Genetic Roulette is Jeffrey Smith’s second book in which he makes unsubstantiated claims against biotechnology. In it, he details 65 separate claims that the technology causes harm in a variety of ways. On these pages each of those claims – addressed in the same eight “sections” that correspond directly with the book – are stacked up against peer-reviewed science.
Showing posts with label Genetics. Show all posts
Showing posts with label Genetics. Show all posts
Saturday, March 27, 2010
Friday, May 05, 2006
Collected links and summaries on natural gene evolution.
This post was inspired by Cédric Feschotte and colleagues' paper just below and collects together comments about natural evolution of genes. Much of this topic is covered in GMO Pundit's Natural GMOs series, and collected links to this series are also given below (see Collected GMO Pundit Posts).
Monday, April 03, 2006
Details about the RAG genes used in the human immune system.
RAG genes are involved in shuffling human antibody genes.
V and J segments mentioned below are the parts of the antibody gene that get shuffled as part of a complex and important normal human reponse to infection.
RAG1 evolved from mobile genes called transposons , otherwise called transposable elements (TEs) that move between species.
This posting is background, documentation of scientific detail, and explanation for an item about Transib transposons which perhaps should be read first
V and J segments mentioned below are the parts of the antibody gene that get shuffled as part of a complex and important normal human reponse to infection.
RAG1 evolved from mobile genes called transposons , otherwise called transposable elements (TEs) that move between species.
This posting is background, documentation of scientific detail, and explanation for an item about Transib transposons which perhaps should be read first
Sunday, February 26, 2006
Some examples of Nina V Fedoroff' s Scientific leadership.
Prehistoric GM Corn
Nina V. Fedoroff
Transposable Elements As a Molecular Evolutionary Force
NINA V. FEDOROFF
Nina Fedoroff
Huck Institute of Life Sciences, Pennsylvania State University
Evan Pugh Professor of Biology
Willaman Professor of Life Sciences, Biology Department
External Faculty, Santa Fe Institute
B.S., Syracuse University, Biology and Chemistry, summa cum laude (1966)
Ph.D., The Rockefeller University, Molecular Biology (1972)
Research Interests:
• Plant stress response
• Hormone signaling
• Transposable elements
• Epigenetic mechanisms
Plant stress response: A major project in the laboratory is investigating the responses of plants to biotic (pathogens) and abiotic (ozone, temperature, chemicals) stresses using DNA microarray gene expression profiling and reverse genetics. We have identified more than 1200 stress-modulated Arabidopsis genes and studying their expression under various conditions. The illustration shows the change in gene expression of 366 genes that are induced (red) or repressed (green) by ozone. Among the genes induced by various stresses are signaling genes, transcription factors, and effector genes that include enzymes that alter the cells structure and properties in response to stress. The signaling molecules include MAP kinases and receptor-like kinases. We are suppressing and overexpressing potential regulatory genes to identify the genes under their control. We want to understand the structure of the stress-response gene networks and to explores molecular genetic approaches to modifying the stress response (see Holter et al, 2000, 2001).
Hormone responses: The hyl1 Arabidopsis mutant (right) has a transposon insertion mutation in a gene that is involved in several hormonal signaling pathways, including those for abscisic acid, auxin and cytokinin. The mutant is affected in many growth parameters, including graviperception. It is not as sensitive to exogenous auxins and cytokinins as the wiltype, but it is hypersensitive to abscisic acid. The HYL1 protein binds to double-stranded RNA and localizes to the nucleus. The mutant is described in Lu and Fedoroff (2000). We are investigating how this protein affects hormone signaling.
Transposable elements: transposable elements or transposons were discovered in corn (maize) plants by the famous geneticist Barbara McClintock through classical genetic analysis of unstable mutations (for a brief history, see http://www.ergito.com or Fedoroff 2001). Maize transposons were cloned in our laboratory almost 20 years ago and are now widely used for insertional mutagenesis. We have created a database of several hundred Arabidopsis transposon insertion lines using a transposon tagging system developed in the laboratory (Smith et al., 1996; Raina et al., 2001). A map of the insertions is shown and the database can be searched at: http://sgio2.biotec.psu.edu/sr.
Epigenetic mechanisms: The maize Suppressor-mutator (Spm) transposon is epigenetically inactivated by methylation and encodes a protein, TnpA, which is capable of reversing the inactivation (Schläppi et al., 1994; Fedoroff et al., 1995). Using an inducible promoter to express TnpA, current experiments seek to understand how it demethylates the Spm promoter. Some ideas about plant transposon evolution are explored in Fedoroff (2000).
MENDEL IN THE KITCHEN: A Scientist's View of Genetically Modified Foods
Nina Fedoroff and Nancy Marie Brown.
Joseph Henry, (352p) ISBN 0-309-09505-1
Wall Street Journal Review
The Miracles of Modifying
By HENRY I. MILLER
Nina V. Fedoroff
Corn (maize) is arguably man's first, and perhaps his greatest, feat of genetic engineering. Its huge ears--each packed with firmly attached kernels filled with starch, protein, and oil--make it a food staple. Contemporary corn, unlike its wild grassy ancestor teosinte, can't survive without people because it can't disperse its own seeds. The origins of maize have long intrigued geneticists, but only recently have new molecular methods enabled evolutionary sleuths to pinpoint its origins and identify the genetic modifications (GMs) that enabled the radical transformation of teosinte into contemporary maize. On page 1206 of this issue, Jaenicke-Després, Doebley, and their colleagues (1) provide the latest chapter in this detective story and suggest that prehistoric people were quick to adopt GM corn.
Teosinte and corn (Zea mays) don't look much alike, but they are interfertile. Teosinte-corn hybrids arise in the wild but look so different from either parent that they were originally classified as a different species (Zea canina). In the 1920s, Beadle examined chromosomes in teosinte-corn hybrids and concluded that the two plants belonged to the same species, and even shared the same chromosomal order of genes...
So how, when, and where was teosinte transformed into maize? Beadle gave his mentor, Emerson, credit for the idea that just a few mutations changed teosinte into maize (4). Analyzing backcrossed maize-teosinte hybrids with molecular probes, Doebley's group came to a startlingly similar conclusion: The differences between maize and teosinte could be traced to just five genomic regions (5). In two of these regions, the differences were attributable to alternative alleles of just one gene: teosinte glume architecture (tga1) and teosinte branched (tb1), which affect kernel structure and plant architecture.
The tga1 gene controls glume hardness, size, and curvature (6). Teosinte kernels are surrounded by a stone-like fruitcase, assuring their unscathed passage through an animal's digestive tract, which is required for seed dispersal. But the plant's reproductive success is the consumer's nutritional failure. Not surprisingly, one of the major differences between maize and teosinte kernels lies in the structures (cupule and outer glume) enclosing the kernel. Maize kernels don't develop a fruitcase because the glume is thinner and shorter and the cupule is collapsed. The hardness of teosinte kernels comes from silica deposits in the glume's epidermal cells and from impregnation of glume cells with the polymer lignin. The maize tga1 allele supports slower glume growth and less silica deposition and lignification than does the teosinte tga1allele.
The tb1 locus is largely responsible for the different architecture of the two plants. Teosinte produces many long side branches, each topped by a male flower (tassel), and its female flowers (ears) are produced by secondary branches growing off the main branches. Modern corn has one main stalk with a tassel at the top. Its lateral branches are short and bear its large ears. Much of the difference is attributable to the tb1 gene, originally identified in a teosinte-like maize mutant. Mutations generally abrogate gene function, indicating that the maize allele acts by suppressing lateral shoot development, converting grassy teosinte into slim, single-stalked modern corn and male into female reproductive structures (7).
Knowing that this cluster of traits is controlled by just two genes makes it less surprising that genetic differences in these genes could render teosinte a much better food plant. Yet however useful to people, a tga1 mutation would have been detrimental to teosinte, making it more vulnerable to destruction in the digestive tract of the consumer and so less able to disperse its seeds. Thus, the only way this mutation could have persisted is if our ancestors propagated the seeds themselves. This implies that people were not only harvesting--and likely grinding and cooking--teosinte seeds before these mutations came along, but also were selecting for favorable features such as kernel quality and cob size. In turn, this suggests a "bottleneck" in corn evolution: Several useful GMs were brought together in a single plant and then the seeds from this plant were propagated, giving rise to all contemporary maize varieties. Such a prediction can be tested by calculating the number of generations and individuals it would take to account for the molecular variability present in contemporary maize. The results of such a test suggest a bottleneck for maize domestication of just 10 generations and a founding population of only 20 individuals (8). Did this happen once or many times? Because genetic differences arise at a fairly constant rate, this question can be answered by constructing family trees using similar sequences from different varieties of teosinte and contemporary maize. The results are unequivocal: All contemporary maize varieties belong to a single family, pointing to a single domestication event.
Knowing how quickly differences arise, how many there are today, and where the family of origin survives, it is possible to determine when--and where--it all started. The answer is that maize most probably arose from teosinte of the subspecies parviglumis in the Balsas River basin of southern Mexico roughly 9000 years ago (9). Recent redating of cobs from the Guilá Naquitz cave (about 500 km from the Balsas River basin) demonstrated that they were more than 6200 years old, providing archaeological support for the molecular findings (10, 11). These earliest corn cobs don't look much like those of modern corn, but they look even less like teosinte cobs (see the figure). They are tough and have several rows of tightly attached kernels, implying that the plants wouldn't have survived without people to detach and plant the seeds. By contrast, teosinte's reproductive structure, the rachis, falls apart when mature to release its hard seeds. Thus, even 6000 years ago, ancient maize cobs were already corn-like.
The GM corn spread far--and fast. Maize appears in the archaeological record of the southwestern United States more than 3000 years ago (12), and it is evident that cob size had already increased under selection. The Jaenicke-Després et al. study (1) examines the selection of traits that can't be observed in fossilized cobs...They report that alleles of these genes typical of modern corn were already present more than 4000 years ago, implying that plant architecture and kernel nutritive properties were selected early, long before corn reached North America.
The authors conclude that "... by 4400 years ago, early farmers had already had a substantial homogenizing effect on allelic diversity at three genes associated with maize morphology and biochemical properties of the corn cob." This suggests that once this special combination of GMs was assembled, the plants proved so superior as a food crop that they were carefully propagated and widely adopted, perhaps causing something of a prehistoric Green Revolution. It also implies that the apparent loss of genetic diversity following the introduction of high-yielding Green Revolution wheat and rice varieties in the 1960s and 1970s, and attending the rapid adoption of superior GM crops today, is far from a new phenomenon.
Science. 2003 Nov 14;302(5648):1158-9.
Transposable Elements As a Molecular Evolutionary Force
NINA V. FEDOROFF
So voluminous is the recent literature on transposable elements that it is difficult to imagine making an original observation; it seems that virtually anything that can be said about them, has been. My modest goal is to reexamine what we already know, viewing transposable elements as central players in a dynamic system of complex chromosome structure. McClintock often expressed the intuition that the genome responds to perturbation as an integrated system and acknowledged that we did not know how to think about such a higher level of integration. Although we still lack the analytic tools, there is a growing appreciation that organisms constitute complex, self-organizing systems whose properties can be understood through the study of interactions within and between networks of mutually interacting components, be they DNA sequences, proteins, or cells. Organisms must also be appreciated as historic entities. Today's genome reveals its evolution, which in turn is shaped and limited by the tools and materials available.
In an endeavor to see the familiar with new eyes, I begin by examining a property of eukaryotic genomes so familiar today that it is largely taken for granted: the presence of repetitive DNA. Whereas a high level of internal redundancy is appreciated as one of the most distinctive features of the complex genomes of higher eukaryotes, the theoretic and practical difficulties associated with the origin and maintenance of redundancy, in my view, have gone largely unrecognized and may be central to understanding contemporary genome structure. Redundant sequences can be either adjacent in the genome or dispersed. Different, albeit related, replication mechanisms give rise to each and pose different challenges to the stability and flexibility of the genome as a system. I will address the evidence that eukaryotes have special mechanisms to process duplications.
A rapidly growing body of data from genome characterization, cloning, and sequencing in a variety of organisms is making it increasingly evident that transposable elements have been instrumental in sculpting the contemporary genomes of all organisms. 1-7 The conversation has shifted from conjecture to fact. An understanding of genome evolution must necessarily include consideration of the role of transposable elements in the derivation of today's genomes. Transposable elements comprise a special category of reduplicated sequence whose inherent propensity for dispersal may be its most important property. I will review some of the mechanisms, both genetic and epigenetic, that regulate the movement of transposons and minimize their impact. Finally, the discussion must address the limits of the epigenetic regulatory systems, asking questions about the short- and long-term stability of eukaryotic genome structure.
My central theses are three: (1) that the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy, (2) that the special contribution of transposable elements is to modularize the genome, maintaining it in a structurally dynamic state despite increasing size and complexity, and (3) that the labilizing forces of recombination and transposition are just barely contained, giving a dynamic system of ever increasing complexity, verging on the chaotic.
Ann N Y Acad Sci. 1999 May 18;870:251-64.
Annals of the New York Academy of Sciences 870:251-264 (1999)
Annals of the New York Academy of Sciences 870:251-264 (1999)
Nina Fedoroff
Huck Institute of Life Sciences, Pennsylvania State University
Evan Pugh Professor of Biology
Willaman Professor of Life Sciences, Biology Department
External Faculty, Santa Fe Institute
B.S., Syracuse University, Biology and Chemistry, summa cum laude (1966)
Ph.D., The Rockefeller University, Molecular Biology (1972)
Research Interests:
• Plant stress response
• Hormone signaling
• Transposable elements
• Epigenetic mechanisms
Plant stress response: A major project in the laboratory is investigating the responses of plants to biotic (pathogens) and abiotic (ozone, temperature, chemicals) stresses using DNA microarray gene expression profiling and reverse genetics. We have identified more than 1200 stress-modulated Arabidopsis genes and studying their expression under various conditions. The illustration shows the change in gene expression of 366 genes that are induced (red) or repressed (green) by ozone. Among the genes induced by various stresses are signaling genes, transcription factors, and effector genes that include enzymes that alter the cells structure and properties in response to stress. The signaling molecules include MAP kinases and receptor-like kinases. We are suppressing and overexpressing potential regulatory genes to identify the genes under their control. We want to understand the structure of the stress-response gene networks and to explores molecular genetic approaches to modifying the stress response (see Holter et al, 2000, 2001).
Hormone responses: The hyl1 Arabidopsis mutant (right) has a transposon insertion mutation in a gene that is involved in several hormonal signaling pathways, including those for abscisic acid, auxin and cytokinin. The mutant is affected in many growth parameters, including graviperception. It is not as sensitive to exogenous auxins and cytokinins as the wiltype, but it is hypersensitive to abscisic acid. The HYL1 protein binds to double-stranded RNA and localizes to the nucleus. The mutant is described in Lu and Fedoroff (2000). We are investigating how this protein affects hormone signaling.
Transposable elements: transposable elements or transposons were discovered in corn (maize) plants by the famous geneticist Barbara McClintock through classical genetic analysis of unstable mutations (for a brief history, see http://www.ergito.com or Fedoroff 2001). Maize transposons were cloned in our laboratory almost 20 years ago and are now widely used for insertional mutagenesis. We have created a database of several hundred Arabidopsis transposon insertion lines using a transposon tagging system developed in the laboratory (Smith et al., 1996; Raina et al., 2001). A map of the insertions is shown and the database can be searched at: http://sgio2.biotec.psu.edu/sr.
Epigenetic mechanisms: The maize Suppressor-mutator (Spm) transposon is epigenetically inactivated by methylation and encodes a protein, TnpA, which is capable of reversing the inactivation (Schläppi et al., 1994; Fedoroff et al., 1995). Using an inducible promoter to express TnpA, current experiments seek to understand how it demethylates the Spm promoter. Some ideas about plant transposon evolution are explored in Fedoroff (2000).
MENDEL IN THE KITCHEN: A Scientist's View of Genetically Modified Foods
Nina Fedoroff and Nancy Marie Brown.
Joseph Henry, (352p) ISBN 0-309-09505-1
Wall Street Journal Review
The Miracles of Modifying
By HENRY I. MILLER
November 11, 2004; Page D9
In the distant past, ruddy husbandmen tilled the earth, yielding the pure bounty of nature. Then scientists came along, and nature gave way to artifice with the use of unnatural hybrids and chemicals, and, inevitably, despoliation of the environment. Or so the story goes.
As it happens, agricultural practices have been "unnatural" for 10,000 years. With the exception of wild berries and wild mushrooms, virtually all the grains, fruits and vegetables in our diets (including "organic" ones) are, strictly speaking, genetically modified. Potatoes, tomatoes, oats, rice and corn, for instance, come from plants created -- during the past half-century -- by "wide cross" hybridizations that transcend "natural breeding boundaries."
This is only one of the many surprises in store for readers of "Mendel in the Kitchen" (John
Henry, 370 pages, $24.95) (Gregor Mendel, a 19th-century Austrian monk, first described the
basic laws of heredity that became the foundation for modern genetics.) Nina V. Fedoroff, a plant biologist, and her co-writer Nancy Marie Brown meticulously depict the past, present and future of genetics in agriculture. They mix didactic science (including diagrams reminiscent of a highschool biology textbook) with accounts of what farmers, naturalists, plant breeders and biologists have wrought over time. The saga brings rationality to the controversy now haunting the newest, most precise and most predictable manifestation of genetic modification -- gene-splicing.
...continues.
Nina V Fedoroff
Evan Pugh professor of biology and Willaman professor of life science at Pennsylvania State University
Scientific ideas can and must be tested and verified in the real world, in order for people to believe in them
Evan Pugh professor of biology and Willaman professor of life science at Pennsylvania State University
Scientific ideas can and must be tested and verified in the real world, in order for people to believe in them
What I wish everyone understood about science is that scientific ideas are like philosophical, political or religious ideas, in the sense that they are the products of people's minds and imaginations. But at the same time, scientific ideas are profoundly different from philosophical, political and religious ideas, because they can - and must - be tested and verified in the real world, in order for people to believe in them.
This means that scientific ideas are constantly changing, self-correcting and useful, as evidenced by the way they have allowed humans to grow food, build buildings and cities, travel, cure diseases, communicate and understand the universe. But I wish people understood that science as a way of living provides us with a viable social organising principle, that does not demand the kinds of rigid loyalty that is at the heart of much of the cultural and religious strife in the world. Science may therefore be the only way that human cultures can get beyond the social, cultural, economic and religious differences that underlie wars.
Wednesday, February 22, 2006
Survey of Recent studies on Mutator like elements (Mules) , mobile DNA that moves and different species and scrambles and mutates the genome.
Mutator mobile genes (Mules) that move around between species such as maize, millet, rice diverse angiosperms, yeast Yarrowia lipolytica, Petunia, flatworm Caenorhabditis, sugarcane, fungus Fusarium oxysporum, fruitfly Drosophila, and grasses, which scramble and delete genes, are genetically unstable, and which are common in nature - and completely NATURAL:
Diao X, Freeling M, Lisch D.
Horizontal Transfer of a Plant Transposon.
PLoS Biol. 2005 Dec 20;4(1):e5 [Epub ahead of print]
McCarty DR, Settles AM, Suzuki M, Tan BC, Latshaw S, Porch T, Robin K, Baier
J, Avigne W, Lai J, Messing J, Koch KE, Hannah LC.
Steady-state transposon mutagenesis in inbred maize.
Plant J. 2005 Oct;44(1):52-61.
Cowan RK, Hoen DR, Schoen DJ, Bureau TE.
MUSTANG is a novel family of domesticated transposase genes found in diverse
angiosperms.
Mol Biol Evol. 2005 Oct;22(10):2084-9. Epub 2005 Jun 29.
6: Mol Biol Evol. 2005 Oct;22(10):2084-9. Epub 2005 Jun 29.
While transposons have traditionally been viewed as genomic parasites or "junk DNA," the discovery of transposon-derived host genes has fueled an ongoing debate over the evolutionary role of transposons. In particular, while mobility-related open reading frames have been known to acquire host functions, the contribution of these types of events to the evolution of genes is not well understood. Here we report that genome-wide searches for Mutator transposase-derived host genes in Arabidopsis thaliana (Columbia-0) and Oryza
sativa ssp. japonica (cv. Nipponbare) (domesticated rice) identified 121 sequences, including the taxonomically conserved MUSTANG1. Syntenic MUSTANG1 orthologs in such varied plant species as rice, poplar, Arabidopsis, and Medicago truncatula appear to be under purifying selection. However, despite the evidence of this pathway of gene evolution, MUSTANG1 belongs to one of only two Mutator-like gene families with members in both monocotyledonous and
dicotyledonous plants, suggesting that Mutator-like elements seldom evolve into taxonomically widespread host genes.
Neuveglise C, Chalvet F, Wincker P, Gaillardin C, Casaregola S.
Mutator-like element in the yeast Yarrowia lipolytica displays multiple
alternative splicings.
Eukaryot Cell. 2005 Mar;4(3):615-24.
Stuurman J, Kuhlemeier C.
Stable two-element control of dTph1 transposition in mutator strains of Petunia
by an inactive ACT1 introgression from a wild species.
Plant J. 2005 Mar;41(6):945-55.
Brownlie JC, Johnson NM, Whyard S.
The Caenorhabditis briggsae genome contains active CbmaT1 and Tcb1 transposons.
Mol Genet Genomics. 2005 Mar;273(1):92-101. Epub 2005 Feb 9.
Rossi M, Araujo PG, de Jesus EM, Varani AM, Van Sluys MA.
Comparative analysis of Mutator -like transposases in sugarcane.
Mol Genet Genomics. 2004 Sep;272(2):194-203. Epub 2004 Aug 24.
The maize Mutator ( Mu) system has been described as the most active and mutagenic plant transposon so far discovered. Mu -like elements (MULEs) are widespread among plants, and many and diverse variants can coexist in a particular genome. The autonomous regulatory element MuDR contains two genes:
mudrA encodes the transposase, while the function of the mudrB gene product remains unknown. Although mudrA -like sequences are ubiquitous in plants, mudrB seems to be restricted to the genus Zea. In the SUCEST (the Brazilian Sugarcane EST Sequencing Project) database, several mudrA -like cDNAs have been identified, suggesting the presence of a transcriptionally active Mu system in sugarcane. Phylogenetic studies have revealed the presence in plants of four classes of mudrA -like sequences, which arose prior to the monocot/eudicot split. At least three of the four classes are also found in the progenitors of
the sugarcane hybrid (Saccharum spp.), Saccharum officinarum and S. spontaneum.
The frequency of putatively functional transposase ORFs varies among the classes, as revealed at both cDNA and genomic levels. The predicted products of some sugarcane mudrA -like transcripts contain both a DNA-binding domain and a transposase catalytic-site motif, supporting the idea that an active Mu system exists in this hybrid genome.
Xu Z, Yan X, Maurais S, Fu H, O'Brien DG, Mottinger J, Dooner HK.
Jittery, a Mutator distant relative with a paradoxical mobile behavior:
excision without reinsertion.
Plant Cell. 2004 May;16(5):1105-14. Epub 2004 Apr 9.
The unstable mutation bz-m039 arose in a maize (Zea mays) stock that originated from a plant infected with barley stripe mosaic virus. The instability of the mutation is caused by a 3.9-kb mobile element that has been named Jittery (Jit).
Jit has terminal inverted repeats (TIRs) of 181 bp, causes a 9-bp direct duplication of the target site, and appears to excise autonomously. It is predicted to encode a single 709-amino acid protein, JITA, which is distantly related to the MURA transposase protein of the Mutator system but is more closely related to the MURA protein of Mutator-like elements (MULEs) from Arabidopsis thaliana and rice (Oryza sativa). Like MULEs, Jit resembles Mutator in the length of the element's TIRs, the size of the target site duplication, and in the makeup of its transposase but differs from the autonomous element Mutator-Don Robertson in that it encodes a single protein. Jit also differs from Mutator elements in the high frequency with which it excises to produce germinal revertants and in its copy number in the maize genome: Jit-like TIRs are present at low copy number in all maize lines and teosinte accessions examined, and JITA sequences occur in only a few maize inbreds. However, Jit cannot be considered a bona fide transposon in its present host line because it does not leave footprints upon excision and does not reinsert in the genome. These unusual mobile element properties are discussed in light of the structure and gene organization of Jit and related elements.
Sijen T, Plasterk RH.
Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi.
Nature. 2003 Nov 20;426(6964):310-4.
Slotkin RK, Freeling M, Lisch D.
Mu killer causes the heritable inactivation of the Mutator family of
transposable elements in Zea mays.
Genetics. 2003 Oct;165(2):781-97.
May BP, Liu H, Vollbrecht E, Senior L, Rabinowicz PD, Roh D, Pan X, Stein
L, Freeling M, Alexander D, Martienssen R.
Maize-targeted mutagenesis: A knockout resource for maize.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11541-6. Epub 2003 Sep 3.
Vastenhouw NL, Fischer SE, Robert VJ, Thijssen KL, Fraser AG, Kamath RS,
Ahringer J, Plasterk RH.
A genome-wide screen identifies 27 genes involved in transposon silencing in C.
elegans.
Curr Biol. 2003 Aug 5;13(15):1311-6.
Chalvet F, Grimaldi C, Kaper F, Langin T, Daboussi MJ.
Hop, an active Mutator-like element in the genome of the fungus Fusarium
oxysporum.
Mol Biol Evol. 2003 Aug;20(8):1362-75. Epub 2003 May 30.
Pooma W, Gersos C, Grotewold E.
Transposon insertions in the promoter of the Zea mays a1 gene differentially
affect transcription by the Myb factors P and C1.
Genetics. 2002 Jun;161(2):793-801.
Bessereau JL, Wright A, Williams DC, Schuske K, Davis MW, Jorgensen EM.
Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ
line.
Nature. 2001 Sep 6;413(6851):70-4.
Lisch DR, Freeling M, Langham RJ, Choy MY.
Mutator transposase is widespread in the grasses.
Plant Physiol. 2001 Mar;125(3):1293-303.
Singer T, Yordan C, Martienssen RA.
Robertson's Mutator transposons in A. thaliana are regulated by the
chromatin-remodeling gene Decrease in DNA Methylation (DDM1).
Genes Dev. 2001 Mar 1;15(5):591-602.
Fedoroff NV.
The suppressor-mutator element and the evolutionary riddle of transposons.
Genes Cells. 1999 Jan;4(1):11-9. Review.
Kloeckener-Gruissem B, Freeling M.
Transposon-induced promoter scrambling: a mechanism for the evolution of new
alleles.
Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1836-40.
Eisen JA, Benito MI, Walbot V.
Sequence similarity of putative transposases links the maize Mutator autonomous
element and a group of bacterial insertion sequences.
Nucleic Acids Res. 1994 Jul 11;22(13):2634-6.
Pan and Peterson (1988) note that it would appear that the corn genome is highly volatile. That is, these transposons are now known to be quiescent in the genome. They appear also to be spontaneously activated. This is evident in almost any line one looks at with appropriate reporter alleles as indicated in the paper by Pan and Peterson (1988), where sectors were pervasive in these lines. It would appear, therefore, that the corn genome has a built-in system of activation and redeployment of genome segments and in a final result, leads to a great deal of variability.
Annual Review of Genetics
Vol. 23: 71-85 (Volume publication date December 1989)
(doi:10.1146/annurev.ge.23.120189.000443)
Maize Transposable Elements
A Gierl, H Saedler, and P A Peterson
Genetics, Vol 128, 823-830, Copyright © 1991
INVESTIGATIONS
Spontaneous Germinal Activation of Quiescent Uq Transposable Elements in Zea mays L
Y. B. Pan and P. A. Peterson
Department of Agronomy and Department of Genetics, Iowa State University, Ames, Iowa 50011 Present address: Department of Immunology/Microbiology, Rush-Presbyterian-St. Luke's Medical Center, 1653 West Congress Parkway, Chicago, Illinois 60612-3864.
The spontaneous germinal activation of quiescent Uq transposable elements is reported. Thirty-nine spotted exceptions were observed at a rate of about 2 X 10(-4) from 687 otherwise colorless ears produced from the cross of a-ruq/a-ruq (colorless or occasionally sectored) X an a-ruq tester (colorless). All exceptions had spotting patterns distinct from the pattern of our original standard Uq (Uq1)-a-ruq spotting. From these spotted exceptions five new Uq elements (Uq2, Uq3, Uq4, Uq5 and Uq6) have been isolated. Genetic evidence for the Uq nature of the five germinal isolates is presented. First, each of the five spotted exceptions was homozygous for the a-ruq reporter allele. Second, four new Uq isolates (Uq2, Uq3, Uq4 and Uq5), after being reconstituted into a a{deg} sh2/a{deg} sh2 (no Uq) line, could transactivate the standard a-ruq allele and continue to produce their distinct spotting phenotypes. Third, these five new Uqs are also capable of transactivating the c-ruq65 and c-ruq67 alleles. However, the transactivation of c-ruq is generally weaker than that of a-ruq.
Tagging of a maize gene involved in kernel development by an activated Uq transposable element
Yong-Bao Pan1 and Peter A. Peterson1 Contact Information
(1) Department of Genetics and Department of Agronomy, Iowa State University, 50011 Ames, IA, USA
Received: 12 April 1989
Communicated by H. Saedler
Summary A quiescent Uq transposable element has been activated in a maize plant treated with 5-aza-2prime-deoxycyti-dine. This activated Uq cosegregates with a heritable dominant miniature (Mn) kernel phenotype, indicating its physical association with a maize miniature locus (Mn:: Uq). The Mn:: Uq mutant is dominant in producing a miniature seed phenotype of variable size and in reducing seedling vigor in the early growth stage. Genetic experiments indicate that the Mn:: Uq mutant also affects the activity of the male gametophyte, whereby pollen germination is inhibited, thus lacking pollen tube growth resulting in the male nontransmissibility of this mutant. Proof for the Uq element in this mutant is derived by its ability to transactivate the standard a-ruq reporter allele to yield spotted aleurone tissue. However, the Mn:: Uq mutant does not transactivate a normally Uq-responsive c-ruq allele, suggesting a structural difference between the two ruq receptors at the A1 and C1 loci. It is anticipated that cloning of the Uq transposable element would facilitate the molecular cloning and characterization of the maize miniature gene.
Key words Zea mays - Uq transposable element - miniature gene - Mn:: Uq - Activation
Journal Paper No. J-13425 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011, USA, Project No. 2850
Genetics, Vol 120, 587-596, Copyright © 1988
INVESTIGATIONS
The Mutator-Related Cy Transposable Element of Zea mays L. Behaves as a Near-Mendelian Factor
P. S. Schnable and P. A. Peterson
Present address: Department of Genetics Iowa State University, Ames, Iowa 50011.
The bz-rcy allele arose in a single gamete of the TEL (transposable-element laden) population, when the rcy receptor element inserted into the Bronze1 locus. This newly arisen receptor allele conditions a stable bronze kernel phenotype in the absence of the independently segregating regulatory element, Cy. In the presence of Cy, bz-rcy conditions fully colored spots on a bronze background. The spots represent clonal sectors arising from mutations of bz-rcy to Bz'. Although Cy exhibits genetic interactions with the Mutator system it differs from Mu-homologous elements in its near-Mendelian behavior which is in contrast to the non-Mendelian inheritance of Mutator and Mu-homologous elements. Evidence is presented which suggests that the timing and mode of Cy transposition differ from those of Mu1.
Diao X, Freeling M, Lisch D.
Horizontal Transfer of a Plant Transposon.
PLoS Biol. 2005 Dec 20;4(1):e5 [Epub ahead of print]
McCarty DR, Settles AM, Suzuki M, Tan BC, Latshaw S, Porch T, Robin K, Baier
J, Avigne W, Lai J, Messing J, Koch KE, Hannah LC.
Steady-state transposon mutagenesis in inbred maize.
Plant J. 2005 Oct;44(1):52-61.
Cowan RK, Hoen DR, Schoen DJ, Bureau TE.
MUSTANG is a novel family of domesticated transposase genes found in diverse
angiosperms.
Mol Biol Evol. 2005 Oct;22(10):2084-9. Epub 2005 Jun 29.
6: Mol Biol Evol. 2005 Oct;22(10):2084-9. Epub 2005 Jun 29.
While transposons have traditionally been viewed as genomic parasites or "junk DNA," the discovery of transposon-derived host genes has fueled an ongoing debate over the evolutionary role of transposons. In particular, while mobility-related open reading frames have been known to acquire host functions, the contribution of these types of events to the evolution of genes is not well understood. Here we report that genome-wide searches for Mutator transposase-derived host genes in Arabidopsis thaliana (Columbia-0) and Oryza
sativa ssp. japonica (cv. Nipponbare) (domesticated rice) identified 121 sequences, including the taxonomically conserved MUSTANG1. Syntenic MUSTANG1 orthologs in such varied plant species as rice, poplar, Arabidopsis, and Medicago truncatula appear to be under purifying selection. However, despite the evidence of this pathway of gene evolution, MUSTANG1 belongs to one of only two Mutator-like gene families with members in both monocotyledonous and
dicotyledonous plants, suggesting that Mutator-like elements seldom evolve into taxonomically widespread host genes.
Neuveglise C, Chalvet F, Wincker P, Gaillardin C, Casaregola S.
Mutator-like element in the yeast Yarrowia lipolytica displays multiple
alternative splicings.
Eukaryot Cell. 2005 Mar;4(3):615-24.
Stuurman J, Kuhlemeier C.
Stable two-element control of dTph1 transposition in mutator strains of Petunia
by an inactive ACT1 introgression from a wild species.
Plant J. 2005 Mar;41(6):945-55.
Brownlie JC, Johnson NM, Whyard S.
The Caenorhabditis briggsae genome contains active CbmaT1 and Tcb1 transposons.
Mol Genet Genomics. 2005 Mar;273(1):92-101. Epub 2005 Feb 9.
Rossi M, Araujo PG, de Jesus EM, Varani AM, Van Sluys MA.
Comparative analysis of Mutator -like transposases in sugarcane.
Mol Genet Genomics. 2004 Sep;272(2):194-203. Epub 2004 Aug 24.
The maize Mutator ( Mu) system has been described as the most active and mutagenic plant transposon so far discovered. Mu -like elements (MULEs) are widespread among plants, and many and diverse variants can coexist in a particular genome. The autonomous regulatory element MuDR contains two genes:
mudrA encodes the transposase, while the function of the mudrB gene product remains unknown. Although mudrA -like sequences are ubiquitous in plants, mudrB seems to be restricted to the genus Zea. In the SUCEST (the Brazilian Sugarcane EST Sequencing Project) database, several mudrA -like cDNAs have been identified, suggesting the presence of a transcriptionally active Mu system in sugarcane. Phylogenetic studies have revealed the presence in plants of four classes of mudrA -like sequences, which arose prior to the monocot/eudicot split. At least three of the four classes are also found in the progenitors of
the sugarcane hybrid (Saccharum spp.), Saccharum officinarum and S. spontaneum.
The frequency of putatively functional transposase ORFs varies among the classes, as revealed at both cDNA and genomic levels. The predicted products of some sugarcane mudrA -like transcripts contain both a DNA-binding domain and a transposase catalytic-site motif, supporting the idea that an active Mu system exists in this hybrid genome.
Xu Z, Yan X, Maurais S, Fu H, O'Brien DG, Mottinger J, Dooner HK.
Jittery, a Mutator distant relative with a paradoxical mobile behavior:
excision without reinsertion.
Plant Cell. 2004 May;16(5):1105-14. Epub 2004 Apr 9.
The unstable mutation bz-m039 arose in a maize (Zea mays) stock that originated from a plant infected with barley stripe mosaic virus. The instability of the mutation is caused by a 3.9-kb mobile element that has been named Jittery (Jit).
Jit has terminal inverted repeats (TIRs) of 181 bp, causes a 9-bp direct duplication of the target site, and appears to excise autonomously. It is predicted to encode a single 709-amino acid protein, JITA, which is distantly related to the MURA transposase protein of the Mutator system but is more closely related to the MURA protein of Mutator-like elements (MULEs) from Arabidopsis thaliana and rice (Oryza sativa). Like MULEs, Jit resembles Mutator in the length of the element's TIRs, the size of the target site duplication, and in the makeup of its transposase but differs from the autonomous element Mutator-Don Robertson in that it encodes a single protein. Jit also differs from Mutator elements in the high frequency with which it excises to produce germinal revertants and in its copy number in the maize genome: Jit-like TIRs are present at low copy number in all maize lines and teosinte accessions examined, and JITA sequences occur in only a few maize inbreds. However, Jit cannot be considered a bona fide transposon in its present host line because it does not leave footprints upon excision and does not reinsert in the genome. These unusual mobile element properties are discussed in light of the structure and gene organization of Jit and related elements.
Sijen T, Plasterk RH.
Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi.
Nature. 2003 Nov 20;426(6964):310-4.
Slotkin RK, Freeling M, Lisch D.
Mu killer causes the heritable inactivation of the Mutator family of
transposable elements in Zea mays.
Genetics. 2003 Oct;165(2):781-97.
May BP, Liu H, Vollbrecht E, Senior L, Rabinowicz PD, Roh D, Pan X, Stein
L, Freeling M, Alexander D, Martienssen R.
Maize-targeted mutagenesis: A knockout resource for maize.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11541-6. Epub 2003 Sep 3.
Vastenhouw NL, Fischer SE, Robert VJ, Thijssen KL, Fraser AG, Kamath RS,
Ahringer J, Plasterk RH.
A genome-wide screen identifies 27 genes involved in transposon silencing in C.
elegans.
Curr Biol. 2003 Aug 5;13(15):1311-6.
Chalvet F, Grimaldi C, Kaper F, Langin T, Daboussi MJ.
Hop, an active Mutator-like element in the genome of the fungus Fusarium
oxysporum.
Mol Biol Evol. 2003 Aug;20(8):1362-75. Epub 2003 May 30.
Pooma W, Gersos C, Grotewold E.
Transposon insertions in the promoter of the Zea mays a1 gene differentially
affect transcription by the Myb factors P and C1.
Genetics. 2002 Jun;161(2):793-801.
Bessereau JL, Wright A, Williams DC, Schuske K, Davis MW, Jorgensen EM.
Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ
line.
Nature. 2001 Sep 6;413(6851):70-4.
Lisch DR, Freeling M, Langham RJ, Choy MY.
Mutator transposase is widespread in the grasses.
Plant Physiol. 2001 Mar;125(3):1293-303.
Singer T, Yordan C, Martienssen RA.
Robertson's Mutator transposons in A. thaliana are regulated by the
chromatin-remodeling gene Decrease in DNA Methylation (DDM1).
Genes Dev. 2001 Mar 1;15(5):591-602.
Fedoroff NV.
The suppressor-mutator element and the evolutionary riddle of transposons.
Genes Cells. 1999 Jan;4(1):11-9. Review.
Kloeckener-Gruissem B, Freeling M.
Transposon-induced promoter scrambling: a mechanism for the evolution of new
alleles.
Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1836-40.
Eisen JA, Benito MI, Walbot V.
Sequence similarity of putative transposases links the maize Mutator autonomous
element and a group of bacterial insertion sequences.
Nucleic Acids Res. 1994 Jul 11;22(13):2634-6.
Pan and Peterson (1988) note that it would appear that the corn genome is highly volatile. That is, these transposons are now known to be quiescent in the genome. They appear also to be spontaneously activated. This is evident in almost any line one looks at with appropriate reporter alleles as indicated in the paper by Pan and Peterson (1988), where sectors were pervasive in these lines. It would appear, therefore, that the corn genome has a built-in system of activation and redeployment of genome segments and in a final result, leads to a great deal of variability.
Annual Review of Genetics
Vol. 23: 71-85 (Volume publication date December 1989)
(doi:10.1146/annurev.ge.23.120189.000443)
Maize Transposable Elements
A Gierl, H Saedler, and P A Peterson
Genetics, Vol 128, 823-830, Copyright © 1991
INVESTIGATIONS
Spontaneous Germinal Activation of Quiescent Uq Transposable Elements in Zea mays L
Y. B. Pan and P. A. Peterson
Department of Agronomy and Department of Genetics, Iowa State University, Ames, Iowa 50011 Present address: Department of Immunology/Microbiology, Rush-Presbyterian-St. Luke's Medical Center, 1653 West Congress Parkway, Chicago, Illinois 60612-3864.
The spontaneous germinal activation of quiescent Uq transposable elements is reported. Thirty-nine spotted exceptions were observed at a rate of about 2 X 10(-4) from 687 otherwise colorless ears produced from the cross of a-ruq/a-ruq (colorless or occasionally sectored) X an a-ruq tester (colorless). All exceptions had spotting patterns distinct from the pattern of our original standard Uq (Uq1)-a-ruq spotting. From these spotted exceptions five new Uq elements (Uq2, Uq3, Uq4, Uq5 and Uq6) have been isolated. Genetic evidence for the Uq nature of the five germinal isolates is presented. First, each of the five spotted exceptions was homozygous for the a-ruq reporter allele. Second, four new Uq isolates (Uq2, Uq3, Uq4 and Uq5), after being reconstituted into a a{deg} sh2/a{deg} sh2 (no Uq) line, could transactivate the standard a-ruq allele and continue to produce their distinct spotting phenotypes. Third, these five new Uqs are also capable of transactivating the c-ruq65 and c-ruq67 alleles. However, the transactivation of c-ruq is generally weaker than that of a-ruq.
Tagging of a maize gene involved in kernel development by an activated Uq transposable element
Yong-Bao Pan1 and Peter A. Peterson1 Contact Information
(1) Department of Genetics and Department of Agronomy, Iowa State University, 50011 Ames, IA, USA
Received: 12 April 1989
Communicated by H. Saedler
Summary A quiescent Uq transposable element has been activated in a maize plant treated with 5-aza-2prime-deoxycyti-dine. This activated Uq cosegregates with a heritable dominant miniature (Mn) kernel phenotype, indicating its physical association with a maize miniature locus (Mn:: Uq). The Mn:: Uq mutant is dominant in producing a miniature seed phenotype of variable size and in reducing seedling vigor in the early growth stage. Genetic experiments indicate that the Mn:: Uq mutant also affects the activity of the male gametophyte, whereby pollen germination is inhibited, thus lacking pollen tube growth resulting in the male nontransmissibility of this mutant. Proof for the Uq element in this mutant is derived by its ability to transactivate the standard a-ruq reporter allele to yield spotted aleurone tissue. However, the Mn:: Uq mutant does not transactivate a normally Uq-responsive c-ruq allele, suggesting a structural difference between the two ruq receptors at the A1 and C1 loci. It is anticipated that cloning of the Uq transposable element would facilitate the molecular cloning and characterization of the maize miniature gene.
Key words Zea mays - Uq transposable element - miniature gene - Mn:: Uq - Activation
Journal Paper No. J-13425 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011, USA, Project No. 2850
Genetics, Vol 120, 587-596, Copyright © 1988
INVESTIGATIONS
The Mutator-Related Cy Transposable Element of Zea mays L. Behaves as a Near-Mendelian Factor
P. S. Schnable and P. A. Peterson
Present address: Department of Genetics Iowa State University, Ames, Iowa 50011.
The bz-rcy allele arose in a single gamete of the TEL (transposable-element laden) population, when the rcy receptor element inserted into the Bronze1 locus. This newly arisen receptor allele conditions a stable bronze kernel phenotype in the absence of the independently segregating regulatory element, Cy. In the presence of Cy, bz-rcy conditions fully colored spots on a bronze background. The spots represent clonal sectors arising from mutations of bz-rcy to Bz'. Although Cy exhibits genetic interactions with the Mutator system it differs from Mu-homologous elements in its near-Mendelian behavior which is in contrast to the non-Mendelian inheritance of Mutator and Mu-homologous elements. Evidence is presented which suggests that the timing and mode of Cy transposition differ from those of Mu1.
Further reading at Academics Review
Friday, December 09, 2005
Collected links to scientific discussions on genetics
Links to Notes on Genetics:
General Format for List:
SOURCE
......# Document
......#2.1—Any DNA Insertion can cause a mutation
......#2.4—Promoters are precise tools
......#2.5—Promoters can insert naturally into DNA
......#2.6—Breeders produce genetically stable crops
......#2.7—Mobile DNA drives evolution
......#2.8—Food Contains Lots of Novel RNAs
......#2.9—All Plant Breeding Causes DNA Scrambling
......#2.10—Chemical Composition of crops is highly variable
......# Textbook bookshelf
MIT
......# Biology Hypertextbook
......# Chales M Rader's Website. A Report on Genetically Engineered Crops
Two sections in the essay are relevant to the question of just how unnatural GMO crops are. These are the sections entitled It's Unlike Anything in Nature and Where Transgenes Go .
SUMANAS INC
Citizens' Compendium
.......# Crop origins and evolution
......# RNA interference
......# Wheat
......# Plant breeding
......# Classical plant breeding
......# Biotechnology and plant breeding
......# Transgenic plants
......# Barbara McClintock
......# Horizontal gene transfer in plants
GMO Pundit
...... # Natural GMOs Part 2. Genes move around, and I mean really around, like in the Ancient Mariner
......# Natural GMOs Part 3. Cereal genes change naturally.
......# Natural GMOs Part 4. All you ever wanted to know about wandering genes
......# Natural GMOs Part 3. Cereal genes change naturally.
......# Natural GMOs Part 4. All you ever wanted to know about wandering genes
......# Natural GMOs Part 5. Jumping genes cause mutations
......# Natural GMOs Part 7. Nanobot Genetic Engineers called Helitrons created food crops we have used for thousands of years
......# Natural GMOs Part 8. Helitrons upclose, unplugged and sweaty.
......# Natural GMOs Part 9. Different flowering plants often add their genes to create new species.
......# Natural GMOs Part 11. Genetic Chaos on in nature.
......# Natural GMOs Part 12. Nanobot mules from rice to millet.
......# Examples of Nina Fedoroff's science relating to mobile DNA and plant genetics.
......# Gene Shuffling Techniques Lead to Practical Advances
......# More on Mobile DNA in Plants.
......# Jumping Genes Cause Dog Mutation.
......# What is JIGMOD? (Includes some discussion of natural transgenic events and DNA transfer).
......# Natural GMOs Part 14. Surprise in the Transib-erian Express.
......# Genetic dissection of particular genes and molecules versus whole organism biology.
......# Genetic dissection (reductionism) part 2.
......# Natural GMOs Part 16. nDart mobile DNA in rice.
......# Direct evidence of phenotypic diversity in conventional food crops.
......# Plant breeding and climate change.
......# Molecular markers and Soy oil fatty acid profiles.
......# Genetics of pathogen detection by Leucine rich repeat proteins in animals insects and plants.
......# The Full Monty on gene evolution.
......# Natural GMOs Part 19. The Evolutionary Arms Race.
......# Natural GMOs Part 20. The Red Queen.
......# How mutants help us understand normal plant life activities.
......# Natural GMOs Part 21. DNA Gymnastics separates humans from chimpanzees.
......# Natural GMOs Part 22. Search for New Mysteries.
......# Natural GMOs Part 23. Power of Parasites.
Maize Genetics......# Natural GMOs Part 7. Nanobot Genetic Engineers called Helitrons created food crops we have used for thousands of years
......# Natural GMOs Part 8. Helitrons upclose, unplugged and sweaty.
......# Natural GMOs Part 9. Different flowering plants often add their genes to create new species.
......# Natural GMOs Part 11. Genetic Chaos on in nature.
......# Natural GMOs Part 12. Nanobot mules from rice to millet.
......# Examples of Nina Fedoroff's science relating to mobile DNA and plant genetics.
......# Gene Shuffling Techniques Lead to Practical Advances
......# More on Mobile DNA in Plants.
......# Jumping Genes Cause Dog Mutation.
......# What is JIGMOD? (Includes some discussion of natural transgenic events and DNA transfer).
......# Natural GMOs Part 14. Surprise in the Transib-erian Express.
......# Genetic dissection of particular genes and molecules versus whole organism biology.
......# Genetic dissection (reductionism) part 2.
......# Natural GMOs Part 16. nDart mobile DNA in rice.
......# Direct evidence of phenotypic diversity in conventional food crops.
......# Plant breeding and climate change.
......# Molecular markers and Soy oil fatty acid profiles.
......# Genetics of pathogen detection by Leucine rich repeat proteins in animals insects and plants.
......# The Full Monty on gene evolution.
......# Natural GMOs Part 19. The Evolutionary Arms Race.
......# Natural GMOs Part 20. The Red Queen.
......# How mutants help us understand normal plant life activities.
......# Natural GMOs Part 21. DNA Gymnastics separates humans from chimpanzees.
......# Natural GMOs Part 22. Search for New Mysteries.
......# Natural GMOs Part 23. Power of Parasites.
......# The MaizeGDB website
USDA Agricultural Research Service comments:
Maize genetics and genomics database available on website
December 15, 2005
Luis Pons
Need some detailed data on the genetics and genomics of maize? Then the Agricultural Research Service (ARS) and Iowa State University (ISU) have just the website for you.
The Maize Genetics and Genomics Database, also known as the MaizeGDB, offers loads of information on the traits, genetic sequences and other related features of maize (Zea mays L. ssp. mays), including those aspects having to do with breeding and crop improvement.
The site is a portal to cutting-edge research on this staple crop, as well as to landmark work done decades ago. It also provides contact information for more than 2,400 cooperative researchers, along with web-based tools for ordering items such as maize stocks and cloned sequences.
MaizeGDB was developed by geneticist Carolyn Lawrence and information technology specialists Trent Seigfried and Darwin Campbell at ARS' Corn Insects and Crop Genetics Research Unit inAmes , Iowa Ames Columbia , Mo.
According toLawrence
Lawrence
MaizeGDB is the successor to, and encapsulates the data from, two pioneer databases devoted to maize research: the Maize Database (MaizeDB), started by former ARS geneticist Ed Coe in 1991, and ZmDB, which was launched by the National Science Foundation-funded Maize Gene Discovery Project (MGDP).
ARS is the U.S. Department of Agriculture's chief in-house scientific research agency.
......# Maize Genetics Conferences
......# Nina Fedoroff on Maize genetics
......# GMO Pundit on why hybrids offer advantages to the farmer
......# Walbot Maize Lab Stanford University
......# Walbot Lab Web Links
Mobile genes, transposons
......# Explanation of jumping genes and variegated corn.
......# Kimball on Mobile DNA
USDA Agricultural Research Service comments:
Maize genetics and genomics database available on website
Luis Pons
Need some detailed data on the genetics and genomics of maize? Then the Agricultural Research Service (ARS) and Iowa State University (ISU) have just the website for you.
The Maize Genetics and Genomics Database, also known as the MaizeGDB, offers loads of information on the traits, genetic sequences and other related features of maize (Zea mays L. ssp. mays), including those aspects having to do with breeding and crop improvement.
The site is a portal to cutting-edge research on this staple crop, as well as to landmark work done decades ago. It also provides contact information for more than 2,400 cooperative researchers, along with web-based tools for ordering items such as maize stocks and cloned sequences.
MaizeGDB was developed by geneticist Carolyn Lawrence and information technology specialists Trent Seigfried and Darwin Campbell at ARS' Corn Insects and Crop Genetics Research Unit in
According to
MaizeGDB is the successor to, and encapsulates the data from, two pioneer databases devoted to maize research: the Maize Database (MaizeDB), started by former ARS geneticist Ed Coe in 1991, and ZmDB, which was launched by the National Science Foundation-funded Maize Gene Discovery Project (MGDP).
ARS is the U.S. Department of Agriculture's chief in-house scientific research agency.
......# Maize Genetics Conferences
......# Nina Fedoroff on Maize genetics
......# GMO Pundit on why hybrids offer advantages to the farmer
......# Walbot Maize Lab Stanford University
......# Walbot Lab Web Links
Mobile genes, transposons
......# Explanation of jumping genes and variegated corn.
......# Kimball on Mobile DNA
Dr. Margaret G. Kidwell, Regents Professor
The University of Arizona
Positions and Education
Regents' Professor, Ecology & Evolutionary Biology, University of Arizona 1994-present
Honors and Awards
Elected Member, National Academy of Sciences, 1996
Regents' Professor of Ecology & Evolutionary Biology, 1994
Wilhelmina Key Invited Lecturer, American Genetic Association, 1993
Elected Fellow, American Academy of Arts and Sciences, 1993
Elected Fellow, American Association for the Advancement of Science, 1992
Research Interests
Margaret Kidwell studies the population genetics and evolution of transposable elements in Drosophila and other Diptera. Recent and ongoing projects include examination of the frequency and possible mechanisms of horizontal transfer of mobile elements and the reconstruction of phylogenetic trees based on molecular data. She also uses computer simulations to model the dynamics of transposable elements in insect populations and population cage studies to explore the feasibility of using transposable elements as genetic drivers in Drosophila and mosquito populations. Other projects include the population genetics of malaria epidemiology and the mechanisms controlling immune responses to infection in Anopheline mosquitoes.
Selected Publications
1. Kidwell, M. G. and D. R. Lisch. 2001. Perspective: Transposable elements, parasitic DNA and genome evolution. Evolution 55: 1-24.
2. Kidwell, M. G. and D. R. Lisch. 2001. Transposable Elements as Sources of Genomic Variation. Chapter In Mobile DNA II. American Society of Microbiology Press. In press.
3. Lyozin, G. T., Makarova, K. S., Velikodvorskaja, V. V., Zelentsova, H. S., Khechumian, R. R., Kidwell, M. G., Koonin, E. V., and M. B. Evgen'ev. 2001. The structure and evolution of Penelope in the Drosophila virilis species group: an ancient lineage of retroelements. J. Mol. Evol. In press.
4. Kidwell, M. G. and D. R. Lisch. 2000. Transposable elements and host genome evolution. Trends Ecol. Evol. 15: 95-99.
5. Kidwell, M. G. and M. B. Evgen'ev. 2000. How valuable are model organisms for transposable element studies? Genetica 107:103-111
6. Evgen'ev, M. B., Zelentsova, H., Mnjoian, L., Poluectova,H., and M. G. Kidwell 2000. Invasion of Drosophila virilis by the Penelope transposable element. Chromosoma 109:350-357.
7. Silva, J. C. and M. G. Kidwell. 2000. Selection and horizontal transfer in the evolution of P elements. Mol. Biol. Evol. 17:1542-1557
8. Evgen'ev, M. B., Zelentsova, H., Poluectova, H., Lyozin, G. T., Veleikodvorskaja, V., Pyatkov, K. I., Zhivotovsky, L. A. and Kidwell, M. G. 2000. Mobile elements and chromosomal evolution in the virilis group of Drosophila. Proc. Natl. Acad. Sci. USA 97:11337-11342.
9. Lee, S. H., Clark, J. B., and M. G. Kidwell. 1999. A P-homologous sequence in the house fly, Musca domestica. Insect Molecular Biology 8:491-500.
10. Zelentsova, H., Poluectova, H., Mnjoian, L., G. Lyozin, V. Veleikodvorskaja, L. Zhivotovski, M. G. Kidwell, and M. B. Evgen'ev. 1999. Distribution and evolution of mobile elements in the virilis species group of Drosophila. Chromosoma 108: 443-456.
11. Kidwell, M. G. 1997. Hybrid dysgenesis determinants and other useful transposable elements. In Drosophila. Encyclopedia of Genetics. E. C. R. Reeve (ed.). Dearborn Publishers. New York.
Older Publications
1. Kidwell, M. G., J. F. Kidwell & J. A. Syed 1977. Hybrid dysgenesis in D. melanogaster: a syndrome of aberrant traits including mutation, sterility & male recombination. Genetics 36: 813-33.
2. Bingham, P. M., M. G. Kidwell & G. M. Rubin 1982. The molecular basis of P-M hybrid dysgenesis: The role of the P element, a P strain-specific transposon family. Cell 29: 995-1004.
3. Kidwell, M. G. 1983. Evolution of hybrid dysgenesis determinants in Drosophila melanogaster. Proc. Nat. Acad. Sci. USA 80: 1655-1659.
4. Anxolabéhère, D., M. G. Kidwell & G. Periquet 1988. Molecular characteristics of diverse populations are consistent with the hypothesis of a recent invasion of Drosophila melanogaster by mobile P elements. Mol. Biol. Evol. 5: 252-269.
5. Daniels, S. B., K. R. Peterson, L. D. Strausbaugh, M. G. Kidwell & A. Chovnick 1990. Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics 124: 339-355.
6. Houck, M. A., J. B. Clark, K. R. Peterson & M. G. Kidwell 1991. Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis. Science 253: 1125-1129.
7. Kidwell, M. G. 1993. Lateral transfer in natural populations of eukaryotes. Ann. Rev. Genet. 27: 235-256.
8. Clark, J. B., W. P. Maddison & M. G. Kidwell 1994. Phylogenetic analysis supports horizontal transfer of P transposable elements. Mol. Biol. Evol. 11:40-50.
9. Kidwell, M. G. and D. Lisch. 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. 94: 7704-7711.
10. Clark, J. B. and M. G. Kidwell 1997. A phylogenetic perspective on P element evolution in Drosophila. Proc. Natl. Acad. Sci. USA 94: 11428-11433.
The University of Arizona
Positions and Education
Regents' Professor, Ecology & Evolutionary Biology, University of Arizona 1994-present
Honors and Awards
Elected Member, National Academy of Sciences, 1996
Regents' Professor of Ecology & Evolutionary Biology, 1994
Wilhelmina Key Invited Lecturer, American Genetic Association, 1993
Elected Fellow, American Academy of Arts and Sciences, 1993
Elected Fellow, American Association for the Advancement of Science, 1992
Research Interests
Margaret Kidwell studies the population genetics and evolution of transposable elements in Drosophila and other Diptera. Recent and ongoing projects include examination of the frequency and possible mechanisms of horizontal transfer of mobile elements and the reconstruction of phylogenetic trees based on molecular data. She also uses computer simulations to model the dynamics of transposable elements in insect populations and population cage studies to explore the feasibility of using transposable elements as genetic drivers in Drosophila and mosquito populations. Other projects include the population genetics of malaria epidemiology and the mechanisms controlling immune responses to infection in Anopheline mosquitoes.
Selected Publications
1. Kidwell, M. G. and D. R. Lisch. 2001. Perspective: Transposable elements, parasitic DNA and genome evolution. Evolution 55: 1-24.
2. Kidwell, M. G. and D. R. Lisch. 2001. Transposable Elements as Sources of Genomic Variation. Chapter In Mobile DNA II. American Society of Microbiology Press. In press.
3. Lyozin, G. T., Makarova, K. S., Velikodvorskaja, V. V., Zelentsova, H. S., Khechumian, R. R., Kidwell, M. G., Koonin, E. V., and M. B. Evgen'ev. 2001. The structure and evolution of Penelope in the Drosophila virilis species group: an ancient lineage of retroelements. J. Mol. Evol. In press.
4. Kidwell, M. G. and D. R. Lisch. 2000. Transposable elements and host genome evolution. Trends Ecol. Evol. 15: 95-99.
5. Kidwell, M. G. and M. B. Evgen'ev. 2000. How valuable are model organisms for transposable element studies? Genetica 107:103-111
6. Evgen'ev, M. B., Zelentsova, H., Mnjoian, L., Poluectova,H., and M. G. Kidwell 2000. Invasion of Drosophila virilis by the Penelope transposable element. Chromosoma 109:350-357.
7. Silva, J. C. and M. G. Kidwell. 2000. Selection and horizontal transfer in the evolution of P elements. Mol. Biol. Evol. 17:1542-1557
8. Evgen'ev, M. B., Zelentsova, H., Poluectova, H., Lyozin, G. T., Veleikodvorskaja, V., Pyatkov, K. I., Zhivotovsky, L. A. and Kidwell, M. G. 2000. Mobile elements and chromosomal evolution in the virilis group of Drosophila. Proc. Natl. Acad. Sci. USA 97:11337-11342.
9. Lee, S. H., Clark, J. B., and M. G. Kidwell. 1999. A P-homologous sequence in the house fly, Musca domestica. Insect Molecular Biology 8:491-500.
10. Zelentsova, H., Poluectova, H., Mnjoian, L., G. Lyozin, V. Veleikodvorskaja, L. Zhivotovski, M. G. Kidwell, and M. B. Evgen'ev. 1999. Distribution and evolution of mobile elements in the virilis species group of Drosophila. Chromosoma 108: 443-456.
11. Kidwell, M. G. 1997. Hybrid dysgenesis determinants and other useful transposable elements. In Drosophila. Encyclopedia of Genetics. E. C. R. Reeve (ed.). Dearborn Publishers. New York.
Older Publications
1. Kidwell, M. G., J. F. Kidwell & J. A. Syed 1977. Hybrid dysgenesis in D. melanogaster: a syndrome of aberrant traits including mutation, sterility & male recombination. Genetics 36: 813-33.
2. Bingham, P. M., M. G. Kidwell & G. M. Rubin 1982. The molecular basis of P-M hybrid dysgenesis: The role of the P element, a P strain-specific transposon family. Cell 29: 995-1004.
3. Kidwell, M. G. 1983. Evolution of hybrid dysgenesis determinants in Drosophila melanogaster. Proc. Nat. Acad. Sci. USA 80: 1655-1659.
4. Anxolabéhère, D., M. G. Kidwell & G. Periquet 1988. Molecular characteristics of diverse populations are consistent with the hypothesis of a recent invasion of Drosophila melanogaster by mobile P elements. Mol. Biol. Evol. 5: 252-269.
5. Daniels, S. B., K. R. Peterson, L. D. Strausbaugh, M. G. Kidwell & A. Chovnick 1990. Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics 124: 339-355.
6. Houck, M. A., J. B. Clark, K. R. Peterson & M. G. Kidwell 1991. Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis. Science 253: 1125-1129.
7. Kidwell, M. G. 1993. Lateral transfer in natural populations of eukaryotes. Ann. Rev. Genet. 27: 235-256.
8. Clark, J. B., W. P. Maddison & M. G. Kidwell 1994. Phylogenetic analysis supports horizontal transfer of P transposable elements. Mol. Biol. Evol. 11:40-50.
9. Kidwell, M. G. and D. Lisch. 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. 94: 7704-7711.
10. Clark, J. B. and M. G. Kidwell 1997. A phylogenetic perspective on P element evolution in Drosophila. Proc. Natl. Acad. Sci. USA 94: 11428-11433.
......# Jumping genes in the dog
......# Nina Fedoroff
......# See also numerous other Natural GMOs posts listed under GMO Pundit above.
......# Uncle Osmar and his friend Stowaway in the rice genome.
......# Throwing nDarts.
......# Margaret Kidwell's 2000 review, and RAG genes too.
......# Nina Fedoroff
......# See also numerous other Natural GMOs posts listed under GMO Pundit above.
......# Uncle Osmar and his friend Stowaway in the rice genome.
......# Throwing nDarts.
......# Margaret Kidwell's 2000 review, and RAG genes too.
Treasures in the attic: Rolling circle transposons discovered in eukaryotic genomes
Cédric Feschotte and Susan R. Wessler
Cédric Feschotte and Susan R. Wessler
Since the advent of methodologies to analyze the content of whole genomes (e.g., renaturation kinetics and Cot analysis), it has been known that a large fraction of eukaryotic genomes is highly repetitive.Recent computer-assisted analysis of several sequenced eukaryotic genomes, including Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, and humans, has demonstrated that most repetitive DNA is composed of or derived from transposable elements (TEs). In the human genome, for example, TEs are the single most abundant component, accounting for over 40% of the total DNA. Although this amount of TEs is viewed as a hindrance to those engaged in the determination and assembly of DNA sequence, the availability of both complete and partial eukaryotic genome sequences is providing TE biologists with a bonanza of raw material that is being used to understand how genomes evolve.
Before the report in PNAS by Kapitonov and Jurka, all eukaryotic TEs were thought to use one of two mechanisms for transposition. Class 1, or retrotransposons, transpose via an RNA intermediate in reactions catalyzed by element-encoded proteins, including reverse transcriptase. In contrast, the transposon itself is the intermediate for class 2 elements where an element-encoded transposase catalyzes reactions, resulting in TE excision from one site and reinsertion elsewhere in the genome (the so-called cut-and-paste mechanism). In addition to these two mechanisms, some prokaryotic TEs (called IS or insertion sequences), move by another mechanism called rolling circle (RC) transposition. This process is similar to the RC replication of some plasmids, single-stranded (ss) bacteriophage, and plant geminiviruses. In a recent issue of PNAS, Kapitonov and Jurka report that RC transposons also occur in eukaryotes where, surprisingly, they comprise about 2% of the genomes of A. thaliana and C. elegans.
PNAS July 31, 2001 vol. 98 no. 16 8923-8924
Genome Research
Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
Benoit Piegu1, Romain Guyot1, Nathalie Picault1, Anne Roulin1, Abhijit Saniyal3, Hyeran Kim4, Kristi Collura4, Darshan S. Brar2, Scott Jackson3, Rod A. Wing4 and Olivier Panaud1,1
Genome Research 16:1262-1269, 2006
1Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD, Université de Perpignan, Perpignan 66860, France; , 2Plant Breeding Genetics and Biochemistry Division, International Rice Research Institute, Manila 1099, Philippines, USA; , 3Agricultural Genomics, Purdue University, West Lafayette, Indiana 47907, USA; , 4Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Benoit Piegu1, Romain Guyot1, Nathalie Picault1, Anne Roulin1, Abhijit Saniyal3, Hyeran Kim4, Kristi Collura4, Darshan S. Brar2, Scott Jackson3, Rod A. Wing4 and Olivier Panaud1,1
Genome Research 16:1262-1269, 2006
1Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD, Université de Perpignan, Perpignan 66860, France; , 2Plant Breeding Genetics and Biochemistry Division, International Rice Research Institute, Manila 1099, Philippines, USA; , 3Agricultural Genomics, Purdue University, West Lafayette, Indiana 47907, USA; , 4Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a "copy and paste" mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis, a wild relative of the Asian cultivated rice O. sativa, has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus.
Nature Magazine.
......# Human Genome Collection
It is now more than 15 years since work began sequencing the 2.85 billion nucleotides of the human genome. While the draft sequence was published in Nature in 2001, researchers at the Human Genome Project continued to fill the gaps and subject individual chromosomes to ever more detailed analyses. Nature is proud to present here the complete and comprehensive DNA sequence of the human genome as a freely available resource. Produced with support from our sponsors. Nature carries sole responsibility for all editorial content........# Role of mobile genes in evolution
5 October 2006 Nature
Volume 443 Number 7111 p521
Editor's Summary
Jump to it
Once dismissed as junk, selfish or parasitic DNA, transposable elements or 'jumping genes' are now regarded as major players in many of the processes that reshape the genome and control the activity of its genes. Christian Biémont and Cristina Vieira consider the two-pronged evolutionary impact of transposable elements as promoters of genetic diversity, and as agents for inflicting genetic damage and causing disease.
News and Views Feature: Genetics: Junk DNA as an evolutionary force, p521
Transposable elements were long dismissed as useless, but they are emerging as major players in evolution. Their interactions with the genome and the environment affect how genes are translated into physical traits.
Christian Biémont and Cristina Vieira
Cite the following:
1: Gene. 2005 Jan 17;345(1):101-11. Epub 2004 Dec 25.
Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals.
Brandt J, Schrauth S, Veith AM, Froschauer A, Haneke T, Schultheis C, Gessler M, Leimeister C, Volff JN.
Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Wurzburg, am Hubland, D-97074 Wurzburg, Germany.
A family of functional neogenes called Mart, related to the gag gene of Sushi-like long terminal repeat retrotransposons from fish and amphibians, is present in the genome of human (11 genes) and other primates, as well as in mouse (11 genes), rat, dog (12 genes), cat, and cow. Mart genes have lost their capacity of retrotransposition through non-functionalizing rearrangements having principally affected long terminal repeats and pol open reading frame. Most Mart genes are located on the X chromosome in different mammals. Sequence database analysis suggested that Mart genes are present in opossum (marsupial), but absent from the genome of chicken. Hence, the Mart gene family might have been formed from Sushi-like retrotransposon(s) after the split of birds and mammals (310 myr ago), but before the divergence between placental mammals and marsupials (170 myr ago). RT-PCR analysis showed that at least six Mart genes are expressed during mouse embryonic development, with in situ hybridization analysis revealing rather ubiquitous expression patterns. Mart expression was
also detected in adult mice, with some genes being expressed in all tissues tested, while others showed a much more restricted expression pattern. Although additional analysis will be required to establish the function of the retrotransposon-derived Mart neogenes, these observations support the evolutionary importance of retrotransposable elements as a source of genetic novelty.
PMID: 15716091 [PubMed - indexed for MEDLINE]
2: Cytogenet Genome Res. 2005;110(1-4):342-52.
Impact of transposable elements on the evolution of mammalian gene regulation.
Medstrand P, van de Lagemaat LN, Dunn CA, Landry JR, Svenback D, Mager DL.
Department of Cell and Molecular Biology, Biomedical Centre, Lund University, Lund, Sweden. patrik.medstrand@medkem.lu.se
Transposable elements (TEs) are present in all organisms and nearly half of the human and mouse genome is derived from ancient transpositions. This fact alone suggests that TEs have played a major role in genome organization and evolution.
Studies undertaken over the last two decades or so clearly show that TEs of various kinds have played an important role in organism evolution. Here we review the impact TEs have on the evolution of gene regulation and gene function with an emphasis on humans. Understanding the mechanisms resulting in genomic change is central to our understanding of gene regulation, genetic disease and genome evolution. Full comprehension of these biological processes is not possible without an in depth knowledge of how TEs impact upon the genome.
Publication Types:
Review
PMID: 16093686 [PubMed - indexed for MEDLINE]
3: Curr Opin Plant Biol. 2006 Apr;9(2):157-63. Epub 2006 Feb 3.
Organization and variability of the maize genome.
Messing J, Dooner HK.
Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA.
With a size approximating that of the human genome, the maize genome is about to become the largest plant genome yet sequenced. Contributing to that size are a whole-genome duplication event and a retrotransposition explosion that produced
a large amount of repetitive DNA. This DNA is greatly under-represented in cDNA collections, so analysis of the maize transcriptome has been an expedient way of assessing the gene content of maize. Over 2 million maize cDNA sequences are now available, making maize the third most widely studied organism, behind mouse and man. To date, the sequencing of large-sized DNA clones has been largely driven by the genetic interests of different investigators. The recent construction of
a physical map that is anchored to the genetic map will aid immensely in the maize genome-sequencing effort. However, studies showing that the repetitive DNA component is highly polymorphic among maize inbred lines point to the need to
sample vertically a few specific regions of the genome to evaluate the extent and importance of this variability.
Publication Types:
Review
PMID: 16459130 [PubMed - indexed for MEDLINE]
4: Genome Res. 2006 Jul;16(7):864-74. Epub 2006 May 22.
Functional noncoding sequences derived from SINEs in the mammalian genome.
Nishihara H, Smit AF, Okada N.
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.
Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective constraint. Here, we report that some of these loci have been derived from a newly defined family of ancient SINEs (short interspersed repetitive elements).
This is a surprising result, as SINEs and other transposable elements are commonly thought to be genomic parasites. We named the ancient SINE family AmnSINE1, for Amniota SINE1, because we found it to be present in mammals as well as in birds, and some copies predate the mammalian-bird split 310 million years ago (Mya). AmnSINE1 has a chimeric structure of a 5S rRNA and a tRNA-derived SINE, and is related to five tRNA-derived SINE families that we characterized here in the coelacanth, dogfish shark, hagfish, and amphioxus genomes. All of the newly described SINE families have a common central domain that is also shared by zebrafish SINE3, and we collectively name them the DeuSINE (Deuterostomia SINE) superfamily. Notably, of the approximately 1000 still identifiable copies of AmnSINE1 in the human genome, 105 correspond to loci phylogenetically highly conserved among mammalian orthologs. The conservation is strongest over the central domain. Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of
the copies have acquired genomic functionality.
PMID: 16717141 [PubMed - indexed for MEDLINE]
5: Dev Cell. 2004 Oct;7(4):597-606.
Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos.
Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, Knowles BB.
The Jackson Laboratory, Bar Harbor, ME 04609, USA.
A comprehensive analysis of transposable element (TE) expression in mammalian full-grown oocytes reveals that LTR class III retrotransposons make an unexpectedly high contribution to the maternal mRNA pool, which persists in cleavage stage embryos. The most abundant transcripts in the mouse oocyte are from the mouse transcript (MT) retrotransposon family, and expression of this and other TE families is developmentally regulated. Furthermore, TEs act as alternative promoters and first exons for a subset of host genes, regulating their expression in full-grown oocytes and cleavage stage embryos. To our
knowledge, this is the first example of TEs initiating synchronous, developmentally regulated expression of multiple genes in mammals. We propose that differential TE expression triggers sequential reprogramming of the embryonic genome during the oocyte to embryo transition and in preimplantation embryos.
PMID: 15469847 [PubMed - indexed for MEDLINE]
6: Cytogenet Genome Res. 2006;113(1-4):109-15.
Repetitive elements in imprinted genes.
Walter J, Hutter B, Khare T, Paulsen M.
Genetik/Epigenetik, FR 8.3 Biowissenschaften, Universitat des Saarlandes, Saarbrucken, Germany.
Genomic imprinting in mammals results in mono-allelic expression of about 80 genes depending on the parental origin of the alleles. Though the epigenetic mechanisms underlying imprinting are rather clear, little is known about the genetic basis for these epigenetic mechanisms. It is still rather enigmatic which sequence features discriminate imprinted from non-imprinted genes/regions and why and how certain sequence elements are recognized and differentially marked in the germlines. It seems likely that specific DNA elements serve as signatures that guide the necessary epigenetic modification machineries to the imprinted regions. Inter- and intraspecific comparative genomic studies suggest that the unusual occurrence and distribution of various types of repetitive elements within imprinted regions may represent such genomic imprinting
signatures. In this review we summarize the various observations made and discuss them in light of experimental data. 2006 S. Karger AG, Basel.
Publication Types:
Review
PMID: 16575169 [PubMed - indexed for MEDLINE]
7: Nucleic Acids Res. 2005 Apr 7;33(6):2052-9. Print 2005.
Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline.
Kalmykova AI, Klenov MS, Gvozdev VA.
Institute of Molecular Genetics RAS Kurchatov square 2, 123 182 Moscow, Russia.
Proteins of the Argonaute family have been identified as key components of RNA interference (RNAi) pathway. RNAi-related mechanisms are implicated in the regulation of gene expression and repression of transposable elements in
eukaryotes. The piwi gene encoding protein of the Drosophila Argonaute family was shown to be required for the germ stem cells maintenance. Here, we show that piwi is involved in silencing of LTR retrotransposons in testes. piwi mutations led to derepression of endogenous retrotransposon copia as well as to upregulation of the reporter gene driven by copia LTR. piwi mutation causes accumulation of retrotransposon mdg1 transcripts at the apical tip of testes, including germinal proliferative center where PIWI protein was shown to be expressed. We applied inverse PCR approach to detect the newly arisen insertions of the mdg1 retrotransposon in the progeny of individual piwi mutant males.
Owing to piwi mutation a high rate of mdg1 transpositions was revealed. Thus, piwi is involved in the silencing of retrotransposons in the precursors of male gametes. Our results provide the first evidence that protein of the Argonaute
family prevents retrotranspositions. It is supposed that the disturbance of RNA silencing system in germinal cells might cause transposition burst.
PMID: 15817569 [PubMed - indexed for MEDLINE]
8: Heredity. 2006 Feb;96(2):195-202.
RNAi: a defensive RNA-silencing against viruses and transposable elements.
Buchon N, Vaury C.
INSERM U384, 28 place Henri Dunant, 63000 Clermont-Ferrand, France.
RNA silencing is a form of nucleic-acid-based immunity, targeting viruses and genomic repeated sequences. First documented in plants and invertebrate animals, this host defence has recently been identified in mammals. RNAi is viewed as a conserved ancient mechanism protecting genomes from nucleic acid invaders.
However, these tamed sequences are known to occasionally escape this host surveillance and invade the genome of their host. This response is consistent with the overall idea that parasitic sequences compete with cells to systematically counter host defences. Using examples taken from the current literature, we illustrate the dynamic move-countermove game played between these two protagonists, the host cell and its parasitic sequences, and discuss the consequences of this game on genome stability.
Publication Types:
Review
PMID: 16369574 [PubMed - indexed for MEDLINE]
9: Nature. 2005 Jun 16;435(7044):903-10.
Comment in:
Nature. 2005 Jun 16;435(7044):890-1.
Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition.
Muotri AR, Chu VT, Marchetto MC, Deng W, Moran JV, Gage FH.
Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.
Revealing the mechanisms for neuronal somatic diversification remains a central challenge for understanding individual differences in brain organization and function. Here we show that an engineered human LINE-1 (for long interspersed
nuclear element-1; also known as L1) element can retrotranspose in neuronal precursors derived from rat hippocampus neural stem cells. The resulting retrotransposition events can alter the expression of neuronal genes, which, in turn, can influence neuronal cell fate in vitro. We further show that retrotransposition of a human L1 in transgenic mice results in neuronal somatic mosaicism. The molecular mechanism of action is probably mediated through Sox2, because a decrease in Sox2 expression during the early stages of neuronal differentiation is correlated with increases in both L1 transcription and
retrotransposition. Our data therefore indicate that neuronal genomes might not be static, but some might be mosaic because of de novo L1 retrotransposition events.
PMID: 15959507 [PubMed - indexed for MEDLINE]
10: Cytogenet Genome Res. 2005;110(1-4):242-9.
Host defenses to transposable elements and the evolution of genomic imprinting.
McDonald JF, Matzke MA, Matzke AJ.
Department of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
john.mcdonald@gatech.edu
Genomic imprinting is the differential expression of maternally and paternally inherited alleles of specific genes. Several organismic level hypotheses have been offered to explain the evolution of genomic imprinting. We argue that evolutionary explanations of the origin of imprinting that focus exclusively on the organismic level are incomplete. We propose that the complex molecular mechanisms that underlie genomic imprinting originally evolved as an adaptive response to the mutagenic potential of transposable elements (TEs). We also present a model of how these mechanisms may have been co-opted by natural selection to evolve molecular features characteristic of genomic imprinting.
Publication Types:
Review
PMID: 16093678 [PubMed - indexed for MEDLINE]
11: Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10604-9. Epub 2005 Jul 11.
Comment in:
Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10413-4.
Epigenetic differences arise during the lifetime of monozygotic twins.
Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suner D, Cigudosa JC, Urioste M, Benitez J, Boix-Chornet M, Sanchez-Aguilera A, Ling C, Carlsson E, Poulsen P, Vaag A, Stephan Z, Spector TD, Wu YZ, Plass C, Esteller
M.
Epigenetics Laboratory, Spanish National Cancer Centre (CNIO), Melchor Fernandez Almagro 3, 28029 Madrid, Spain.
Monozygous twins share a common genotype. However, most monozygotic twin pairs are not identical; several types of phenotypic discordance may be observed, such as differences in susceptibilities to disease and a wide range of anthropomorphic features. There are several possible explanations for these observations, but one is the existence of epigenetic differences. To address this issue, we examined the global and locus-specific differences in DNA methylation and histone acetylation of a large cohort of monozygotic twins. We found that, although twins are epigenetically indistinguishable during the early years of life, older monozygous twins exhibited remarkable differences in their overall content and genomic distribution of 5-methylcytosine DNA and histone acetylation, affecting their gene-expression portrait. These findings indicate
how an appreciation of epigenetics is missing from our understanding of how different phenotypes can be originated from the same genotype.
PMID: 16009939 [PubMed - indexed for MEDLINE]
12: Plant Cell. 2005 Dec;17(12):3301-10. Epub 2005 Oct 28.
Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase.
Kim SY, He Y, Jacob Y, Noh YS, Michaels S, Amasino R.
Department of Biology, Indiana University, Bloomington, 47405, USA.
Winter-annual accessions of Arabidopsis thaliana are often characterized by a requirement for exposure to the cold of winter to initiate flowering in the spring. The block to flowering prior to cold exposure is due to high levels of the flowering repressor FLOWERING LOCUS C (FLC). Exposure to cold promotes flowering through a process known as vernalization that epigenetically represses FLC expression. Rapid-cycling accessions typically have low levels of FLC expression and therefore do not require vernalization. A screen for mutants in which a winter-annual Arabidopsis is converted to a rapid-cycling type has identified a putative histone H3 methyl transferase that is required for FLC expression. Lesions in this methyl transferase, EARLY FLOWERING IN SHORT DAYS (EFS), result in reduced levels of histone H3 Lys 4 trimethylation in FLC chromatin. EFS is also required for expression of other genes in the FLC clade, such as MADS AFFECTING FLOWERING2 and FLOWERING LOCUS M. The requirement for EFS to permit expression of several FLC clade genes accounts for the ability of efs lesions to suppress delayed flowering due to the presence of FRIGIDA, autonomous pathway mutations, or growth in noninductive photoperiods. efs mutants exhibit pleiotropic phenotypes, indicating that the role of EFS is not limited to the
regulation of flowering time.
PMID: 16258034 [PubMed - indexed for MEDLINE]
13: Nature. 2004 Jul 22;430(6998):471-6.
Role of transposable elements in heterochromatin and epigenetic control.
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R.
Watson School of Biological Sciences and Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation.
Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that
is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that
heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond
to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1
and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.
PMID: 15269773 [PubMed - indexed for MEDLINE]
14: Nutrition. 2004 Jan;20(1):63-8.
Early nutrition, epigenetic changes at transposons and imprinted genes, and enhanced susceptibility to adult chronic diseases.
Waterland RA, Jirtle RL.
Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA. waterland@radonc.duke.edu
Publication Types:
Review
PMID: 14698016 [PubMed - indexed for MEDLINE]
15: Genetics. 2005 Nov;171(3):1183-94. Epub 2005 Sep 12.
Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome.
Hughes JF, Coffin JM.
Department of Molecular Microbiology and Program in Genetics, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
HERV elements make up a significant fraction of the human genome and, as interspersed repetitive elements, have the capacity to provide substrates for ectopic recombination and gene conversion events. To understand the extent to
which these events occur and gain further insight into the complex evolutionary history of these elements in our genome, we undertook a phylogenetic study of the long terminal repeat sequences of 15 HERV-K(HML-2) elements in various
primate species. This family of human endogenous retroviruses first entered the primate genome between 35 and 45 million years ago. Throughout primate evolution, these elements have undergone bursts of amplification. From this analysis, which is the largest-scale study of HERV sequence dynamics during primate evolution to date, we were able to detect intraelement gene conversion and recombination at five HERV-K loci. We also found evidence for replacement of an ancient element by another HERV-K provirus, apparently reflecting an occurrence of retroviral integration by homologous recombination. The high
frequency of these events casts doubt on the accuracy of integration time estimates based only on divergence between retroelement LTRs.
PMID: 16157677 [PubMed - indexed for MEDLINE]
16: Curr Opin Genet Dev. 1998 Jun;8(3):343-50.
Mobile elements and disease.
Kazazian HH Jr.
Department of Genetics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania 19104, USA. kazazian@mail.med.upenn.edu
A substantial fraction of mammalian genomes is composed of mobile elements and their remnants. Recent insertions of LTR-retrotransposons, non-LTR retrotransposons, and non-autonomous retrotransposons have caused disease frequently in mice, but infrequently in humans. Although many of these elements are defective, a number of mammalian non-LTR retrotransposons of the L1 type are capable of autonomous retrotransposition. The mechanism by which they
retrotranspose and in turn aide the retrotransposition of non-autonomous elements is being elucidated.
Publication Types:
Review
PMID: 9690999 [PubMed - indexed for MEDLINE]
17: Mol Cell Biol. 2003 May;23(10):3566-74.
Direct involvement of HERV-W Env glycoprotein in human trophoblast cell fusion and differentiation.
Frendo JL, Olivier D, Cheynet V, Blond JL, Bouton O, Vidaud M, Rabreau M, Evain-Brion D, Mallet F.
Unite INSERM 427, Faculte des Sciences Pharmaceutiques et Biologiques, Universite Rene Descartes, 75006 Paris, France.
We recently demonstrated that the product of the HERV-W env gene, a retroviral envelope protein also dubbed syncytin, is a highly fusogenic membrane glycoprotein inducing the formation of syncytia on interaction with the type D mammalian retrovirus receptor. In addition, the detection of HERV-W Env protein (Env-W) expression in placental tissue sections led us to propose a role for this fusogenic glycoprotein in placenta formation. To evaluate this hypothesis, we analyzed the involvement of Env-W in the differentiation of primary cultures of human villous cytotrophoblasts that spontaneously differentiate by cell
fusion into syncytiotrophoblasts in vitro. First, we observed that HERV-W env mRNA and glycoprotein expression are colinear with primary cytotrophoblast differentiation and with expression of human chorionic gonadotropin (hCG), a marker of syncytiotrophoblast formation. Second, we observed that in vitro stimulation of trophoblast cell fusion and differentiation by cyclic AMP is also associated with a concomitant increase in HERV-W env and hCG mRNA and protein expression. Finally, by using specific antisense oligonucleotides, we demonstrated that inhibition of Env-W protein expression leads to a decrease of trophoblast fusion and differentiation, with the secretion of hCG in culture medium of antisense oligonucleotide-treated cells being decreased by fivefold.
Taken together, these results strongly support a direct role for Env-W in human trophoblast cell fusion and differentiation.
PMID: 12724415 [PubMed - indexed for MEDLINE]
18: Cytogenet Genome Res. 2005;110(1-4):25-34.
What transposable elements tell us about genome organization and evolution: the case of Drosophila.
Biemont C, Vieira C.
Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558, Universite Lyon
1, Villeurbanne, France. biemont@bioserv.univ-lyon1.fr
Transposable elements (TEs) have been identified in every organism in which they have been looked for. The sequencing of large genomes, such as the human genome and those of Drosophila, Arabidopsis, Caenorhabditis, has also shown that they
are a major constituent of these genomes, accounting for 15% of the genome of Drosophila, 45% of the human genome, and more than 70% in some plants and amphibians. Compared with the 1% of genomic DNA dedicated to protein-coding
sequences in the human genome, this has prompted various researchers to suggest that the TEs and the other repetitive sequences that constitute the so-called "noncoding DNA", are where the most stimulating discoveries will be made in the
future (Bromham, 2002). We are therefore getting further and further from the original idea that this DNA was simply "junk DNA", that owed its presence in the genome entirely to its capacity for selfish transposition. Our understanding of
the structures of TEs, their distribution along the genomes, their sequence and insertion polymorphisms within genomes, and within and between populations and species, their impact on genes and on the regulatory mechanisms of genetic
expression, their effects on exon shuffling and other phenomena that reshape the genome, and their impact on genome size has increased dramatically in recent years. This leads to a more general picture of the impact of TEs on genomes,
though many copies are still mainly selfish or junk DNA. In this review we focus mainly on discoveries made in Drosophila, but we also use information about other genomes when this helps to elucidate the general processes involved in the organization, plasticity, and evolution of genomes.
Publication Types:
Review
PMID: 16093655 [PubMed - indexed for MEDLINE]
19: Science. 2003 Nov 21;302(5649):1401-4.
Comment in:
Science. 2004 Apr 16;304(5669):389-90; author reply 389-90.
Science. 2004 Nov 5;306(5698):978; author reply 978.
The origins of genome complexity.
Lynch M, Conery JS.
Department of Biology, Indiana University, Bloomington, IN 47405, USA.
mlynch@bio.indiana.edu
Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention
of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that
accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic
complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.
PMID: 14631042 [PubMed - indexed for MEDLINE]
20: Evolution Int J Org Evolution. 2001 Jan;55(1):1-24.
Perspective: transposable elements, parasitic DNA, and genome evolution.
Kidwell MG, Lisch DR.
Department of Ecology and Evolutionary Biology, The University of Arizona,
Tucson 85721, USA. kidwell@azstarnet.com
The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as "selfish DNA" and "junk DNA"
may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum,
endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level
but at a later stage of evolution are co-opted for new host functions.
Publication Types:
Review
PMID: 11263730 [PubMed - indexed for MEDLINE]
21: PLoS Genet. 2006 Mar;2(3):e36. Epub 2006 Mar 17.
Meiotically stable natural epialleles of Sadhu, a novel Arabidopsis retroposon.
Rangwala SH, Elumalai R, Vanier C, Ozkan H, Galbraith DW, Richards EJ.
Department of Biology, Washington University in St. Louis, St. Louis, Missouri,
USA.
Epigenetic variation is a potential source of genomic and phenotypic variation among different individuals in a population, and among different varieties within a species. We used a two-tiered approach to identify naturally occurring epigenetic alleles in the flowering plant Arabidopsis: a primary screen for transcript level polymorphisms among three strains (Col, Cvi, Ler), followed by a secondary screen for epigenetic alleles. Here, we describe the identification of stable, meiotically transmissible epigenetic alleles that correspond to one member of a previously uncharacterized non-LTR retroposon family, which we have
designated Sadhu. The pericentromeric At2g10410 element is highly expressed in strain Col, but silenced in Ler and 18 other strains surveyed. Transcription of this locus is inversely correlated with cytosine methylation and both the expression and DNA methylation states map in a Mendelian manner to stable cis-acting variation. The silent Ler allele can be converted by the epigenetic modifier mutation ddm1 to a meiotically stable expressing allele with an identical primary nucleotide sequence, demonstrating that the variation responsible for transcript level polymorphism among Arabidopsis strains is epigenetic. We extended our characterization of the Sadhu family members and show that different elements are subject to both genetic and epigenetic variation in natural populations. These findings support the view that an important component of natural variation in retroelements is epigenetic.
PMID: 16552445 [PubMed - indexed for MEDLINE]
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