Searching journal content for articles similar to Lee et al. 32 (7): 1424.

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  1. Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
    • Liangxi Wang,
    • Tiegh Taylor,
    • Kumaragurubaran Rathnakumar,
    • Nadiya Khyzha,
    • Minggao Liang,
    • Azad Alizada,
    • Laura F. Campitelli,
    • Sara E. Pour,
    • Zain M. Patel,
    • Lina Antounians,
    • Ian C. Tobias,
    • Huayun Hou,
    • Timothy R. Hughes,
    • Sushmita Roy,
    • Jennifer A. Mitchell,
    • Jason E. Fish,
    • and Michael D. Wilson
    Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
    ..., act as a source of cis-regulatory elements, which primarily innovate regulatory programs in a species- and tissue-specific manner (Buecker and Wysocka 2012; Chuong et al. 2016; Fuentes et al. 2018; Todd et al. 2019; Du et al. 2022; Kelly et al. 2022; Lee et al. 2022; Choudhary et al. 2023). Although...
  2. Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
    • David C.H. Metzger,
    • Imogen Porter,
    • Brendan Mobley,
    • Benjamin A. Sandkam,
    • Lydia J.M. Fong,
    • Andrew P. Anderson,
    • and Judith E. Mank
    Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
    ...levels, whereas genes with higher expression had lower promoter methylation in somatic but not gonadal tissue (Supplemental Fig. 4). These data suggest the relationship between promoter methylation and gene expression is tissue-specific. It is possible that this pattern is the result of the breakdown...
  3. Research: Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
    • Yaqiang Cao,
    • Guoyu Chen,
    • Gang Wu,
    • Xiaoli Zhang,
    • Joseph McDermott,
    • Xingwei Chen,
    • Chi Xu,
    • Quanlong Jiang,
    • Zhaoxiong Chen,
    • Yingying Zeng,
    • Daosheng Ai,
    • Yi Huang,
    • and Jing-Dong J. Han
    Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
    ...equally to this work. Corresponding author: jdhan@picb.ac.cnAbstractA few families of transposable elements (TEs) have been shown to evolve into cis-regulatory elements (CREs). Here, to extend these studies to all classes of TEs in the human , we identified widespread enhancer-like repeats (ELRs) and find...
    OPEN ACCESS ARTICLE
  4. Perspective: Functional transcriptomics in the post-ENCODE era
    • Jonathan M. Mudge,
    • Adam Frankish,
    • and Jennifer Harrow
    Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
    ...). Second, it is noteworthy that 62% of lncRNA transcripts in GENCODE overlap transposable elements (TEs) (JM Mudge, unpubl.). Furthermore, there is a well-established link between TEs and AS in protein-coding genes; certain TE families such as Alu contain DNAmotifs that resemble splicing signals, making...
    OPEN ACCESS ARTICLE
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