Searching journal content for articles similar to Zhou et al. 31 (2): 265.

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  1. Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
    • Olga M. Sigalova,
    • Mattia Forneris,
    • Frosina Stojanovska,
    • Bingqing Zhao,
    • Rebecca R. Viales,
    • Adam Rabinowitz,
    • Fayrouz Hammal,
    • Benoît Ballester,
    • Judith B. Zaugg,
    • and Eileen E.M. Furlong
    Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
    ...genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several time points...
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  2. Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
    • Belle A. Moyers,
    • E. Christopher Partridge,
    • Mark Mackiewicz,
    • Michael J. Betti,
    • Roshan Darji,
    • Sarah K. Meadows,
    • Kimberly M. Newberry,
    • Laurel A. Brandsmeier,
    • Barbara J. Wold,
    • Eric M. Mendenhall,
    • and Richard M. Myers
    Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
    ...fewer peaks than candidate activators (Supplemental Fig. 15), consistent with a “hit and run” model of transcriptional repression (Shah et al. 2019). Comparing the distribution of peaks across cCRE types, we found that the majority of peaks for each type were found in promoter-like signature (PLS...
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  3. 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
    ...tissues. Here we report that most of the commonly expressed mouse or human genes across different cell types, including more than half of the previously identified housekeeping genes, are associated with cell type–specific enhancers. Furthermore, the binding of most transcription factors (TFs) is cell...
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  4. Research: An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
    • Zhizhuo Zhang,
    • Kern Rei Chng,
    • Shreyas Lingadahalli,
    • Zikai Chen,
    • Mei Hui Liu,
    • Huy Hoang Do,
    • Shaojiang Cai,
    • Nicola Rinaldi,
    • Huay Mei Poh,
    • Guoliang Li,
    • Ying Ying Sung,
    • Charlie L. Heng,
    • Leighton J. Core,
    • Si Kee Tan,
    • Xiaoan Ruan,
    • John T. Lis,
    • Manolis Kellis,
    • Yijun Ruan,
    • Wing-Kin Sung,
    • and Edwin Cheung
    Genome Res. February 2019 29: 223-235; Published in Advance January 3, 2019, doi:10.1101/gr.230243.117
    ...coordinated regulation of a subset of AR target genes. Through multifaceted functional data analysis, we found that AR-ERG interaction hub regions are characterized by distinct functional signatures, including bidirectional transcription and cotranscription factor binding. In addition, cancer-associated long...
  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
    ...@bwh.harvard.eduAbstractDeciphering the interplay between chromatin accessibility and transcription factor (TF) binding is fundamental to understanding transcriptional regulation, control of cellular states, and the establishment of new phenotypes. Recent -wide chromatin accessibility profiling studies have provided catalogs of putative open...
  6. Research: Relationship between histone modifications and transcription factor binding is protein family specific
    • Beibei Xin and
    • Remo Rohs
    Genome Res. March 2018 28: 321-333; Published in Advance January 11, 2018, doi:10.1101/gr.220079.116
    ...to regulate transcriptional processes cooperatively. Our analysis revealed a dependency between the HM pattern preferences of TF pairs and their tendency to cobind the , even if they have different DNA sequence preferences. This interdependency indicates that HM patterns in regions where BSs are located...
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  7. Research: Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state
    • Connor Rogerson,
    • Edward Britton,
    • Sarah Withey,
    • Neil Hanley,
    • Yeng S. Ang,
    • and Andrew D. Sharrocks
    Genome Res. May 2019 29: 723-736; Published in Advance April 8, 2019, doi:10.1101/gr.243345.118
    ...the expression of several Barrett's-specific markers (Colleypriest et al. 2017). This activity of HNF4A is akin to pioneering activity that has been demonstrated for several transcription factors (Zaret and Carroll 2011). However, GATA6 did not demonstrate widespread pioneering activity, and there is a distinct...
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  8. Research: CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
    • Kosuke Hashimoto,
    • Ana Maria Suzuki,
    • Alexandre Dos Santos,
    • Christophe Desterke,
    • Agnese Collino,
    • Serena Ghisletti,
    • Emilie Braun,
    • Alessandro Bonetti,
    • Alexandre Fort,
    • Xian-Yang Qin,
    • Enrico Radaelli,
    • Bogumil Kaczkowski,
    • Alistair R.R. Forrest,
    • Soichi Kojima,
    • Didier Samuel,
    • Gioacchino Natoli,
    • Marie Annick Buendia,
    • Jamila Faivre,
    • and Piero Carninci
    Genome Res. December 2015 25: 1812-1824; Published in Advance October 28, 2015, doi:10.1101/gr.191031.115
    ...is a shared feature of human HCC and the mouse HCCmodel studied. Molecular signature of HCC comprising top 43 up-regulated LTR-derived transcripts Having found significantly up-regulated distal peaks with a low (<0.05) FDR threshold in human and mouse HCCs, we sought to select human ncRNA candidates...
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  9. Research: Widespread contribution of transposable elements to the innovation of gene regulatory networks
    • Vasavi Sundaram,
    • Yong Cheng,
    • Zhihai Ma,
    • Daofeng Li,
    • Xiaoyun Xing,
    • Peter Edge,
    • Michael P. Snyder,
    • and Ting Wang
    Genome Res. December 2014 24: 1963-1976; Published in Advance October 15, 2014, doi:10.1101/gr.168872.113
    ...Widespread contribution of transposable elements to the innovation of gene regulatory networks Vasavi Sundaram 1 , 4 , Yong Cheng 2 , 4 , Zhihai Ma 2 , Daofeng Li 1 , Xiaoyun Xing 1 , Peter Edge 3 , Michael...
  10. Research: ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors
    • Stephan R. Starick,
    • Jonas Ibn-Salem,
    • Marcel Jurk,
    • Céline Hernandez,
    • Michael I. Love,
    • Ho-Ryun Chung,
    • Martin Vingron,
    • Morgane Thomas-Chollier,
    • and Sebastiaan H. Meijsing
    Genome Res. June 2015 25: 825-835; Published in Advance February 26, 2015, doi:10.1101/gr.185157.114
    ...ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors Stephan R. Starick 1 , 3 , Jonas Ibn-Salem 1 , 2 , 3 , Marcel Jurk 1 , 3 , Céline...
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