Searching journal content for articles similar to Singh et al. 31 (4): 564.

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  1. Research: Functional characterization of enhancer activity during a long terminal repeat's evolution
    • Alan Y. Du,
    • Xiaoyu Zhuo,
    • Vasavi Sundaram,
    • Nicholas O. Jensen,
    • Hemangi G. Chaudhari,
    • Nancy L. Saccone,
    • Barak A. Cohen,
    • and Ting Wang
    Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
    ...widespread enhancer turnover (Arnold et al. 2014; Klein et al. 2018).Transposable elements (TEs) are repetitive DNA elements that represent a rich source of genetic material for regulatory innovation (Feschotte 2008). In mammalian s, TEs have made substantial contributions to the collection of transcription...
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  2. Research: Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
    • Iris Zhu and
    • David Landsman
    Genome Res. October 2023 33: 1662-1672; Published in Advance October 26, 2023, doi:10.1101/gr.278130.123
    ..., including their position, order, and spacing. This results in cell type–specific enhancer sites formed through recruitment of a flexible repertoire of TFs uniquely present in each cell type while preserving the function to facilitate the transcription of a nearby gene.DiscussionIn this study, we examined...
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  3. Method: MEDEA: analysis of transcription factor binding motifs in accessible chromatin
    • Luca Mariani,
    • Kathryn Weinand,
    • Stephen S. Gisselbrecht,
    • and Martha L. Bulyk
    Genome Res. May 2020 30: 736-748; Published in Advance May 18, 2020, doi:10.1101/gr.260877.120
    ...in embryonic stem cells, MEF2A and JUND in GM12878 B cells, and NR2F2 and JUND in K562 erythroleukemia cells. We evaluated these predictions by checking for the enrichment of these candidate motifs in their associated TF ChIP-seq peaks in factorbook (Wang et al. 2012). Analysis of ChIP-seq data for those TFs...
  4. Research: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells
    • Jennifer Y. Tan,
    • Tamara Sirey,
    • Frantisek Honti,
    • Bryony Graham,
    • Allison Piovesan,
    • Matthias Merkenschlager,
    • Caleb Webber,
    • Chris P. Ponting,
    • and Ana C. Marques
    Genome Res. May 2015 25: 655-666; Published in Advance March 19, 2015, doi:10.1101/gr.181974.114
    ...consequences of miRNA-mediated regulation of mRNA levels by lncRNAs. To gain further insight into lncRNA-mRNA miRNA-mediated crosstalk, we reanalyzed transcriptome-wide changes induced by the targeted knockdown of over 100 lncRNA transcripts in mouse embryonic stem cells (mESCs). We predicted that, on average...
  5. Research: Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes
    • Sakthi D. Moorthy,
    • Scott Davidson,
    • Virlana M. Shchuka,
    • Gurdeep Singh,
    • Nakisa Malek-Gilani,
    • Lida Langroudi,
    • Alexandre Martchenko,
    • Vincent So,
    • Neil N. Macpherson,
    • and Jennifer A. Mitchell
    Genome Res. February 2017 27: 246-258; Published in Advance November 28, 2016, doi:10.1101/gr.210930.116
    ...; Tuan et al. 1989;Higgs et al. 1990; Chen et al. 1997;Mitchell et al. 2012). Furthermore, both the Hbb and Hba LCRs were recently determined to fit the bioinformatic criteria for super-enhancers (Hay et al. 2016). The transcriptional regulatory networks that control cell identity of embryonic stem (ES...
  6. Research: TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
    • Helen M. Rowe,
    • Adamandia Kapopoulou,
    • Andrea Corsinotti,
    • Liana Fasching,
    • Todd S. Macfarlan,
    • Yara Tarabay,
    • Stéphane Viville,
    • Johan Jakobsson,
    • Samuel L. Pfaff,
    • and Didier Trono
    Genome Res. March 2013 23: 452-461; Published in Advance December 10, 2012, doi:10.1101/gr.147678.112
    ...TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells Helen M. Rowe 1 , Adamandia Kapopoulou 1 , 2 , Andrea Corsinotti 1 , Liana Fasching 3 , Todd S. Macfarlan 4...
  7. Research: Enhancer transcripts mark active estrogen receptor binding sites
    • Nasun Hah,
    • Shino Murakami,
    • Anusha Nagari,
    • Charles G. Danko,
    • and W. Lee Kraus
    Genome Res. August 2013 23: 1210-1223; Published in Advance May 1, 2013, doi:10.1101/gr.152306.112
    ...by contacting W. Lee Kraus. Read alignment, transcript calling, determination of regulation by E2, and the generation of heat maps were performed as described previously (Hah et al. 2011). Defining classes of ESR1 enhancer transcripts (eRNAs) The repertoire of genomic ESR1 binding sites (ERBSs) was extracted...
  8. Research: Combinatorial binding of transcription factors in the pluripotency control regions of the genome
    • Luciana Ferraris,
    • Allan P. Stewart,
    • Jinsuk Kang,
    • Alec M. DeSimone,
    • Matthew Gemberling,
    • Dean Tantin,
    • and William G. Fairbrother
    Genome Res. July 2011 21: 1055-1064; Published in Advance April 28, 2011, doi:10.1101/gr.115824.110
    ...in stem cells (Boyer et al. 2005). The loss of POU5F1 or NANOG causes embryonic stem (ES) cells to lose pluripotency and differentiate inappropriately (Hough et al. 2006). Precise POU5F1 levels are also critical to maintaining pluripotency and are at least partially controlled by SOX2, a factor that can...
  9. REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
    • Laura Elnitski,
    • Victor X. Jin,
    • Peggy J. Farnham,
    • and Steven J.M. Jones
    Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
    ...approaches is required for the -wide elucidation of cis -acting transcriptional regulatory elements. These include promoters, enhancers, and repressor elements, along with structural components like origins of replication and boundary elements. For instance, experimentally based oligo-capping methods...
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  10. LETTER: Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
    • A. Gordon Robertson,
    • Mikhail Bilenky,
    • Angela Tam,
    • Yongjun Zhao,
    • Thomas Zeng,
    • Nina Thiessen,
    • Timothee Cezard,
    • Anthony P. Fejes,
    • Elizabeth D. Wederell,
    • Rebecca Cullum,
    • Ghia Euskirchen,
    • Martin Krzywinski,
    • Inanc Birol,
    • Michael Snyder,
    • Pamela A. Hoodless,
    • Martin Hirst,
    • Marco A. Marra,
    • and Steven J.M. Jones
    Genome Res. December 2008 18: 1906-1917; Published in Advance September 11, 2008, doi:10.1101/gr.078519.108
    ...and for two functionally different transcription factors: STAT1 in the immortalized HeLa S3 cell line, with and without interferon-gamma (IFNG) stimulation; and FOXA2 in mouse adult liver tissue. In unstimulated and stimulated HeLa cells, respectively, we determined ∼270,000 and ∼301,000 H3K4me1-enriched...
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