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LETTER: Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
- David C. King,
- James Taylor,
- Ying Zhang,
- Yong Cheng,
- Heather A. Lawson,
- Joel Martin,
- ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. June 2007 17: 775-786; doi:10.1101/gr.5592107
...expanded to a representative genomic region covering at least 100 bp. In defining this set only experiments for the following factors were included: SP1, SP3, E2F1, E2F4, MYC, STAT1, JUN, CEBPE, PU.1 (SPI1), RARecA. All of these factors bind to DNA with sequence specificity and are not known...
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Methods: Systematic functional characterization of cis-regulatory motifs in human core promoters
- Saurabh Sinha,
- Adam S. Adler,
- Yair Field,
- Howard Y. Chang,
- and Eran Segal
Genome Res. March 2008 18: 477-488; Published in Advance February 6, 2008, doi:10.1101/gr.6828808
...repressed in their normal tissue counterparts, supporting a role for these factors in regulating cell proliferation of these tumors ( Fig. 4B ; Supplemental Fig. S2). Consistent with a role in regulating the motif modules, E2F1 (along with additional E2F genes) and NFYA gene expression levels were highly...
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Research: Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns
- Elisheva Javasky,
- Inbal Shamir,
- Shashi Gandhi,
- Shawn Egri,
- Oded Sandler,
- Scott B. Rothbart,
- Noam Kaplan,
- Jacob D. Jaffe,
- Alon Goren,
- and Itamar Simon
Genome Res. October 2018 28: 1455-1466; Published in Advance August 30, 2018, doi:10.1101/gr.230300.117
...II), or by determining the maximal P-value from all pairwise comparisons (for HA-E2F1 and USF1). For a comprehensive list of all P-values, see Supplemental Table S2. The same analysis for all available ENCODE HeLa-S3 data is shown in Supplemental Figures S11, S12. (E) Profiles showing transcription reactivation kinetics...
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Method: Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes
- Sushmita Roy and
- Rupa Sridharan
Genome Res. July 2017 27: 1250-1262; Published in Advance April 19, 2017, doi:10.1101/gr.215004.116
..., modules 10, 11, and 12, which were relatively depleted for H3K14ac and H3K18ac, were enriched for MYC binding in iPSCs and not enriched for any of the other factors (Fig. 3C). The combination of MYC (includes both MYC and MYCN), E2F1, and ZFX were again enriched in the modules that lacked H3K14ac and H3K...
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ARTICLE: A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members
- Xiaoqin Xu,
- Mark Bieda,
- Victor X. Jin,
- Alina Rabinovich,
- Mathew J. Oberley,
- Roland Green,
- and Peggy J. Farnham
Genome Res. November 2007 17: 1550-1561; Published in Advance October 1, 2007, doi:10.1101/gr.6783507
...these assays in the context of five different cell types, including both normal and tumor cells. Results E2F family members localize to core promoter regions in both normal and tumor cells Using ChIP–chip analysis and genomic tiling arrays, we had previously shown that E2F1 binds predominantly within 2 kb...
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LETTER: Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
- Victor X. Jin,
- Henriette O’Geen,
- Sushma Iyengar,
- Roland Green,
- and Peggy J. Farnham
Genome Res. June 2007 17: 807-817; doi:10.1101/gr.6006107
...Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches Victor X. Jin 1 , Henriette O’Geen 1 , Sushma Iyengar 1 , Roland Green 2 , and Peggy J. Farnham 1 , 3 1...
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Letter: Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns
- Michael P. Schnetz,
- Cynthia F. Bartels,
- Kuntal Shastri,
- Dheepa Balasubramanian,
- Gabriel E. Zentner,
- Ravishankar Balaji,
- Xiaodong Zhang,
- Lingyun Song,
- Zhenghe Wang,
- Thomas LaFramboise,
- Gregory E. Crawford,
- and Peter C. Scacheri
Genome Res. April 2009 19: 590-601; Published in Advance February 27, 2009, doi:10.1101/gr.086983.108
...of the CHD7 protein on chromatin using the approach of chromatin immunoprecipitation on tiled microarrays (ChIP-chip). These studies were performed in human colorectal carcinoma cells, human neuroblastoma cells, and mouse embryonic stem (ES) cells before and after differentiation into neural precursor cells...
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Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
- Joseph D. Fleming,
- Giulio Pavesi,
- Paolo Benatti,
- Carol Imbriano,
- Roberto Mantovani,
- and Kevin Struhl
Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
...is shown; see Supplemental Figure 13 for all TFs analyzed. Fleming et al. 1202 Genome Research www..org By preventing accessibility to target sites, chromatin is a formidable barrier for binding by most TFs. This creates a dilemma as to how cis-regulatory motifs can provide transcriptional competency...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
.... ↵ Bieda, M. , Xu, X. , Singer, M.A. , Green, R. , Farnham, P.J. ( 2006 ) Unbiased location analysis of E3F1-binding sites suggests a widespread role for E2F1 in the human . Genome Res. 16 : 595 – 605 . ↵ Birney, E. , Andrews, D. , Caccamo, M. , Chen, Y. , Clarke, L. , Coates, G. , Cox, T. , Cunningham, F...
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LETTER: E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites
- Alina Rabinovich,
- Victor X. Jin,
- Roman Rabinovich,
- Xiaoqin Xu,
- and Peggy J. Farnham
Genome Res. November 2008 18: 1763-1777; Published in Advance October 3, 2008, doi:10.1101/gr.080622.108
...consensus motifs were bound by other E2Fs or were unavailable for binding due to being located in silenced chromatin. To determine why the 1566 E2F consensus motifs were not bound by E2F1 in MCF7 cells, we examined the results of MCF7 ChIP-chip assays performed using antibodies to E2F4 and E2F6 ( Xu et al...

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