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  1. 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
    ...reads reveal potential tissue-specific activity for certain TFs, such as limb-specific activity for E2F4 HCTs, or forebrain-specific activity for NOBOX HCTs (Fig. 7B). The latter reinforces the association between NOBOX and forebrain specificity observed with the set of human enhancers. In fact...
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  2. 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
    .... Although the specific genes regulated by E2F1 alone versus E2F1 plus AP-2α are different, the two classes of target genes are both enriched in transcription factors. These results suggest that the major role of E2F1 in the cell is to regulate other transcription factors. Interestingly, although E2F1...
  3. 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
    ...factors in MCF7 cells, ESR1 and E2F1, also revealed greater FAIRE enrichment at sites that were bound versus unbound ( Bieda et al. 2006 ; Carroll et al. 2006 ; Rabinovich et al. 2008 ; Supplemental Fig. S2). View larger version: In this window In a new window Figure 1. FAIRE-chip signal from MCF7 cells...
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