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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
..., albeit without marked differences between brain regions (Fig. 2B; Supplemental Tables S4, S5). Similarly to KZFP genes, TEs have emerged continuously throughout evolution, with both young integrants and relics of ancient TEs reflective of different waves of genomic invasion. Using TE subfamily age...
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Research: Widespread contribution of transposable elements to the innovation of gene regulatory networks
- Vasavi Sundaram,
- Yong Cheng,
- Zhihai Ma,
- Daofeng Li,
- Xiaoyun Xing,
- Peter Edge,
- Michael P. Snyder,
- and Ting Wang
Genome Res. December 2014 24: 1963-1976; Published in Advance October 15, 2014, doi:10.1101/gr.168872.113
...expect that TE sequences of ancient subfamilies (prior to the human-mouse split) might not be detectible in mouse. However, this could also reflect a limitation in annotating TE sequences at the -wide level, because a further examination of sequences not annotated as TEs revealed that they shared...
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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
.... 2006). Two such studies estimated that 5%– 10% of mammal-specific functional elements were TE-derived (Lowe et al. 2007; Mikkelsen et al. 2007). However, it was acknowledged that these figures based on ancestral mammalian gain of function (>100 Mya) may represent severe underestimates, since ancient...
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Perspective: Reading TE leaves: New approaches to the identification of transposable element insertions
- David A. Ray and
- Mark A. Batzer
Genome Res. June 2011 21: 813-820; doi:10.1101/gr.110528.110
...to ascertaining human demography and its extension, forensic identification of particular individuals or groups. For example, Bamshad et al. (2003), Witherspoon et al. (2006), and Watkins et al. (2003) utilized either Alu or L1 (or a combination of both) to not only explore ancient human origins and migrations...
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LETTER: Functional noncoding sequences derived from SINEs in the mammalian genome
- Hidenori Nishihara,
- Arian F.A. Smit,
- and Norihiro Okada
Genome Res. July 2006 16: 864-874; Published in Advance May 22, 2006, doi:10.1101/gr.5255506
...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...
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LETTER: Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs)
- Maren Krull,
- Mirjan Petrusma,
- Wojciech Makalowski,
- Jürgen Brosius,
- and Jürgen Schmitz
Genome Res. August 2007 17: 1139-1145; Published in Advance July 10, 2007, doi:10.1101/gr.6320607
...that requires exonization, and when expressed via alternative splicing, they increase the complexity of the proteome ( Xing and Lee 2006 ). In rare cases, when their sequences or parts thereof are under strong negative selection, retroposed elements can be identified as very ancient exaptations dating as far...
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Research: Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
- Coralie Zangarelli,
- Olivier Arnaiz,
- Mickaël Bourge,
- Kevin Gorrichon,
- Yan Jaszczyszyn,
- Nathalie Mathy,
- Loïc Escoriza,
- Mireille Bétermier,
- and Vinciane Régnier
Genome Res. November/December 2022 32: 2028-2042; Published in Advance November 23, 2022, doi:10.1101/gr.277027.122
.... The earliest excised IESs tend to be independent of epigenetic factors, display strong sequence signals at their ends, and originate from the most ancient integration events. We conclude that old IESs have been optimized during evolution for early and accurate excision by acquiring stronger sequence...
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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
...) and ancient recombination events are difficult to detect, it is possible that recombination also contributed to the rapid evolution of SINE/LINE-associated TSSs.A third contributing factor is the instability of tandem repeats. Previous research showed that the mutability of microsatellites (also known...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...approximate range estimates for these basal divergence dates. Consequent of their close common ancestry, metatherians and eutherians share basic genetic structures and molecular processes that reflect elemental and ancient mammalian characteristics; yet as a result of their long separation, each group has...
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PERSPECTIVE: Raising the estimate of functional human sequences
- Michael Pheasant and
- John S. Mattick
Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
...numbers of transposon-derived sequences of all classes, both ancient and modern, including lineage-specific repeats, that have been shown to have undergone functional exaptation ( Brosius 1999 ; Volff 2006 ) (also referred to as exaption, co-option, recruitment, or domestication; Silva et al. 2003...

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