Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

Zhihao Ding,Gregory E Crawford,Vishwanath R Iyer,Sander W Timmer,Anna Battenhouse,Fengtang Yang,Sandra Louzada,Richard Durbin,Ian Dunham,Jason D Lieb,Ewan Birney,Yunyun Ni,Bum-Kyu Lee,Greg Gibson

doi:10.1371/journal.pgen.1004798

Abstract

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.

Highlights

A major challenge in human genetics is to understand the mechanisms that link variation in genomic sequence to phenotypes of interest, including disease
We have systematically measured the effect of normal genetic variation present in a human population on the binding of a specific chromatin protein (CTCF) to DNA by measuring its binding in 51 human cell lines
We observed a large number of changes in protein binding that we can confidently attribute to genetic effects

Summary

Introduction

A major challenge in human genetics is to understand the mechanisms that link variation in genomic sequence to phenotypes of interest, including disease. Considerable effort has been invested in identifying potential causative variants, because this is essential to understanding the mechanistic route from the change in genomic sequence to final phenotype. The majority of the loci that have been found are not in strong linkage disequilibrium with a protein coding variant, suggesting that a change in a non-protein coding DNA sequence is often responsible for the phenotypic effect [2]. One route to finding intermediates between genotype and whole organism phenotype is to study the effect of genetic variants on gene regulation. New technologies such as microarrays and RNA sequencing (RNA-seq) have enabled quantification of transcript levels for every gene in a genome. Using DNase I hypersensitivity and binding assays for the CTCF transcription factor on two family trios with known genome sequences, we showed that allele-specific binding patterns consistent with strong

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Discussion

Conclusion