Searching journal content for articles similar to Ramagopalan et al. 20 (10): 1352.

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  1. Research: Alu insertion variants alter gene transcript levels
    • Lindsay M. Payer,
    • Jared P. Steranka,
    • Maria S. Kryatova,
    • Giacomo Grillo,
    • Mathieu Lupien,
    • Pedro P. Rocha,
    • and Kathleen H. Burns
    Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
    ...numbers of loci in a model that was then tractable for follow-up studies to dissect sequence requirements. In all, we tested 110 polymorphic Alu loci (Supplemental Table S1) selected because these are common variants, many of which map to Genome-Wide Association Studies (GWAS) signals and therefore may...
  2. Research: Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses
    • Hitoshi Ohtani,
    • Minmin Liu,
    • Wanding Zhou,
    • Gangning Liang,
    • and Peter A. Jones
    Genome Res. August 2018 28: 1147-1157; Published in Advance July 3, 2018, doi:10.1101/gr.234229.118
    ...to particular genomic regions.We first determined the location of ERVs based on RepeatMasker (Smit et al. 2013–2015) and their associated epigenetic marks by whole- bisulfite sequencing (WGBS) and H3K9me3 ChIP-seq in the human colon cancer cell line HCT116 (Fig. 1A). To simplify the epigenetic profiles, we...
  3. Research: The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions
    • Julie Dubois-Chevalier,
    • Vanessa Dubois,
    • Hélène Dehondt,
    • Parisa Mazrooei,
    • Claire Mazuy,
    • Aurélien A. Sérandour,
    • Céline Gheeraert,
    • Penderia Guillaume,
    • Eric Baugé,
    • Bruno Derudas,
    • Nathalie Hennuyer,
    • Réjane Paumelle,
    • Guillemette Marot,
    • Jason S. Carroll,
    • Mathieu Lupien,
    • Bart Staels,
    • Philippe Lefebvre,
    • and Jérôme Eeckhoute
    Genome Res. June 2017 27: 985-996; Published in Advance April 11, 2017, doi:10.1101/gr.217075.116
    ...of specific biological pathways/functions. Results A large set of TRs share their recruitment sites with NR1H4 in the mouse liver , defining distinct classes of CRMs In order to define TRs interconnected with NR1H4, we used our chromatin immunoprecipitation-high throughput sequencing (ChIP-seq) data from Lien...
  4. Research: Personal and population genomics of human regulatory variation
    • Benjamin Vernot,
    • Andrew B. Stergachis,
    • Matthew T. Maurano,
    • Jeff Vierstra,
    • Shane Neph,
    • Robert E. Thurman,
    • John A. Stamatoyannopoulos,
    • and Joshua M. Akey
    Genome Res. September 2012 22: 1689-1697; doi:10.1101/gr.134890.111
    ...perform a genome-wide scan of recent positive selection and identify hundreds of novel substrates of adaptive regulatory evolution that are enriched for biologically interesting pathways such as melanogenesis and adipocytokine signaling. These data and results provide new insights into patterns...
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  5. 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
    ...regions and lineage-specific motifs associated with TF binding therein. To benchmark MEDEA, we used a panel of reference cell lines profiled by ENCODE and curated by the ENCODE Project Consortium for the ENCODE-DREAM Challenge. By comparing results with RNA-seq data, ChIP-seq peaks, and DNase...
  6. Method: Time course regulatory analysis based on paired expression and chromatin accessibility data
    • Zhana Duren,
    • Xi Chen,
    • Jingxue Xin,
    • Yong Wang,
    • and Wing Hung Wong
    Genome Res. April 2020 30: 622-634; Published in Advance March 18, 2020, doi:10.1101/gr.257063.119
    ...knockdown, ChIP-seq, and HiChIP experiments. After validating these key concepts, we will apply our method to study a time course of retinoic acid (RA)–induced differentiation of mouse embryonic stem cells (mESCs), in which gene expression and chromatin accessibility are measured at baseline (day 0...
    OPEN ACCESS ARTICLE
  7. Research: Reconstructed cell fate–regulatory programs in stem cells reveal hierarchies and key factors of neurogenesis
    • Marco-Antonio Mendoza-Parra,
    • Valeriya Malysheva,
    • Mohamed Ashick Mohamed Saleem,
    • Michele Lieb,
    • Aurelie Godel,
    • and Hinrich Gronemeyer
    Genome Res. November 2016 26: 1505-1519; Published in Advance September 20, 2016, doi:10.1101/gr.208926.116
    ...and BMS753 or RA and BMS961 and presenting a proximal FAIRE and RXRA binding site, stratified for the cell-specific (P19, F9) and common programs. (E) RT-qPCR revealing the temporal RA-induced mRNA expression profiles of bona fide RA target genes. (F ) FAIRE-seq, RXRA, and RNAPII ChIP-seq profiles...
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