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Topic: Retrotransposon

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	Missing steps of jumping-gene replication discovered
		Retrotransposons are one class of jumping genes, with the L1 family being the most abundant in the human genome.
		Retrotransposons move by having their DNA sequence transcribed or copied to RNA, and then instead of the genetic code being translated directly into a protein sequence, the RNA is copied back to DNA by the retrotransposon's own enzyme called reverse transcriptase.
		In subsequent generations, the retrotransposons moved within the offsprings' genomes and each new insertion could be detected by the investigators.
	www.eurekalert.org /pub_releases/2006-01/uops-mso013106.php (844 words)

	Reference.com/Encyclopedia/Retrotransposon
		Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms.
		Transposition and survival of retrotransposons within the host genome are possibly regulated both by retrotransposon- and host-encoded factors, to avoid deleterious effects on host and retrotransposon as well, in a relationship that has existed for many millions of years between retrotransposons and their plant hosts.
		The integrase is the retrotransposon equivalent of the transposase of DNA-transposons.
	www.reference.com /browse/wiki/Retrotransposon (680 words)

	Nup124p Is a Nuclear Pore Factor of Schizosaccharomyces pombe That Is Important for Nuclear Import and Activity of ...
		Nup124p Is a Nuclear Pore Factor of Schizosaccharomyces pombe That Is Important for Nuclear Import and Activity of Retrotransposon Tf1 -- Balasundaram et al.
		Sistla, S., Pang, J. V., Wang, C. X., Balasundaram, D. Multiple Conserved Domains of the Nucleoporin Nup124p and Its Orthologs Nup1p and Nup153 Are Critical for Nuclear Import and Activity of the Fission Yeast Tf1 Retrotransposon.
		Dang, V.-D., Levin, H. Nuclear Import of the Retrotransposon Tf1 Is Governed by a Nuclear Localization Signal That Possesses a Unique Requirement for the FXFG Nuclear Pore Factor Nup124p.
	mcb.asm.org /cgi/content/abstract/19/8/5768 (627 words)

	Ylli, a Non-LTR Retrotransposon L1 Family in the Dimorphic Yeast Yarrowia lipolytica -- Casaregola et al. 19 (5): 664 ...
		with the non–LTR retrotransposon RT and hybridized to
		A, The three yeast non–LTR retrotransposon ORF1 (Ylli, Zorro-1, Zorro-3) amino acid sequences and the human (L1Hs) and mouse (L1Md) ORF1 amino acid sequences were aligned with CLUSTAL W and CLUSTAL X with minor manual adjustments.
		2001 The diversity of retrotransposons in the yeast Cryptococcus neoformans Yeast 18:865-880
	mbe.oxfordjournals.org /cgi/content/full/19/5/664 (7243 words)

	VIDO - Solutions Through Research
		TCa2 is a Tyl/copia retrotransposon from the pathogenic yeast Candida albicans.
		The invention also provides a novel retrotransposon comprising at least one polypeptide positioned between at least two long terminal repeats, and wherein the retrotransposon is capable of integrating into the DNA in a genome providing a copy number of between 40 150 copies per genome.
		Retrotransposons can be used for gene insertion and expression studies in cell culture, gene therapy, for the generation of transgenic animals, and in where traditional RNA retroviral vectors may be used (as well as in instances where such RNA retroviral vectors theoretically may be employed but may be considered unsafe or undesirable).
	www.vido.org /patents/patent.php?patentnumber=5,969,126 (17904 words)

	Retrotransposon Summary
		Retrotransposons are mobile genetic elements and are ubiquitous in the genomes of many eukaryotic organisms.
		Transposition and survival of retrotransposons within the host genome are possibly regulated both by retrotransposon- and host-encoded factors, to avoid deleterious effects on host and retrotransposon as well, in a relationship that has existed for many millions of years between retrotransposons and their plant hosts.
		The integrase is the retrotransposon equivalent of the transposase of DNA-transposons.
	www.bookrags.com /Retrotransposon (1241 words)

	BioMed Central \| Full text \| Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
		The retrotransposon Tnt1, first characterised in tobacco, is one of the few plant retrotransposons for which transpositional activity has been demonstrated [8].
		Considering the Tnt1 superfamily of retrotransposons in the genera Solanum, Lycopersicon and Nicotiana as a population of sequences with a common ancestor, a Network study was carried out with the aim of testing the hypothesis that a common α master sequence exists in Tnt1-superfamily.
		Co-evolution and co-adaptation of retrotransposon with its host genome is expected to play a particularly important role in the long-term survival of these genetic elements [22].
	www.biomedcentral.com /1471-2148/7/34 (4984 words)

	Involvement of Ethylene in Stress-Induced Expression of the TLC1.1 Retrotransposon From Lycopersicon Chilense Dun.1[W] ... (Site not responding. Last check: )
		Retrotransposons are mobile genetic elements that share several structural and functional characteristics with retroviruses (Boeke and Corces, 1989).
		Complete copies of the TLC1 retrotransposon were obtained by screening a genomic library from L. chilense with a DNA probe corresponding to a conserved domain in the reverse transcriptase coding region within the TLC1 retrotransposon family (Yaez et al., 1998).
		Retrotransposons are major constituents of higher-plant genomes and provide much of the raw material for the evolution of genome structure and function.
	www.redorbit.com /news/display?id=229629&source=r_scienc (8225 words)

	Genome Biology \| Full text \| Long terminal repeat retrotransposons of Oryza sativa
		Our estimate that LTR retrotransposons make up 17% of the rice genome is conservative, inasmuch as our study was based primarily on euchromatic sequences and did not include elements present within the traditionally retrotransposon-rich heterochromatin [14,17].
		This disproportionate increase in the percentage of LTR retrotransposons as a function of genome size is consistent with the view that genome size variability in plants is often heavily dependent on variation in LTR retrotransposon content [27,28].
		It remains to be determined whether or not this hypothesis is an adequate explanation of the apparent lack of older full-length LTR retrotransposons in the euchromatic portion of the rice genome.
	genomebiology.com /2002/3/10/research/0053 (5864 words)

	Spartanburg SC \| GoUpstate.com \| Spartanburg Herald-Journal (Site not responding. Last check: )
		Retrotransposon integrations are assumed to be irreversible events since no eminent biological mechanisms have yet been described for the precise re-excision of class I transposons (but see van de Lagemaat et al., 2005).
		The 'presence' of a given Retrotransposon in related taxa implies their orthologues integration, a derived condition acquired via a common ancestry, while the 'absence' of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa.
		Examples for phylogenetic studies based on Retrotransposon presence/absence data are the definition of whales as members of the order Cetartiodactyla with hippos being their closest living relatives (Nikaido et al., 1999), hominoid relationships (Salem et al.
	www.goupstate.com /apps/pbcs.dll/section?category=NEWS&template=wiki&text=Retrotransposon_Marker (630 words)

	Genome Biology \| Full text \| Long terminal repeat retrotransposons of Mus musculus
		Retrotransposons fall into two main categories: those with long terminal repeats (LTRs), such as retroviruses and LTR retrotransposons, and those that lack such repeats, for example, long interspersed nuclear elements (LINEs).
		An LTR retrotransposon 'family' is defined as a group of elements with RTs at least 90% similar at the amino acid level [7].
		In using these names for the three main categories of murine LTR retrotransposons we follow the usage of the Mouse Genome Sequencing Consortium [4], but the reader is cautioned that the same terminology has been used to designate RNA-based transposons (Class I) and DNA-based transposons (Class II).
	genomebiology.com /2004/5/3/R14 (3666 words)

	Spartanburg SC \| GoUpstate.com \| Spartanburg Herald-Journal (Site not responding. Last check: )
		Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms.
		Retrotransposons, also known as class I transposable elements, consist of two sub-types, the long terminal repeat (LTR) and the non-LTR retrotransposons.
		LTR retrotransposons are further sub-classified into the Ty1-copia-like (Pseudoviridae) and the Ty3-gypsy-like (Metaviridae) groups based on both their degree of sequence similarity and the order of encoded gene products.
	www.goupstate.com /apps/pbcs.dll/section?category=NEWS&template=wiki&text=Retrotransposon (911 words)

	Analysis of Phytophthora parasitica by retrotransposon-derived DNA fingerprinting
		Retrotransposons are mobile genetic elements, which replicate through an RNA intermediate prior to integration into the chromosomal DNA of their host.
		PCR with ty1A and ty1B, which were designed according to the conserved reverse transcriptase sequence of Ty1-copia retrotransposons (Flavell et al., 1992), gave rise to a DNA fragment of the expected size, approximately 260 bp in length (data not shown).
		Retrotransposons are mobile genetic elements, which replicate by successive transcription, reverse transcription, and insertion of the new cDNA copies back into the genome.
	ejournal.sinica.edu.tw /bbas/content/2002/1/bot431-03.html (3860 words)

	BioBeat Online Magazine
		Fukuyama-type congenital muscular dystrophy (FCMD), an unusual form of muscular dystrophy that is particularly common in Japan, appears to be caused by the presence of an ancient retrotransposon insertion in a newly identified gene called the FCMD gene, according to a recent report in Nature (Kobayashi, K., et al., Nature 394: 388—392, July 23, 1998).
		The authors suggest that the retrotransposon insertion, or other mutations in the FCMD gene, are likely to cause a decrease in the gene’s transcription, and/or an instability in its mRNA, resulting in a loss of function.
		They note that the retrotransposon insertion, which is approximately 3,000 bases long, is located in the 3’-untranslated region of the FCMD gene, and could theoretically result in an altered secondary structure for the FCMD mRNA, possibly rendering it unstable.
	www.appliedbiosystems.com /biobeat/index.jsp?articleId=08a7de0a-97b3-27ac-fd70911fd454a521&type=0 (613 words)

	[No title]
		Retrotransposon diversity in Deuterostomia, as shown by phylogenetic analyses, was found to be much greater than previously expected.
		To investigate the tempo and mode of retrotransposon evolution in Deuterostomia, I examined the retrotransposon repertoire in the most ancestral deuterostomian lineage, in echinoderms.
		Thus, deciphering the ancestral state of retrotransposon repertoire in Deuterostomia is pivotal to understanding their evolution in vertebrates.The first global analysis of the tempo and mode of retrotransposon evolution in the genomes of Deuterostomia will be presented.
	www.up.univ-mrs.fr /evol-cgr/home_page/meeting2004/02.html (312 words)

	Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition ...
		Retrotransposons occur in all eukaryotes and are the
		Boeke, J.D. and Stoye, J.P. Retrotransposons, endogenous retro-viruses, and the evolution.
		Peterson-Burch, B.D. and Voytas, D.F. Genes of the Pseudoviridae (Ty1/copia retrotransposons).
	www.rnajournal.org /cgi/content/full/11/8/1181 (6154 words)

	Complex patterns of transcription at the insertion site of a retrotransposon in the mouse -- Druker et al. 32 (19): ...
		retrotransposon affects the expression of the adjacent gene.
		Han,J.S., Szak,S.T. and Boeke,J.D. ((2004)) Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes.
		Dupressoir,A. and Heidmann,T. ((1996)) Germ line-specific expression of intracisternal A-particle retrotransposons in transgenic mice.
	nar.oxfordjournals.org /cgi/content/full/32/19/5800 (3877 words)

	Target Site Specificity of the Tos17 Retrotransposon Shows a Preference for Insertion within Genes and against ...
		of the fava bean genome are occupied by retrotransposons.
		Tos17 is not excised in regenerated rice and is inherited stably;
		Devine, S.E., and Boeke, J.D. Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III.
	www.plantcell.org /cgi/content/full/15/8/1771 (6338 words)

	Poster 549 - Evolutionary genomics of Deuterostomia: tempo and mode of non-LTR retrotransposon evolution (Site not responding. Last check: )
		Retrotransposons are playing a central role in the structure, evolution and function of eukaryotic genomes.
		Thus, deciphering the ancestral state of non-LTR retrotransposon repertoire in Deuterostomia is pivotal to understanding their evolution in vertebrates.
		We found that in Deuterostomia each non-LTR retrotransposon clade shows their specific pattern of short- and long-term evolutionary dynamics that could be in some cases simple but in the other very complex.
	hgm2002.hgu.mrc.ac.uk /HGM2002/Abstracts/Publish/WorkshopPosters/WorkshopPoster11/hgm0549.htm (323 words)

	Cancer Cell International \| Full text \| Human LINE-1 retrotransposon induces DNA damage and apoptosis in cancer cells
		Thus, the role of retrotransoposons in general, and of L1 in particular, in DNA damage and repair assumes larger significance both for the understanding of mutagenicity and, potentially, for the control of cell proliferation and apoptosis.
		Retrotransposons are mobile retroelements that utilize reverse transcriptase and RNA intermediates to relocate within the cellular genome.
		LINE-1 (Long Interspersed Nuclear Element type 1, or L1), is the most common family of non-LTR retrotransposons in the human genome; with about 500,000 copies, it comprises about 17% of the genome [1,2].
	www.cancerci.com /content/6/1/13 (4260 words)

	CiteULike: TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p ... (Site not responding. Last check: )
		TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs.
		Retrotransposons are RNA elements that reverse transcribe their RNA genomes and make a cDNA copy that is inserted back into a new genomic location by the element-encoded integrase protein.
		Ty1 is a long terminal repeat (LTR) retrotransposon in Saccharomyces cerevisiae that inserts into an approximately 700-bp integration window upstream of tRNA genes with a periodicity of approximately 80 bp.
	www.citeulike.org /user/sameetmehta/article/1077556 (489 words)

	Voytas Lab: Publications
		The Sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, ineract with a family of proteins to dynein light chain 8.
		The yeast retrotransposon Ty5 uses the anticondon stem-loop of the initiator methionine tRNA as a primer for reverse transcription.
		(1995) The Saccharomyces Ty5 retrotransposon family is associated with origins of DNA replication at the telomeres and the silent mating locus HMR.
	www.public.iastate.edu /~voytas/Publications.html (1013 words)

	Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum -- Vicient et al. 11 (9): 1769 -- THE ...
		Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum -- Vicient et al.
		Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum
		SanMiguel, P., Gaut, B.S., Tikhoniv, A., Nakajima, Y., and Bennetzen, J.L. (1998) The paleontology of intergene retrotransposons in maize.
	www.plantcell.org /cgi/content/full/11/9/1769 (7191 words)

	Active Retrotransposons Are a Common Feature of Grass Genomes -- Vicient et al. 125 (3): 1283 -- PLANT PHYSIOLOGY
		Retrotransposons are well established as ubiquitous and highly prevalent components of plant genomes in general.
		Hirochika H (1997) Retrotransposons of rice: their regulation and use for genome analysis.
		Suoniemi A, Tanskanen J, Schulman AH (1998) Gypsy-like retrotransposons are widespread in the plant kingdom.
	www.plantphysiol.org /cgi/content/full/125/3/1283 (5095 words)

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