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

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

doi:10.1038/ncomms7178

Cited by 200 publications

(167 citation statements)

References 61 publications

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“…A number of such modifications have been published (Fig. 3b), called Capture C, Capture Hi-C (CHi-C), HiCap, and targeted chromatin capture (T2C) (Dryden et al 2014;Hughes et al 2014;Jager et al 2015;Kolovos et al 2014;Mifsud et al 2015;Sahlen et al 2015;Schoenfelder et al 2015). Most of these assays are based on hybridization of sequencing adaptor-ligated 3C (Capture C) and Hi-C samples (CHi-C and HiCap) respectively, followed by pull-down using biotinylated RNA molecules (120 nucleotides).…”

Section: Technical Limitations and Further Improvements In Hi-c Technmentioning

confidence: 99%

“…that are already available to chromatin interaction data in order to identify their putative target genes, which can then be validated by analyzing chromatin changes in the presence of these genomic aberrations. Integrative approaches involving epigenetic, genomic, and chromatin conformation analyses are beginning to deliver exciting results (Jager et al 2015), and their widespread application may lead to the understanding of hidden principles of Fullwood et al (2009) genome function and regulation, both in normal conditions and in disease. Finally, all the present methods capture bipartite interactions.…”

Section: Future Perspectivesmentioning

confidence: 99%

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Chromosome conformation capture technologies and their impact in understanding genome function

2016

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It has been more than a decade since the first chromosome conformation capture (3C) assay was described. The assay was originally devised to measure the frequency with which two genomic loci interact within the three-dimensional (3D) nuclear space. Over time, this method has evolved both qualitatively and quantitatively, from detection of pairwise interaction of two unique loci to generating maps for the global chromatin interactome. Combined with the analysis of the epigenetic chromatin context, these advances led to the unmasking of general genome folding principles. The evolution of 3C-based methods has been supported first by the revolution in ChIP and then by sequencingbased approaches, methods that were primarily tools to study the unidimensional genome. The gradual improvement of 3C-based methods illustrates how the field adapted to the need to gradually address more subtle questions, beginning with enquiries of reductionist nature to reach more holistic perspectives, as the technology advanced, in a process that is greatly improving our knowledge on genome behavior and regulation. Here, we describe the evolution of 3C and other 3C-based methods for the analysis of chromatin interactions, along with a brief summary of their contribution in uncovering the significance of the threedimensional world within the nucleus. We also discuss their inherent limitations and caveats in order to provide a critical view of the power and the limits of this technology.

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Section: Technical Limitations and Further Improvements In Hi-c Technmentioning

confidence: 99%

Section: Future Perspectivesmentioning

confidence: 99%

Chromosome conformation capture technologies and their impact in understanding genome function

2016

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“…This 'Capture-HiC' greatly increases the obtained resolution and allows multiple interacting regions to be investigated simultaneously [162]. Capture HiC shows great promise for post-GWAS work and has been used to follow up risk-SNPs at both breast and colorectal cancer loci [162,173].…”

Section: C (Chromosome Conformation Capture Carbon Copy) and Hicmentioning

confidence: 99%

“…The power of this technique has been greatly enhanced by next-generation sequencing which allows the creation of a genome wide map of loci that interact with the genomic element being studied [172]. It is of particular use to investigate those GWAS loci where the candidate causal SNPs can be mapped to one or two regulatory elements allowing genome-wide interaction data to be generated from a single experiment [173]. It has not yet been employed to investigate breast cancer GWAS loci and should prove a powerful tool for post-GWAS analysis.…”

Section: C (Circular Chromosome Conformation Capture)mentioning

confidence: 99%

“…5C examines interactions within a defined genomic region and can identify enhancer-promoter looping or give a broader picture of local chromatin structure [174]. 5C has not yet been used to characterise risk loci although a related technique (capture Hi-C) has recently been employed to find targets of putative enhancers at the 2q35, 8q24 and 9q31 breast cancer risk loci and at 14 colorectal carcinoma loci [162,173].…”

Section: Introductionmentioning

confidence: 99%

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The long range regulation of breast cancer associated genes

Betts¹

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PrefacePage iBreast cancer is the most common non-cutaneous cancer of women and a major cause of mortality [1]. Genetic factors are the single biggest risk factor and 75% of the risk derives from common but low penetrance single nucleotide polymorphisms (SNPs) [2]. These are found using genome-wide association studies (GWAS) and the majority localize to non-coding regions of the genome [3] The identification of CCND1 as an interacting partner of PRE1 and PRE2 was done using a candidate gene approach with 3C (chromosome conformation capture) targeted confirmation of interaction. To detect other potential targets of PRE1 and PRE2 at the 11q13 locus using an agnostic approach, the 4Cseq and 5C techniques were used. These revealed a number of local interaction regions covering six gene promoters. A novel strategy using knockdown of enhancer RNA transcribed from PRE1 then identified the IGHMBP2 and CPT1A genes as likely additional targets of PRE1. Genome editing with transcription activator-like effector nucleases (TALENS) was also used, creating isogenic cell lines to clarify the effects of the SNPs in their native genomic context. Further functional work is required, however the range of techniques employed has substantially expanded our understanding of the 11q13 breast cancer risk locus and forms a template for future investigations of GWAS risk loci.To identify noncoding RNAs expressed at the 11q13 locus that may be interacting with PRE1 or PRE2 required the use of RNA Capture-seq. RNA Capture-seq involves a targeted enrichment step that greatly increases the sequencing depth at regions of interest and can reveal lowly expressed transcripts that may have not been found by traditional RNA-seq [7]. This identified one novel long non-coding RNA expressed from the (+) strand that was named CUPID1 and a second arising from the same locus on the (-) strand named CUPID2. They were located in the nucleus, oestrogen induced and both expressed relatively highly in ERα positive breast cancer cell lines but not in ERα The 11q13 locus is amplified in around 20% of breast cancers and is thought to contain a number of driver genes including CCND1 [8]. Given that CUPID1 and CUPID2 are widely over-expressed inERα positive breast cancer cell lines, it was hypothesized that they may also have a role in driving tumour growth. Publically available RNAseq data showed CUPID2 to be highly expressed in breast and renal cancer but not in normal tissue. Stable cell lines over-expressing the lncRNAs were then generated and subsequent oncogenic assays revealed that CUPID2 increased cellular proliferation and the efficiency of colony formation in breast cancer cells. A murine xenograft model confirmed these findings in vivo by demonstrating a marked increase in tumour size for the mice injected with cells over-expressing CUPID2. There is thus evidence that CUPID2 behaves as an oncogene and may be an additional driver of the 11q13 amplicon in ERα positive breast cancer.In summary, CPT1A and IGHMBP2 were identified as potential mediat...

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Capture Hi‐C Library Generation and Analysis to Detect Chromatin Interactions

2018

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Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. The recently implemented modification, in situ Hi-C, maintains nuclear integrity during digestion and ligation steps, reducing random ligation of Hi-C fragments. Although Hi-C allows for genome-wide characterization of chromatin contacts, it requires high-depth sequencing to discover significant contacts. To address this, Capture Hi-C (CHi-C) enriches standard Hi-C libraries for regions of biological interest, for example by specifically targeting gene promoters, aiding identification of biologically significant chromatin interactions compared to conventional Hi-C, for an equivalent number of sequence reads. Illustrating the application of CHi-C applied to genome-wide analysis of chromatin interactions with promoters, we detail the protocols for in situ Hi-C and CHi-C library generation for sequencing, as well as the bioinformatics tools for data analysis. © 2018 by John Wiley & Sons, Inc.

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

Cited by 200 publications

References 61 publications

Chromosome conformation capture technologies and their impact in understanding genome function

Chromosome conformation capture technologies and their impact in understanding genome function

The long range regulation of breast cancer associated genes

Capture Hi‐C Library Generation and Analysis to Detect Chromatin Interactions

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