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Review: Origins, evolution, and phenotypic impact of new genes
- Henrik Kaessmann
Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
...to the evolution of lineage- or species-specific phenotypic traits. Consequently, the process of the ‘‘birth’’ and evolution of novel genes has attracted much attention from biologists in the past. Indeed, quite remarkably, considerations pertaining to the origin and functional fate of new genes trace back...
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LETTER: Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus
- David A. Ray,
- Cedric Feschotte,
- Heidi J.T. Pagan,
- Jeremy D. Smith,
- Ellen J. Pritham,
- Peter Arensburger,
- Peter W. Atkinson,
- and Nancy L. Craig
Genome Res. May 2008 18: 717-728; Published in Advance March 13, 2008, doi:10.1101/gr.071886.107
...full-length and potentially functional autonomous hAT transposon ( Ray et al. 2007 ). In a separate report, an extensive and recently amplified population of Helitron s, a distinct subclass of DNA transposons, was discovered in the M. lucifugus ( Pritham and Feschotte 2007 ). These surprising...
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Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
..., the parallel need to annotate transposable element (TE) sequences that have been shown to alter architecture, rewire gene regulatory networks, and contribute to the evolution of host traits is becoming ever more evident. However, accurate -wide annotation of TE sequences is still technically challenging...
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Research: Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters
- Vibhor Kumar,
- Nirmala Arul Rayan,
- Masafumi Muratani,
- Stefan Lim,
- Bavani Elanggovan,
- Lixia Xin,
- Tess Lu,
- Harshyaa Makhija,
- Jeremie Poschmann,
- Thomas Lufkin,
- Huck Hui Ng,
- and Shyam Prabhakar
Genome Res. May 2016 26: 612-623; Published in Advance March 8, 2016, doi:10.1101/gr.201038.115
.... Abstract Although over 35 different histone acetylation marks have been described, the overwhelming majority of regulatory genomics studies focus exclusively on H3K27ac and H3K9ac. In order to identify novel epigenomic traits of regulatory elements, we constructed a benchmark set of validated enhancers...
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Research: Alu insertion variants alter gene transcript levels
- Lindsay M. Payer,
- Jared P. Steranka,
- Maria S. Kryatova,
- Giacomo Grillo,
- Mathieu Lupien,
- Pedro P. Rocha,
- and Kathleen H. Burns
Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
...transcripts that show tissue specificity and have only been identified in cancers. PVT1 is a long noncoding RNA (lncRNA) that is overexpressed in many cancers, including breast cancer, although its function is not well understood (Colombo et al. 2015); it maps >500 kb away from the polymorphic Alu. At 391 kb...
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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
...these questions can we begin to understand how regulatory innovations arise in the and how they contribute to biological diversity and adaptation.Here, to gain detailed insights into young TSSs in the human , we integrated cross-species evolutionary and functional genomic data to investigate the origin of new...
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Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
..., Rayan NA, Prabhakar S. 2014. Noncoding origins of anthropoid traits and a new model of transposon functionalization. Genome Res 24: 1469–1484. DeLaForest A, Nagaoka M, Si-Tayeb K, Noto FK, Konopka G, Battle MA, Duncan SA. 2011. HNF4A is essential for specification of hepatic progenitors from human...
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