Searching journal content for articles similar to Yáñez-Cuna et al. 22 (10): 2018.

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  1. Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
    • Anna Nordin,
    • Chaitali Chakraborty,
    • Mattias Jonasson,
    • Orgena Dano,
    • Gianluca Zambanini,
    • Pierfrancesco Pagella,
    • Silvia Remeseiro,
    • and Claudio Cantù
    Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
    ...be considered as potential partners in recruiting CTCF to the chromatin. Additionally, it was recently reported that CTCF binding can be context-specific and dependent on the activity of other transcription factors that bind upstream of the CTCF motif and stabilize CTCF binding (Do et al. 2025); we consider...
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  2. Research: Enhancers display constrained sequence flexibility and context-specific modulation of motif function
    • Franziska Reiter,
    • Bernardo P. de Almeida,
    • and Alexander Stark
    Genome Res. March 2023 33: 346-358; Published in Advance March 20, 2023, doi:10.1101/gr.277246.122
    ...positions within 496 enhancers. These complementary strategies reveal that enhancers display constrained sequence flexibility and the context-specific modulation of motif function. Important motifs can be functionally replaced by hundreds of sequences constituting several distinct motif types...
  3. Research: Local sequence features that influence AP-1 cis-regulatory activity
    • Hemangi G. Chaudhari and
    • Barak A. Cohen
    Genome Res. February 2018 28: 171-181; Published in Advance January 5, 2018, doi:10.1101/gr.226530.117
    ...Corresponding author: cohen@wustl.eduAbstractIn the , most occurrences of transcription factor binding sites (TFBS) have no cis-regulatory activity, which suggests that flanking sequences contain information that distinguishes functional from nonfunctional TFBS. We interrogated the role of flanking sequences...
  4. Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
    • Alexander Morin,
    • Eric Ching-Pan Chu,
    • Aman Sharma,
    • Alex Adrian-Hamazaki,
    • and Paul Pavlidis
    Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
    ...Data S5).To show an application of these bound loci, we examined their overlap with candidate cis-regulatory elements (cCREs) (Moore et al. 2020). These regions, which encompass predicted promoter- and enhancer-like regions, were previously defined through the integration of multiple genomic features...
  5. Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
    • Jungkyun Seo,
    • D. Dewran Koçak,
    • Luke C. Bartelt,
    • Courtney A. Williams,
    • Alejandro Barrera,
    • Charles A. Gersbach,
    • and Timothy E. Reddy
    Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
    ...in vitro have suggested differences in TRE or CRE affinity (Isakova et al. 2017). Massively parallel reporter assay (MPRA) analyses have also shown that AP-1-mediated cis-regulatory activity depends on sequences beyond the core TRE (Chaudhari and Cohen 2018). It remains unresolved whether AP-1 subunits...
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  6. Method: A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes
    • Shang Gao,
    • Yang Dai,
    • and Jalees Rehman
    Genome Res. July 2021 31: 1296-1311; Published in Advance June 30, 2021, doi:10.1101/gr.265595.120
    ...be overcome in the future with the emerging availability of context-specific single-cell chromatin accessibility data as seen in studies of the transcription factor targets and regulatory mechanism by scATAC-seq (Buenrostro et al. 2015; Cusanovich et al. 2018; Duren et al. 2018; Jia et al. 2018...
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  7. Method: Integrated analysis of motif activity and gene expression changes of transcription factors
    • Jesper Grud Skat Madsen,
    • Alexander Rauch,
    • Elvira Laila Van Hauwaert,
    • Søren Fisker Schmidt,
    • Marc Winnefeld,
    • and Susanne Mandrup
    Genome Res. February 2018 28: 243-255; Published in Advance December 12, 2017, doi:10.1101/gr.227231.117
    ..., Germany ↵3 These authors contributed equally to this work. ↵4 Present address: Institute for Diabetes and Cancer, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany Corresponding author: s.mandrup@bmb.sdu.dkAbstractThe ability to predict transcription...
  8. 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
    ...-dependent function of a cis regulatory region requires binding of a specific combination of TFs. This modularity contributes to morphological evolution through changes in cis elements controlling transcriptionwhile avoiding the pleiotropic effects of a TF gene’s expression change (Prud’homme et al. 2007). Shared...
  9. Research: A widespread role of the motif environment in transcription factor binding across diverse protein families
    • Iris Dror,
    • Tamar Golan,
    • Carmit Levy,
    • Remo Rohs,
    • and Yael Mandel-Gutfreund
    Genome Res. September 2015 25: 1268-1280; Published in Advance July 9, 2015, doi:10.1101/gr.184671.114
    ...Science, University of Southern California, Los Angeles, California 90089, USA; 3Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel Transcriptional regulation requires the binding of transcription factors (TFs) to short sequence...
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  10. Method: Unraveling determinants of transcription factor binding outside the core binding site
    • Michal Levo,
    • Einat Zalckvar,
    • Eilon Sharon,
    • Ana Carolina Dantas Machado,
    • Yael Kalma,
    • Maya Lotam-Pompan,
    • Adina Weinberger,
    • Zohar Yakhini,
    • Remo Rohs,
    • and Eran Segal
    Genome Res. July 2015 25: 1018-1029; Published in Advance March 11, 2015, doi:10.1101/gr.185033.114
    ...). The pattern observed was highly reproducible across several TF concentrations tested (Supplemental Fig. S3), and more importantly, it is TFand context-specific, indicating that it does not stem from an inherent property of the binding in our assay, such as the relative location of the binding site within...
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