Searching journal content for articles similar to Raveh-Sadka et al. 19 (8): 1480.

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  1. Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
    • Kaixuan Luo,
    • Jianling Zhong,
    • Alexias Safi,
    • Linda K. Hong,
    • Alok K. Tewari,
    • Lingyun Song,
    • Timothy E. Reddy,
    • Li Ma,
    • Gregory E. Crawford,
    • and Alexander J. Hartemink
    Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
    ...in a population) in accordance with prevailing energetic and thermodynamic conditions, including competition with other TFs and nucleosomes (Narlikar et al. 2007; Gordân and Hartemink 2008; Wasson and Hartemink 2009; Li et al. 2011; Lickwar et al. 2012; Neph et al. 2012). Also, growing evidence suggests...
  2. Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
    • Yuning Zhang,
    • Tiffany D. Ho,
    • Nicolas E. Buchler,
    • and Raluca Gordân
    Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
    ...by Cbf1 and Pho4 (Supplemental Fig. S4D), and we considered longer sequences flanking the E-box binding sites, which can significantly influence TF binding (Supplemental Fig. S4C).Next, we incorporated the competition between paralogous TFs into the equilibrium thermodynamics model in Equation (1...
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  3. Research: Nascent RNA folding mitigates transcription-associated mutagenesis
    • Xiaoshu Chen,
    • Jian-Rong Yang,
    • and Jianzhi Zhang
    Genome Res. January 2016 26: 50-59; Published in Advance October 30, 2015, doi:10.1101/gr.195164.115
    ...Nascent RNA folding mitigates transcription-associated mutagenesis Xiaoshu Chen , Jian-Rong Yang and Jianzhi Zhang Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding...
  4. 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
    ...predictive TF-specific binding specificity models based on sequences flanking the core binding site), the likelihood of co-occurring TF binding events (e.g., characterizing the dependency on TFBS multiplicity), and the propensity of each of the examined sequences to form nucleosomes. Our results demonstrate...
  5. 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
    ...whether environmental properties could help to discriminate between bound and unbound sequences. To this end, we employed L2-regularized multiple linear regression (MLR) models that incorporated different environmental features surrounding each motif as described in the Methods. Since it has been shown...
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  6. Letter: A novel strategy of transcription regulation by intragenic nucleosome ordering
    • Cédric Vaillant,
    • Leonor Palmeira,
    • Guillaume Chevereau,
    • Benjamin Audit,
    • Yves d'Aubenton-Carafa,
    • Claude Thermes,
    • and Alain Arneodo
    Genome Res. January 2010 20: 59-67; Published in Advance October 26, 2009, doi:10.1101/gr.096644.109
    ...the intragenic nucleosome organization only depend on the properties (distance and nucleosome exclusion strength) of the 59 and 39NFRs? To test this hypothesis, we predicted the nucleosome occupancy profile inside the 4554 yeast genes using a thermodynamical model of nucleosome assembly that depends...
  7. Method: Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
    • Daniel Marbach,
    • Sushmita Roy,
    • Ferhat Ay,
    • Patrick E. Meyer,
    • Rogerio Candeias,
    • Tamer Kahveci,
    • Christopher A. Bristow,
    • and Manolis Kellis
    Genome Res. July 2012 22: 1334-1349; Published in Advance March 28, 2012, doi:10.1101/gr.127191.111
    ...Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks Daniel Marbach 1 , 2 , 7 , Sushmita Roy 1 , 2 , 3 , 7 , Ferhat Ay 1 , 2 , 4 , 5 , Patrick E. Meyer 1 , 2 , 6...
  8. Method: Mapping nucleosome positions using DNase-seq
    • Jianling Zhong,
    • Kaixuan Luo,
    • Peter S. Winter,
    • Gregory E. Crawford,
    • Edwin S. Iversen,
    • and Alexander J. Hartemink
    Genome Res. March 2016 26: 351-364; Published in Advance January 15, 2016, doi:10.1101/gr.195602.115
    ...to nucleosome rotational positioning, it also reveals the rotational context of transcription factor (TF) binding sites. We show that potential binding sites within nucleosome-associated DNA are often centered preferentially on an exposed major or minor groove. This preferential localization may modulate TF...
  9. Research: Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development
    • Vladimir B. Teif,
    • Daria A. Beshnova,
    • Yevhen Vainshtein,
    • Caroline Marth,
    • Jan-Philipp Mallm,
    • Thomas Höfer,
    • and Karsten Rippe
    Genome Res. August 2014 24: 1285-1295; Published in Advance May 8, 2014, doi:10.1101/gr.164418.113
    ...(5hmC), nucleosome repositioning, and binding of the transcription factor CTCF during this process. By integrating MNase-seq and ChIP-seq experiments in mouse embryonic stem cells (ESC) and their differentiated counterparts with biophysical modeling, we found that the interplay between these factors...
  10. Research: DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
    • Deborah R. Winter,
    • Lingyun Song,
    • Sayan Mukherjee,
    • Terrence S. Furey,
    • and Gregory E. Crawford
    Genome Res. July 2013 23: 1118-1129; Published in Advance May 8, 2013, doi:10.1101/gr.150482.112
    ...and Davey 2003; Wang et al. 2008). As the basic unit of packaging in chromatin, nucleosomes incorporate themajority of bases in the (Felsenfeld andGroudine 2003; Valouev et al. 2011). Nucleosomes plays a role in regulating gene transcription by controlling the accessibility of transcription factor (TF...
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