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LETTER: Active Alu retrotransposons in the human genome
- E. Andrew Bennett,
- Heiko Keller,
- Ryan E. Mills,
- Steffen Schmidt,
- John V. Moran,
- Oliver Weichenrieder,
- and Scott E. Devine
Genome Res. December 2008 18: 1875-1883; Published in Advance October 3, 2008, doi:10.1101/gr.081737.108
....J. ( 2000 ) Statistics with Confidence ( BMJ books , Bristol, UK ) 2d edition . ↵ Batzer, M.A. , Deininger, P.L. ( 2002 ) Alu repeats and human genomic diversity . Nat. Rev. Genet. 35 : 501 – 538 . ↵ Belancio, V.P. , Hedges, D.J. , Deininger, P. ( 2008 ) Mammalian non-LTR retrotransposons: For better...
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Research: Discovery of a new repeat family in the Callithrix jacchus genome
- Miriam K. Konkel,
- Brygg Ullmer,
- Erika L. Arceneaux,
- Sreeja Sanampudi,
- Sarah A. Brantley,
- Robert Hubley,
- Arian F.A. Smit,
- and Mark A. Batzer
Genome Res. May 2016 26: 649-659; Published in Advance February 25, 2016, doi:10.1101/gr.199075.115
..., Hoppens CL, Deininger PL. 1990. Structure and variability of recently inserted Alu family members. Nucleic Acids Res 18: 6793–6798. Platy-1 , a New World monkey-specific repeat family Genome Research 657 www..org Belancio VP, Hedges DJ, Deininger P. 2008. Mammalian non-LTR retrotransposons: for better...
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Letter: 5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genome
- Annette Damert,
- Julija Raiz,
- Axel V. Horn,
- Johannes Löwer,
- Hui Wang,
- Jinchuan Xing,
- Mark A. Batzer,
- Roswitha Löwer,
- and Gerald G. Schumann
Genome Res. November 2009 19: 1992-2008; Published in Advance August 3, 2009, doi:10.1101/gr.093435.109
...via cis- or trans-splicing must have covered at least this fraction of MAST2 exon 1 (Fig. 8A). The MAST2 promoter that was most likely recruited by the ancestral SVA source element 1A for its mobilization is reported to be highly active in mammalian testicular tissue, although the promoter sequence...
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Letter: Exon-trapping mediated by the human retrotransposon SVA
- Dustin C. Hancks,
- Adam D. Ewing,
- Jesse E. Chen,
- Katsushi Tokunaga,
- and Haig H. Kazazian, Jr
Genome Res. November 2009 19: 1983-1991; Published in Advance July 27, 2009, doi:10.1101/gr.093153.109
...on mammalian gene expression. Nucleic Acids Res 34: 1512– 1521. Belancio VP, Hedges DJ, Deininger P. 2008. Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health. Genome Res 18: 343–358. Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. 2004. Natural genetic variation caused...
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Letter: Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius
- Fangqing Zhao,
- Ji Qi,
- and Stephan C. Schuster
Genome Res. August 2009 19: 1384-1392; Published in Advance June 9, 2009, doi:10.1101/gr.091363.109
...25: 3389–3402. Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37–48. Belancio VP, Hedges DJ, Deininger P. 2008. Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health. Genome Res 18: 343...
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Letter: Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard
- Nicolas Di-Poï,
- Juan I. Montoya-Burgos,
- and Denis Duboule
Genome Res. April 2009 19: 602-610; Published in Advance February 18, 2009, doi:10.1101/gr.087932.108
.... ↵ Belancio, V.P. , Hedges, D.J. , Deininger, P. ( 2008 ) Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health . Genome Res. 18 : 343 – 358 . ↵ Brown, W.M. , Taylor, G.R. ( 1994 ) The 5′-sequence of the murine Hox-b3 (Hox-2.7) gene and its intron contain multiple transcription...
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Research: Characteristics of de novo structural changes in the human genome
- Wigard P. Kloosterman,
- Laurent C. Francioli,
- Fereydoun Hormozdiari,
- Tobias Marschall,
- Jayne Y. Hehir-Kwa,
- Abdel Abdellaoui,
- Eric-Wubbo Lameijer,
- Matthijs H. Moed,
- Vyacheslav Koval,
- Ivo Renkens,
- Markus J. van Roosmalen,
- Pascal Arp,
- Lennart C. Karssen,
- Bradley P. Coe,
- Robert E. Handsaker,
- Eka D. Suchiman,
- Edwin Cuppen,
- Djie Tjwan Thung,
- Mitch McVey,
- Michael C. Wendl,
- Genome of the Netherlands Consortium,
- André Uitterlinden,
- Cornelia M. van Duijn,
- Morris A. Swertz,
- Cisca Wijmenga,
- GertJan B. van Ommen,
- P. Eline Slagboom,
- Dorret I. Boomsma,
- Alexander Schönhuth,
- Evan E. Eichler,
- Paul I.W. de Bakker,
- Kai Ye,
- and Victor Guryev
Genome Res. June 2015 25: 792-801; Published in Advance April 16, 2015, doi:10.1101/gr.185041.114
...analysis of a complex chromosomal rearrangement and a review of familial cases. Am J Med Genet 53: 255–263. Belancio VP, Hedges DJ, Deininger P. 2008. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res 18: 343–358. Besenbacher S, Liu S, Izarzugaza JMG, Grove J...
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Letter: Mobile elements create structural variation: Analysis of a complete human genome
- Jinchuan Xing,
- Yuhua Zhang,
- Kyudong Han,
- Abdel Halim Salem,
- Shurjo K. Sen,
- Chad D. Huff,
- Qiong Zhou,
- Ewen F. Kirkness,
- Samuel Levy,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. September 2009 19: 1516-1526; Published in Advance May 13, 2009, doi:10.1101/gr.091827.109
...Sequencing and Analysis Consortium2005;Wang et al. 2005;Mills et al. 2006; Han et al. 2007a). Non-LTR retrotransposons, including L1s, Alus, and SVAs, mobilize via RNA intermediates using a mechanism called target site-primed reverse transcription (TPRT) (Luan et al. 1993; Feng et al. 1996; Cost et al. 2002...
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Resource: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
- Adam D. Ewing and
- Haig H. Kazazian, Jr.
Genome Res. June 2011 21: 985-990; Published in Advance October 27, 2010, doi:10.1101/gr.114777.110
...RM, Moran JV. 2010. LINE-1 retrotransposition activity in human s. Cell 141: 1159–1170. Belancio VP, Hedges DJ, Deininger P. 2008. Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health. Genome Res 18: 343–358. Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. 2004...
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Article: Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die?
- Matthew S. Comeaux,
- Astrid M. Roy-Engel,
- Dale J. Hedges,
- and Prescott L. Deininger
Genome Res. April 2009 19: 545-555; Published in Advance March 9, 2009, doi:10.1101/gr.089789.108
...further tested the relative influences of thymine (T), cytosine (C), and guanine (G) disruptions to the A-tail ( Fig. 4C ) and observed a general trend where T &lt;&lt; C &lt; G when it comes to disruptions in the A-tail influencing Alu activity. The A3T construct retrotransposed much better than the A5C...
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