Searching journal content for articles similar to Gotea et al. 20 (5): 565.

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  1. Research: Systematic interrogation of human promoters
    • Shira Weingarten-Gabbay,
    • Ronit Nir,
    • Shai Lubliner,
    • Eilon Sharon,
    • Yael Kalma,
    • Adina Weinberger,
    • and Eran Segal
    Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
    .... Moreover, the spatial organization of TF binding sites in the is an important feature of transcriptional regulation. Multiple binding sites for a single TF, known as homotypic clusters of TF binding sites (HCTs), are statistically enriched in proximal promoters and distal enhancers (Gotea et al. 2010...
  2. Method: Evidence of widespread, independent sequence signature for transcription factor cobinding
    • Manqi Zhou,
    • Hongyang Li,
    • Xueqing Wang,
    • and Yuanfang Guan
    Genome Res. February 2021 31: 265-278; Published in Advance December 10, 2020, doi:10.1101/gr.267310.120
    ...Manqi Zhou1, Hongyang Li1, Xueqing Wang and Yuanfang Guan Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA ↵1 These authors contributed equally to this work. Corresponding author: gyuanfan@umich.eduAbstractTranscription factors (TFs...
  3. Method: Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks
    • Seyed Ali Madani Tonekaboni,
    • Parisa Mazrooei,
    • Victor Kofia,
    • Benjamin Haibe-Kains,
    • and Mathieu Lupien
    Genome Res. October 2019 29: 1733-1743; Published in Advance September 18, 2019, doi:10.1101/gr.248658.119
    ...of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 20: 565–577. doi:10.1101/gr.104471.109 ↵Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP. 2014. Genome-wide map of regulatory interactions in the human . Genome Res 24: 1905...
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  4. Research: The role of insulators and transcription in 3D chromatin organization of flies
    • Keerthi T. Chathoth,
    • Liudmila A. Mikheeva,
    • Gilles Crevel,
    • Jareth C. Wolfe,
    • Ioni Hunter,
    • Saskia Beckett-Doyle,
    • Sue Cotterill,
    • Hongsheng Dai,
    • Andrew Harrison,
    • and Nicolae Radu Zabet
    Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
    ...borders (in BG3 BEAF-32RNAi and BG3 Cp190RNAi ChroRNAi), there is less DNA accessibility and transcription, indicating that these borders are in a repressed chromatin state (Fig. 4B; Supplemental Fig. S8B).Maintained borders are associated with active promoters and enhancers, whereas lost borders...
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  5. Research: A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells
    • Gurdeep Singh,
    • Shanelle Mullany,
    • Sakthi D. Moorthy,
    • Richard Zhang,
    • Tahmid Mehdi,
    • Ruxiao Tian,
    • Andrew G. Duncan,
    • Alan M. Moses,
    • and Jennifer A. Mitchell
    Genome Res. April 2021 31: 564-575; Published in Advance March 12, 2021, doi:10.1101/gr.272468.120
    ...enhancer activity (Ballester et al. 2014). To identify these regions, 1-kb segments bound by at least one transcription factor from the following set of nine transcription factors—POU5F1, SOX2, NANOG, KLF4, KLF2, ESRRB, SMAD1, STAT3, and TFCP2L1—in mouse were clustered based on active enhancer features...
  6. Method: Probing the effect of promoters on noise in gene expression using thousands of designed sequences
    • Eilon Sharon,
    • David van Dijk,
    • Yael Kalma,
    • Leeat Keren,
    • Ohad Manor,
    • Zohar Yakhini,
    • and Eran Segal
    Genome Res. October 2014 24: 1698-1706; Published in Advance July 16, 2014, doi:10.1101/gr.168773.113
    ...search for their target sites. We show that this assumption can improve the prediction of the mean-independent component of expression noise for our designed promoter sequences, suggesting that a transcription factor target search may affect gene expression noise. Consistent with our findings in designed...
  7. Methods: Genome-wide discovery of human heart enhancers
    • Leelavati Narlikar,
    • Noboru J. Sakabe,
    • Alexander A. Blanski,
    • Fabio E. Arimura,
    • John M. Westlund,
    • Marcelo A. Nobrega,
    • and Ivan Ovcharenko
    Genome Res. March 2010 20: 381-392; Published in Advance January 14, 2010, doi:10.1101/gr.098657.109
    ...mainly relied on detection of clusters of binding sites specific to activator proteins for which appropriate tissue specificity has been previously reported (Thompson et al. 2004; Segal et al. 2008). In Drosophila, the homotypic structure of enhancers, withmultiple transcription factor binding sites...
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  8. Method: Discriminative prediction of mammalian enhancers from DNA sequence
    • Dongwon Lee,
    • Rachel Karchin,
    • and Michael A. Beer
    Genome Res. December 2011 21: 2167-2180; Published in Advance August 29, 2011, doi:10.1101/gr.121905.111
    ...genes (Banerji 1981). Enhancer activity ismodulated by interactions between sequence specific DNA binding proteins and sequence elements in the enhancer. Since individual transcription factor binding sites (TFBSs) can be relatively short and degenerate, TFBSs tend to be clustered to achieve precise...
  9. Method: Heterogeneity of transcription factor binding specificity models within and across cell lines
    • Mahfuza Sharmin,
    • Héctor Corrada Bravo,
    • and Sridhar Hannenhalli
    Genome Res. August 2016 26: 1110-1123; Published in Advance June 16, 2016, doi:10.1101/gr.199166.115
    ...2013), homotypic clusters of binding sites (Dror et al. 2015), cooperative binding of the TF with its partners (Wang et al. 2006; Liu et al. 2016), condition-specific chromatin context (Wang et al. 2006; Heintzman et al. 2009; Gheldof et al. 2010; Kumar and Bucher 2016), and local DNAproperties (Dror...
  10. Method: Discovery and assessment of conserved Pax6 target genes and enhancers
    • Pedro Coutinho,
    • Sofia Pavlou,
    • Shipra Bhatia,
    • Kevin J. Chalmers,
    • Dirk A. Kleinjan,
    • and Veronica van Heyningen
    Genome Res. August 2011 21: 1349-1359; Published in Advance May 26, 2011, doi:10.1101/gr.124115.111
    ...in Supplemental Tables S5–S8. Gene targets that coincide between the two mammals are highlighted in yellow. Multiple binding sites associated with a single gene are clearly observed, reinforcing the concept of homotypic clustering (Gotea et al. 2010). To characterize the identified sets of mouse and human genes...
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