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REVIEW: Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
- Victoria P. Belancio,
- Dale J. Hedges,
- and Prescott Deininger
Genome Res. March 2008 18: 343-358; Published in Advance February 6, 2008, doi:10.1101/gr.5558208
...or theoretical considerations. Autonomous retrotransposons LINE-1 The most active autonomous non-LTR element identified within currently sequenced mammalian s is the LINE-1 (L1) element. Transcription of L1 generates a retrotranspositionally competent, full-length L1 mRNA ( Skowronski and Singer 1985 ; Dombroski...
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Method: The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism
- Maximilian P.A. Salm,
- Stuart D. Horswell,
- Claire E. Hutchison,
- Helen E. Speedy,
- Xia Yang,
- Liming Liang,
- Eric E. Schadt,
- William O. Cookson,
- Anthony S. Wierzbicki,
- Rossi P. Naoumova,
- and Carol C. Shoulders
Genome Res. June 2012 22: 1144-1153; Published in Advance March 7, 2012, doi:10.1101/gr.126037.111
...and chimpanzee s are products of NAHR between Alu or LINE-1 elements (Lee et al. 2008). Similarly, >16% of human HERV-K elements may have mediated large-scale rearrangements during primate evolution (Hughes and Coffin 2001). Retrotransposons promote genomic instability through replication-fork stalling...
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Research: The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important
- Erika M. Kvikstad and
- Kateryna D. Makova
Genome Res. May 2010 20: 600-613; Published in Advance March 10, 2010, doi:10.1101/gr.099044.109
...The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important Erika M. Kvikstad 1 and Kateryna D. Makova 2 Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...↵11 These authors contributed equally to this work. Corresponding authors: adam.ewing@mater.uq.edu.au, carbone@ohsu.edu, faulknergj@gmail.comAbstractThe retrotransposon LINE-1 (L1) is central to the recent evolutionary history of the human and continues to drive genetic diversity and germline...
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Research: LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
- Shengjun Tan,
- Margarida Cardoso-Moreira,
- Wenwen Shi,
- Dan Zhang,
- Jiawei Huang,
- Yanan Mao,
- Hangxing Jia,
- Yaqiong Zhang,
- Chunyan Chen,
- Yi Shao,
- Liang Leng,
- Zhonghua Liu,
- Xun Huang,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. December 2016 26: 1663-1675; Published in Advance October 20, 2016, doi:10.1101/gr.204925.116
...it has been conclusively shown that retrocopies can be generated by the reverse transcriptase (RT) of LINE1 or L1 retrotransposons (Eickbush 1999; Moran et al. 1999; Esnault et al. 2000;Wei et al. 2001). L1-mediated retrocopies harbor several hallmark sequences in their flanking regions: a TTTT...
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Research: Noncoding origins of anthropoid traits and a new null model of transposon functionalization
- Ricardo C.H. del Rosario,
- Nirmala Arul Rayan,
- and Shyam Prabhakar
Genome Res. September 2014 24: 1469-1484; Published in Advance July 20, 2014, doi:10.1101/gr.168963.113
...functionalization applies to enhancers in vivo. Our study provides fundamental insights into genome evolution and the origins of anthropoid phenotypes and supports an elegantly simple new model of TE exaptation. Footnotes [Supplemental material is available for this article.] Article...
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Method: Epigenomic differences in the human and chimpanzee genomes are associated with structural variation
- Xiaoyu Zhuo,
- Alan Y. Du,
- Erica C. Pehrsson,
- Daofeng Li,
- and Ting Wang
Genome Res. February 2021 31: 279-290; Published in Advance December 10, 2020, doi:10.1101/gr.263491.120
...in Escherichia coli. Nature 274: 775–780. doi:10.1038/274775a0 ↵Danko CG, Choate LA, Marks BA, Rice EJ, Wang Z, Chu T, Martins AL, Dukler N, Coonrod SA, Tait Wojno ED, et al. 2018. Dynamic evolution of regulatory element ensembles in primate CD4+ T cells. Nature Ecology & Evolution 2: 537–548. doi:10.1038/s41559...
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Research: Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
- Cai Li,
- Boris Lenhard,
- and Nicholas M. Luscombe
Genome Res. May 2018 28: 676-688; Published in Advance April 4, 2018, doi:10.1101/gr.231449.117
...-less promoters may have originated as LTR-derived TATA-box-containing promoters.LINE-1 (L1) is the most abundant LINE family, covering ∼20% of the human . The overall distribution of TSSs along L1 elements (Fig. 2C) is similar to that of Faulkner et al. (2009); however, there are further observations...
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Research: A matter of life or death: How microsatellites emerge in and vanish from the human genome
- Yogeshwar D. Kelkar,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2011 21: 2038-2048; Published in Advance October 12, 2011, doi:10.1101/gr.122937.111
...; e.g., they are associated with over 40 genetic diseases (Pearson et al. 2005). The evolution of a microsatellite can be represented as a ‘‘life cycle’’ (Amos 1999; Buschiazzo and Gemmell 2006), comprised of (a) birth, when a locus acquires the number of repeats (a threshold) required for high rates...
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LETTER: The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage
- John K. Pace II and
- Cédric Feschotte
Genome Res. April 2007 17: 422-432; Published in Advance March 5, 2007, doi:10.1101/gr.5826307
...transpositionally active in the primate lineage. Below we first discuss the value of combining various methods for estimating the age of TEs, then turn to the specific implications of our findings for primate evolution and for understanding the forces underlying the amplification dynamics of TEs in mammalian s...

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