Searching journal content for articles similar to Wang et al. 29 (2): 293.

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  1. Research: Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis
    • Arun B. Dutta,
    • Daniel S. Lank,
    • Roza K. Przanowska,
    • Piotr Przanowski,
    • Lixin Wang,
    • Bao Nguyen,
    • Ninad M. Walavalkar,
    • Fabiana M. Duarte,
    • and Michael J. Guertin
    Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
    ...). We used discriminative regulatory-element detection (dREG) to identify peaks of bidirectional transcription from our PRO-seq data (Wang et al. 2019). We identified more than 180,000 dREG peaks (Fig. 2A,B) and an 18% change significantly over the time course (Supplemental Fig. S2A). ATAC-seq and PRO...
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  2. Research: Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol
    • Noah Dukler,
    • Gregory T. Booth,
    • Yi-Fei Huang,
    • Nathaniel Tippens,
    • Colin T. Waters,
    • Charles G. Danko,
    • John T. Lis,
    • and Adam Siepel
    Genome Res. November 2017 27: 1816-1829; Published in Advance October 12, 2017, doi:10.1101/gr.222935.117
    ...associations and pausing patterns to genes Previous studies have shown that putative enhancers are divergently transcribed, producing nascent RNAs that can be detected via PRO-seq (De Santa et al. 2010; Core et al. 2014; Danko et al. 2015). Using dREG (Danko et al. 2015), which predicts divergent transcription...
  3. Research: Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
    • Lisa Barros de Andrade e Sousa,
    • Iris Jonkers,
    • Laurène Syx,
    • Ilona Dunkel,
    • Julie Chaumeil,
    • Christel Picard,
    • Benjamin Foret,
    • Chong-Jian Chen,
    • John T. Lis,
    • Edith Heard,
    • Edda G. Schulz,
    • and Annalisa Marsico
    Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
    ...over the entire gene body (Supplemental Table S7). The active TSS for each gene was identified based on the PRO-seq data at time point t = 0 through the dREG method, which finds regions that harbor bidirectional transcription (Supplemental Fig. S18; Danko et al. 2015). In addition to epigenetic...
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