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Letter: Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
- Alexander W. Bruce,
- Andrés J. López-Contreras,
- Paul Flicek,
- Thomas A. Down,
- Pawandeep Dhami,
- Shane C. Dillon,
- Christoph M. Koch,
- Cordelia F. Langford,
- Ian Dunham,
- Robert M. Andrews,
- and David Vetrie
Genome Res. June 2009 19: 994-1005; Published in Advance April 28, 2009, doi:10.1101/gr.089086.108
.... We demonstrate that variations within the DNA sequence motifs that bind the transcriptional repressor REST (NRSF) encode in vivo DNA binding affinity hierarchies that contribute to regulatory function during lineage-specific and developmental programs in fundamental ways. First, canonical sequence...
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Resource: Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
- Ali Mortazavi,
- Shirley Pepke,
- Camden Jansen,
- Georgi K. Marinov,
- Jason Ernst,
- Manolis Kellis,
- Ross C. Hardison,
- Richard M. Myers,
- and Barbara J. Wold
Genome Res. December 2013 23: 2136-2148; Published in Advance October 29, 2013, doi:10.1101/gr.158261.113
...online through the Genome Research Open Access option. 2136 Genome Research www..org 23:2136–2148 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/13; www..org Models (HMMs) or Dynamic Bayesian Networks (e.g., Ernst and Kellis 2010; Hoffman et al. 2012). The resulting machine...
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Method: Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
- Antonio L.C. Gomes,
- Thomas Abeel,
- Matthew Peterson,
- Elham Azizi,
- Anna Lyubetskaya,
- Luís Carvalho,
- and James Galagan
Genome Res. October 2014 24: 1686-1697; Published in Advance July 14, 2014, doi:10.1101/gr.161711.113
..., with value » 0.85 (Fig. 5; see also Supplemental Figs. S5, S6). Cooperative interaction predictions for the human TFs CTCF, REST, andGABPA are shown in Supplemental Figures S12 and S14. High-throughput application and orphan regions Our method was designed with a level of computational efficiency that makes...
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Resource: Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
- Jie Wang,
- Jiali Zhuang,
- Sowmya Iyer,
- XinYing Lin,
- Troy W. Whitfield,
- Melissa C. Greven,
- Brian G. Pierce,
- Xianjun Dong,
- Anshul Kundaje,
- Yong Cheng,
- Oliver J. Rando,
- Ewan Birney,
- Richard M. Myers,
- William S. Noble,
- Michael Snyder,
- and Zhiping Weng
Genome Res. September 2012 22: 1798-1812; doi:10.1101/gr.139105.112
..., shown as a periodic oscillatory pattern in the average nucleosome occupancy profile centered on CTCF binding sites (Fu et al. 2008). Another study showed thatNRSF (also called REST) binding sites are flanked by positioned nucleosomes in CD4+ T cells, CD8+ T cells, and granulocytes (Valouev...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
...suggest that ungapped sequence comparisons can predict regulatory elements genome-wide. Footnotes ↵ 3 Corresponding authors. ↵ 3 E-mail woldb@caltech.edu ; fax (626) 395-5750. ↵ 3 E-mail pws@caltech.edu ; fax (626) 568-8012. [Supplemental material is available online...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...expression by altering pre-mRNA splicing (Lin et al. 2008) or regulatory networks (Jacques et al. 2013; Chuong et al. 2016). For example, lineage-specific transposons can carry binding sites for regulators including the repressor NRSF/REST (Mortazavi et al. 2006; Johnson et al. 2007) and CTCF (Bourque et al...
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