Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
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Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes. In order to identify quantitative trait loci (QTLs) that influence the binding of a transcription factor in humans, we measured binding of the multifunctional transcription and chromatin factor CTCF in 51 HapMap cell lines. We identified thousands of QTLs in which genotype differences were associated with differences in CTCF binding strength, hundreds of them confirmed by directly observable allele-specific binding bias. The majority of QTLs were either within 1 kb of the CTCF binding motif, or in linkage disequilibrium with a variant within 1 kb of the motif. On the X chromosome we observed three classes of binding sites: a minority class bound only to the active copy of the X chromosome, the majority class bound to both the active and inactive X, and a small set of female-specific CTCF sites associated with two non-coding RNA genes. In sum, our data reveal extensive genetic effects on CTCF binding, both direct and indirect, and identify a diversity of patterns of CTCF binding on the X chromosome.
Chromosomes, Human, X
Quantitative Trait Loci
Published Version (Please cite this version)10.1371/journal.pgen.1004798
Publication InfoBattenhouse, A; Birney, E; Crawford, Gregory E; Ding, Z; Dunham, I; Durbin, R; ... Yang, F (2014). Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLoS Genet, 10(11). pp. e1004798. 10.1371/journal.pgen.1004798. Retrieved from https://hdl.handle.net/10161/10680.
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Associate Professor in Pediatrics
My research involves identifying gene regulatory elements across the genome to help us understand how chromatin structure dictates cell function and fate. For the last 30 years, mapping DNase I hypersensitive sites has been the gold standard method to identify the location of active regulatory elements, including promoters, enhancers, silencers, and locus control regions. I have developed technologies that can identify most DNase I hypersensitive sites from potentially any cell type from an