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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
..., among several key activities, catalyze genomic DNA nicking and reverse transcription of the L1 mRNA (Feng et al. 1996; Moran et al. 1996; Kazazian and Moran 2017; Scott and Devine 2017). New L1 insertions typically carry retrotransposition hallmarks, including target site duplications (TSDs) and a long...
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Research: Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region
- Cemalettin Bekpen,
- Ibrahim Tastekin,
- Priscillia Siswara,
- Cezmi A. Akdis,
- and Evan E. Eichler
Genome Res. June 2012 22: 1050-1058; Published in Advance March 14, 2012, doi:10.1101/gr.134098.111
...occurred in a stepwise manner, acquiring foreign promoters from BPTF and DND1 via segmental duplication. This unusual evolutionary trajectory altered the regulation of the LRRC37 family, leading to increased expression in the fetal brain and cerebellum. Footnotes ↵ 5 Corresponding...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...emerge within species (Ohno 1970). Many of these evolutionary events occur in segmental duplications (SDs), genomic units that are at least 1 kbp in length and whose duplications are ≥90% identical to one another (Bailey and Eichler 2006). Many human-specific genes reside in SDs, which often continue...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...al. 2016; Wu and Knudson 2018). Some genes that emerge de novo not only provide new functions, but have even become essential to the species in which they emerged. For example, the human-specific de novo gene ESRG is required for the maintenance of pluripotency in human naive stem cells (Wang et al...
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LETTER: Gene Content and Function of the Ancestral Chromosome Fusion Site in Human Chromosome 2q13–2q14.1 and Paralogous Regions
- Yuxin Fan,
- Tera Newman,
- Elena Linardopoulou,
- and Barbara J. Trask
Genome Res. November 1, 2002 12: 1663-1672; doi:10.1101/gr.338402
....E. ( 2002 ) Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70 : 83 – 100 . ↵ Blot S. , Poirier C. , Dreyfus P.A. ( 1995 ) The mouse mutation muscle deficient (mdf) is characterized by a progressive motoneuron disease. J. Neuropathol...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
...et al. 2009). Instead, we identified and masked 661 (3%) genes that show patchy phylogenetic distribution of orthologs, which often suggest problematic synteny inference (Methods). For example, a well-known human-specific duplicated fusion gene, CHRFAM7A (Costantini et al. 2015), showed reciprocal...
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ARTICLE: Reevaluating Human Gene Annotation: A Second-Generation Analysis of Chromosome 22
- John E. Collins,
- Melanie E. Goward,
- Charlotte G. Cole,
- Luc J. Smink,
- Elizabeth J. Huckle,
- Sarah Knowles,
- Jacqueline M. Bye,
- David M. Beare,
- and Ian Dunham
Genome Res. January 1, 2003 13: 27-36; Published in Advance December 30, 2002, doi:10.1101/gr.695703
...A.M. , Viggiano L. , Misceo D. , Horvath J.E. , Archidiacono N. , Schwartz S. , Rocchi M. , Eichler E.E. ( 2002 ) Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70 : 83 – 100 . ↵ Bairoch A. , Apweiler R. ( 2000 ) The SWISS...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...human-specific transcripts, whereas an alternative acceptor site produces a macaque-specific transcript. Another example is interferon induced protein 44 like (IFI44L), which is involved in the immune response to infection and autoimmune disorders (Herberg et al. 2016; Zhao et al. 2016; de Oyarzabal et...
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Research: A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
- Elisabeth J. van Bree,
- Rita L.F.P. Guimarães,
- Mischa Lundberg,
- Elena R. Blujdea,
- Jimi L. Rosenkrantz,
- Fred T.G. White,
- Josse Poppinga,
- Paula Ferrer-Raventós,
- Anne-Fleur E. Schneider,
- Isabella Clayton,
- David Haussler,
- Marcel J.T. Reinders,
- Henne Holstege,
- Adam D. Ewing,
- Colette Moses,
- and Frank M.J. Jacobs
Genome Res. April 2022 32: 656-670; Published in Advance March 24, 2022, doi:10.1101/gr.275515.121
...classes was comparable to previous analysis, with most SV-SVA elements belonging to the youngest types.To rule out sequencing or assembly errors leading to the observed variation, we selected five human-specific SVAs in which to validate the structural variations by PCR analysis. We confirmed structural...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
...contributed an extra layer of species-specific gene regulation by providing novel transcription factor binding sites. In humans, SINE-VNTR-Alu (SVA) elements are one of three still active TE families; approximately 2800 SVA insertions exist in the human , half of which are human-specific. TEs are often...
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