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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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Methods: A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1
- Victor X. Jin,
- Alina Rabinovich,
- Sharon L. Squazzo,
- Roland Green,
- and Peggy J. Farnham
Genome Res. December 2006 16: 1585-1595; Published in Advance October 19, 2006, doi:10.1101/gr.5520206
...matrices constructed from transcription factor binding sites, a comparative genomics approach, and statistical learning methods to identify transcriptional regulatory modules. We began with E2F1 binding site information obtained from ChIP–chip analyses of ENCODE regions, from both HeLa and MCF7 cells. Our...
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LETTER: Suz12 binds to silenced regions of the genome in a cell-type-specific manner
- Sharon L. Squazzo,
- Henriette O’Geen,
- Vitalina M. Komashko,
- Sheryl R. Krig,
- Victor X. Jin,
- Sung-wook Jang,
- Raphael Margueron,
- Danny Reinberg,
- Roland Green,
- and Peggy J. Farnham
Genome Res. July 2006 16: 890-900; Published in Advance June 2, 2006, doi:10.1101/gr.5306606
...by E2F1 in ChIP assays ( Weinmann et al. 2001 ). Also, SUZ12, EZH2, EED, RbAP46, and RbAP48 have been identified as E2F target genes in overexpression and ChIP-chip experiments ( Bracken et al. 2003 ; Oberley et al. 2003 ; Bieda et al. 2006 ). Thus, it is believed that the frequent deregulation...
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Article: Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- Yong Cheng,
- Weisheng Wu,
- Swathi Ashok Kumar,
- Duonan Yu,
- Wulan Deng,
- Tamara Tripic,
- David C. King,
- Kuan-Bei Chen,
- Ying Zhang,
- Daniela Drautz,
- Belinda Giardine,
- Stephan C. Schuster,
- Webb Miller,
- Francesca Chiaromonte,
- Yu Zhang,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2009 19: 2172-2184; Published in Advance November 3, 2009, doi:10.1101/gr.098921.109
...and trimethylation of H3K27, and the location of the Hbb locus (purple). (Expr change) Change in expression level; (GATA1 peaks) those deduced from the -wide ChIP-chip data. The image was generated on a customized installation of the UCSC Genome Browser (Kent et al. 2002). Cheng et al. 2174 Genome Research www...
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LETTER: Transcription factor binding and modified histones in human bidirectional promoters
- Jane M. Lin,
- Patrick J. Collins,
- Nathan D. Trinklein,
- Yutao Fu,
- Hualin Xi,
- Richard M. Myers,
- and Zhiping Weng
Genome Res. June 2007 17: 818-827; doi:10.1101/gr.5623407
...categorized the presence of DNA sequence motifs, binding of transcription factors, and modified histones as overrepresented, shared, or underrepresented in bidirectional promoters with respect to unidirectional promoters. We found that a small set of motifs, including GABPA, MYC, E2F1, E2F4, NRF-1, CCAAT, YY1...
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Letter: Evolutionary descent of a human chromosome 6 neocentromere: A jump back to 17 million years ago
- Oronzo Capozzi,
- Stefania Purgato,
- Pietro D'Addabbo,
- Nicoletta Archidiacono,
- Paola Battaglia,
- Anna Baroncini,
- Antonella Capucci,
- Roscoe Stanyon,
- Giuliano Della Valle,
- and Mariano Rocchi
Genome Res. May 2009 19: 778-784; doi:10.1101/gr.085688.108
....A., Green, R., and Farnham, P.J. 2006. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human . Genome Res. 16: 595–605. Capozzi, O., Purgato, S., Verdun di Cantogno, L., Grosso, E., Ciccone, R., Zuffardi, O., Della Valle, G., and Rocchi, M. 2008. Evolutionary...
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Research: Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
- Valer Gotea,
- Axel Visel,
- John M. Westlund,
- Marcelo A. Nobrega,
- Len A. Pennacchio,
- and Ivan Ovcharenko
Genome Res. May 2010 20: 565-577; Published in Advance April 2, 2010, doi:10.1101/gr.104471.109
...2007). In the case of E2F1, E2F4, and MYC, experimental data, and therefore our analysis, were limited to the ENCODE regions (The ENCODE Project Consortium 2007). We evaluated the fraction of HCTs that correspond to regions bound by the corresponding TF by overlapping the genomic coordinates of HCTs...
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Letter: Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers
- Jérôme Eeckhoute,
- Mathieu Lupien,
- Clifford A. Meyer,
- Michael P. Verzi,
- Ramesh A. Shivdasani,
- X. Shirley Liu,
- and Myles Brown
Genome Res. March 2009 19: 372-380; Published in Advance January 7, 2009, doi:10.1101/gr.084582.108
...) Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human . Genome Res. 16 : 595 – 605 . ↵ Bolton, E.C. , So, A.Y. , Chaivorapol, C. , Haqq, C.M. , Li, H. , Yamamoto, K.R. ( 2007 ) Cell- and gene-specific regulation of primary target genes by the androgen receptor...
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LETTER: Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- David S. Johnson,
- Wei Li,
- D. Benjamin Gordon,
- Arindam Bhattacharjee,
- Bo Curry,
- Jayati Ghosh,
- Leonardo Brizuela,
- Jason S. Carroll,
- Myles Brown,
- Paul Flicek,
- Christoph M. Koch,
- Ian Dunham,
- Mark Bieda,
- Xiaoqin Xu,
- Peggy J. Farnham,
- Philipp Kapranov,
- David A. Nix,
- Thomas R. Gingeras,
- Xinmin Zhang,
- Heather Holster,
- Nan Jiang,
- Roland D. Green,
- Jun S. Song,
- Scott A. McCuine,
- Elizabeth Anton,
- Loan Nguyen,
- Nathan D. Trinklein,
- Zhen Ye,
- Keith Ching,
- David Hawkins,
- Bing Ren,
- Peter C. Scacheri,
- Joel Rozowsky,
- Alexander Karpikov,
- Ghia Euskirchen,
- Sherman Weissman,
- Mark Gerstein,
- Michael Snyder,
- Annie Yang,
- Zarmik Moqtaderi,
- Heather Hirsch,
- Hennady P. Shulha,
- Yutao Fu,
- Zhiping Weng,
- Kevin Struhl,
- Richard M. Myers,
- Jason D. Lieb,
- and X. Shirley Liu
Genome Res. March 2008 18: 393-403; Published in Advance February 7, 2008, doi:10.1101/gr.7080508
...; 6 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; 7 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; 8 Department of Pharmacology and the Genome...
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REVIEW: Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
- Albertha J.M. Walhout
Genome Res. December 2006 16: 1445-1454; Published in Advance October 19, 2006, doi:10.1101/gr.5321506
...304 : 1321 – 1325 . ↵ Bieda, M. , Xu, X. , Singer, M.A. , Green, R. , Farnham, P.J. ( 2006 ) Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human . Genome Res. 16 : 595 – 605 . ↵ Blais, A. , Dynlacht, B.D. ( 2005 ) Constructing transcriptional regulatory...

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