Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.

By Jason S. Carroll, X. S. Liu, A. Brodsky, Clifford A. Meyer, A. J. Szary, J. Eeckhoute, W. Shao, E. Hestermann, T. Geistlinger, E. Fox and 2 more. Cell, 2005

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Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/556d6f9a2d19fc82cfda040fe78a03bac764be81

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ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing (2010, background): “Three-dimensional chromatin interactions have been shown to bring distal transcription factor binding sites into close spatial proximity to gene promoters [6], but global analysis of three-dimensional chromatin interactions has been limited by the lack of techniques for high-resolution and whole-gen”
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. (2007, methodology): “ChIP combined with tiled DNA oligonucleotide microarray analysis (ChIP-on-chip) has recently evolved as an unbiased technique for mapping the in vivo binding sites of transcription factors in the genome (Carroll et al., 2005, 2006).”
GATA-3 maintains the differentiation of the luminal cell fate in the mammary gland. (2006, neutral): “GATA-1 is essential for the specification of erythroid cells from myelo-erythroid progenitors, whereas the Ets family transcription factor PU.1 is essential for the specification of myeloid cells ( Cantor and Orkin, 2001 ).”
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. (2008, positive): “Accordingly, this distribution contrasted with that of RNA polymerase II (RNA PolII) (Carroll et al., 2005), which is foundprimarily at proximal promoters (FigureS4C).”
Pioneer transcription factors: establishing competence for gene expression. (2011, background): “Such ‘‘priming’’ can increase the rapidity of a transcriptional response and is seen during development and in hormonal regulation (Gualdi et al. 1996; Carroll et al. 2005).”
Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer (2009, background): “Given our previous findings that collaborating transcription factors and coactivators may assist nuclear receptor binding in certain regions (Carroll et al., 2005; Shao et al., 2004; Wang et al., 2007), we then investigated whether the previously identified AR collaborating factors FoxA1, Wang et al”
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer (2011, background): “…transcription start sites of their target genes, which implies that distal enhancers are the primary receptor loading sites and suggests that the receptors utilize a distal regulatory mode of transcriptional control (Carroll et al, 2005; John et al, 2008; Lin et al, 2009; Cheung and Kraus, 2010).”
Somatic sex reprogramming of adult ovaries to testes by FOXL2 ablation. (2009, neutral): “Indeed, a recent study claims that, in addition to the ‘classical’ forkhead site, FOXL2 can bind a DNA binding motif that resembles two estrogen receptor DNA binding half-sites and the consensus binding site for SF1 (Benayoun et al., 2008; Carroll et al., 2005).”
Genome-wide analysis of estrogen receptor binding sites (2006, background): “We recently expanded on these analyses to map estrogen receptor binding sites in a less biased way that did not depend on preexisting concepts of classic promoter domain”
The evolution of Fox genes and their role in development and disease (2009, background): “Recent findings on the contribution of FOXA1-mediated gene regulation in breast and prostate cancer (see below) further show the large contribution of this gene family to human healt”
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. (2008, background): “In addition, for many domain classes, and in organisms ranging from yeast to human, in vivo binding sites detected by ChIP-chip typically contain sequences that reflect those preferred in vitro (Carroll et al., 2005; Harbison et al., 2004).”