Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

Roland Jäger; Gabriele Migliorini; Marc Henrion; Radhika Kandaswamy; Helen E. Speedy; Andreas Heindl; Nicola Whiffin; Maria J. Carnicer; Laura Broome; Nicola Dryden; Takashi Nagano; Stefan Schoenfelder; Martin Enge; Yinyin Yuan; Jussi Taipale; Peter Fraser; Olivia Fletcher; Richard S. Houlston

doi:10.1038/ncomms7178

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

Roland Jäger, Gabriele Migliorini, Marc Henrion, Radhika Kandaswamy, Helen E. Speedy, Andreas Heindl, Nicola Whiffin, Maria J. Carnicer, Laura Broome, Nicola Dryden, Takashi Nagano, Stefan Schoenfelder, Martin Enge, Yinyin Yuan, Jussi Taipale, Peter Fraser, Olivia Fletcher, Richard S. Houlston

Research output: Contribution to journal › Article › peer-review

160 Citations (Scopus)

Abstract

Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.

Original language	English
Article number	6178
Journal	Nature Communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms7178
Publication status	Published - 1 Feb 2015
Externally published	Yes

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Jäger, R., Migliorini, G., Henrion, M., Kandaswamy, R., Speedy, H. E., Heindl, A., Whiffin, N., Carnicer, M. J., Broome, L., Dryden, N., Nagano, T., Schoenfelder, S., Enge, M., Yuan, Y., Taipale, J., Fraser, P., Fletcher, O., & Houlston, R. S. (2015). Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nature Communications, 6, Article 6178. https://doi.org/10.1038/ncomms7178

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title = "Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci",

abstract = "Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.",

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Jäger, R, Migliorini, G, Henrion, M, Kandaswamy, R, Speedy, HE, Heindl, A, Whiffin, N, Carnicer, MJ, Broome, L, Dryden, N, Nagano, T, Schoenfelder, S, Enge, M, Yuan, Y, Taipale, J, Fraser, P, Fletcher, O & Houlston, RS 2015, 'Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci', Nature Communications, vol. 6, 6178. https://doi.org/10.1038/ncomms7178

TY - JOUR

T1 - Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

AU - Jäger, Roland

AU - Migliorini, Gabriele

AU - Henrion, Marc

AU - Kandaswamy, Radhika

AU - Speedy, Helen E.

AU - Heindl, Andreas

AU - Whiffin, Nicola

AU - Carnicer, Maria J.

AU - Broome, Laura

AU - Dryden, Nicola

AU - Nagano, Takashi

AU - Schoenfelder, Stefan

AU - Enge, Martin

AU - Yuan, Yinyin

AU - Taipale, Jussi

AU - Fraser, Peter

AU - Fletcher, Olivia

AU - Houlston, Richard S.

PY - 2015/2/1

Y1 - 2015/2/1

N2 - Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.

AB - Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.

U2 - 10.1038/ncomms7178

DO - 10.1038/ncomms7178

M3 - Article

SN - 2041-1723

VL - 6

JO - Nature Communications

JF - Nature Communications

M1 - 6178

ER -

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

Abstract

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