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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...signaling. Immunity 39: 454-469. Rebollo R, Romanish MT, Mager DL. 2012. Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annual review of genetics 46: 21-42. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A...
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Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
- Xiaofei Song,
- Christine R. Beck,
- Renqian Du,
- Ian M. Campbell,
- Zeynep Coban-Akdemir,
- Shen Gu,
- Amy M. Breman,
- Pawel Stankiewicz,
- Grzegorz Ira,
- Chad A. Shaw,
- and James R. Lupski
Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
.... These data further underscore the importance of Alu elements in gene and evolution and in mediating human disease and point to a potentially underappreciated source of CNVs, particularly those resulting in exonic deletions. Such information may help elucidate novel disease–gene associations, assist molecular...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...diverse cancer types (Jang et al. 2019). The best-characterized example is an intergenic TE AluJB in human lung cancers that has been exapted to be an alternative promoter, up-regulating the oncogene LIN28B. The MIRb element located in the intronic region of the ACE2 gene serves as an alternative promoter...
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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
...1631 www..org Brown CD, Johnson DS, Sidow A. 2007. Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 317: 1557–1560. Brown CD, Mangravite L, Engelhardt B. 2013. Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying...
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Research: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
- Alexandra J. Scott,
- Colby Chiang,
- and Ira M. Hall
Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
...patterns. We also identified 539 rare SVs associated with nearby gene expression outliers. Of these, 62.34% are noncoding SVs that affect gene expression but have modest enrichment at regulatory elements, showing that rare noncoding SVs are a major source of gene expression differences but remain difficult...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...looked in more detail at intergenic insertions. For each family, we measured the median distance of intergenic insertions to the nearest gene on the same strand, as well as on the opposite strand (Fig. 2E); we find that LTR elements and LINEs are located significantly further away from genes on the same...
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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
...–specific activation of TE-derived alternative promoters driving the expression of neurogenesis-associated genes. Long-read sequencing confirmed these TE-driven isoforms as significant contributors to neurogenic transcripts. We also show experimentally that a co-opted antisense L2 element drives temporal protein...
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Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
...of repetitive origin are necessary for a defined function: The structured A-repeat of XIST, of retroviral origin, recruits the PRC2 silencing complex (Elisaphenko et al. 2008); Watson–Crick hybridization between RNA and DNA Alu elements recruits ANRIL to target genes (Holdt et al. 2013); and a SINEB2 repeat...
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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 embryonic development (Fort et al. 2014; Grow et al. 2015; Durruthy-Durruthy et al. 2016), and immune systems (Chuong et al. 2016; Manghera et al. 2016). A recent H3K27ac and H3K4me1 ChIP-seq study profiling cis-regulatory elements suggests that transposable elements are the primary source of gene...
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LETTER: Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome
- Dennis D.Y. Kim,
- Thomas T.Y. Kim,
- Thomas Walsh,
- Yoshifumi Kobayashi,
- Tara C. Matise,
- Steven Buyske,
- and Abram Gabriel
Genome Res. September 2004 14: 1719-1725; doi:10.1101/gr.2855504
...element are interspersed throughout the human genome, with up to 75% of all known genes having Alu insertions within their introns and/or UTRs. Transcribed Alu sequences can alter splicing patterns by generating new exons, but other impacts of intragenic Alu elements on their host RNA are largely...

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