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Method: The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- Eugene J. Gardner,
- Vincent K. Lam,
- Daniel N. Harris,
- Nelson T. Chuang,
- Emma C. Scott,
- W. Stephen Pittard,
- Ryan E. Mills,
- The 1000 Genomes Project Consortium,
- and Scott E. Devine
Genome Res. November 2017 27: 1916-1929; Published in Advance August 30, 2017, doi:10.1101/gr.218032.116
...MELT-SGEmultiple sample modes are engineered for population-scale studies involving hundreds or thousands of s. Mobile Element Locator Tool (MELT) Genome Research 1917 www..org As outlined above, an additional advantage of the multiple samplemodes is that evidence for eachMEI is drawn frommultiple s (instead of just one...
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Research: Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency
- Marc Friedli,
- Priscilla Turelli,
- Adamandia Kapopoulou,
- Benjamin Rauwel,
- Nathaly Castro-Díaz,
- Helen M. Rowe,
- Gabriela Ecco,
- Carmen Unzu,
- Evarist Planet,
- Angelo Lombardo,
- Bastien Mangeat,
- Barbara E. Wildhaber,
- Luigi Naldini,
- and Didier Trono
Genome Res. August 2014 24: 1251-1259; Published in Advance May 30, 2014, doi:10.1101/gr.172809.114
...transposable elements. Genome Res 18: 1752–1762. Chuong EB, Rumi MA, Soares MJ, Baker JC. 2013. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet 45: 325–329. Corsinotti A, Kapopoulou A, Gubelmann C, Imbeault M, Santoni de Sio FR, Rowe HM, Mouscaz Y, Deplancke B...
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Method: Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations
- David J. Witherspoon,
- Yuhua Zhang,
- Jinchuan Xing,
- W. Scott Watkins,
- Hongseok Ha,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. July 2013 23: 1170-1181; Published in Advance April 18, 2013, doi:10.1101/gr.148973.112
...Watkins, W Watkins, WS Xing Jinchuan Lynn Jorde L Jorde L.B. Jorde Xing, Jinchuan Zhang, Yuhua Witherspoon, David J LB Jorde Yuhua genome;gr.148973.112 10.1101/gr.148973.112 1088-9051 Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations Method Mobile...
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Research: Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
- Jingfeng Li,
- Keiko Akagi,
- Yongjun Hu,
- Anna L. Trivett,
- Christopher J.W. Hlynialuk,
- Deborah A. Swing,
- Natalia Volfovsky,
- Tamara C. Morgan,
- Yelena Golubeva,
- Robert M. Stephens,
- David E. Smith,
- and David E. Symer
Genome Res. May 2012 22: 870-884; Published in Advance February 23, 2012, doi:10.1101/gr.130740.111
...or disrupting gene expression since they comprise almost half of the mouse and certain elements are still actively mobilized. Approximately 10% of naturally occurring mutations in the mouse have been attributed to insertional mutagenesis of coding sequences due to endogenous retrotransposition (Waterston et al...
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Research: Alu repeat discovery and characterization within human genomes
- Fereydoun Hormozdiari,
- Can Alkan,
- Mario Ventura,
- Iman Hajirasouliha,
- Maika Malig,
- Faraz Hach,
- Deniz Yorukoglu,
- Phuong Dao,
- Marzieh Bakhshi,
- S. Cenk Sahinalp,
- and Evan E. Eichler
Genome Res. June 2011 21: 840-849; Published in Advance December 3, 2010, doi:10.1101/gr.115956.110
.... References The 1000 Genomes Project Consortium. 2010. A map of human variation from population-scale sequencing. Nature 467: 1061–1073. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, et al. 2009. Personalized copy number and segmental...
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ARTICLE: The Complete Genome and Proteome of Mycoplasma mobile
- Jacob D. Jaffe,
- Nicole Stange-Thomann,
- Cherylyn Smith,
- David DeCaprio,
- Sheila Fisher,
- Jonathan Butler,
- Sarah Calvo,
- Tim Elkins,
- Michael G. FitzGerald,
- Nabil Hafez,
- Chinnappa D. Kodira,
- John Major,
- Shunguang Wang,
- Jane Wilkinson,
- Robert Nicol,
- Chad Nusbaum,
- Bruce Birren,
- Howard C. Berg,
- and George M. Church
Genome Res. August 2004 14: 1447-1461; doi:10.1101/gr.2674004
..., and the tmRNA in the genomic sequence. No insertion sequences (ISs), transposons, or endogenous plasmids were found in the , although the presence of these elements has been reported in several other mycoplasma s ( Sasaki et al. 2002 ; Papazisi et al. 2003 ; Westberg et al. 2004 ). View larger version...
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Letter: A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains
- Yongming Wang,
- František Liška,
- Claudia Gosele,
- Lucie Šedová,
- Vladimír Křen,
- Drahomíra Křenová,
- Zoltán Ivics,
- Norbert Hubner,
- and Zsuzsanna Izsvák
Genome Res. January 2010 20: 19-27; Published in Advance November 3, 2009, doi:10.1101/gr.100073.109
.... However, autonomous retrotransposition of potentially active elements has not been demonstrated in the rat genome. We cloned an insertion that disrupted the normal splicing of the Cntrob gene that was subsequently identified as a nonautonomous, novel endogenous retrovirus of the RnERV-K8e family. The Rn...
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LETTER: Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
- Keiko Akagi,
- Jingfeng Li,
- Robert M. Stephens,
- Natalia Volfovsky,
- and David E. Symer
Genome Res. June 2008 18: 869-880; Published in Advance April 1, 2008, doi:10.1101/gr.075770.107
...of the identified genomic variants between mouse strains were caused by recent mobilization of endogenous transposable elements, of which L1 retrotransposons were most active. Additionally, as described here, we found that a substantial number of these polymorphic transposons directly altered transcript structures...
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LETTER: Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements
- Marie Dewannieux,
- Francis Harper,
- Aurélien Richaud,
- Claire Letzelter,
- David Ribet,
- Gérard Pierron,
- and Thierry Heidmann
Genome Res. December 2006 16: 1548-1556; Published in Advance October 31, 2006, doi:10.1101/gr.5565706
...be characterized at both the structural and functional level. Actually, following “endogenization,” which transformed its retroviral status into that of a host genomic locus and thus dramatically reduced its evolutionary rate, this element has been frozen in time in its ancestral state, which we have recovered...
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Letter: Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
- Jian Lu and
- Andrew G. Clark
Genome Res. February 2010 20: 212-227; Published in Advance November 30, 2009, doi:10.1101/gr.095406.109
...) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-interacting RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruit flies...

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