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Nucleic Acids Res. 2013 Jul;41(13):e132. doi: 10.1093/nar/gkt373. Epub 2013 May 13.

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.

Author information

1
Computational Biology Unit, Uni Computing, Uni Research AS, N-5020 Bergen, Norway.

Abstract

The coupling of chromosome conformation capture (3C) with next-generation sequencing technologies enables the high-throughput detection of long-range genomic interactions, via the generation of ligation products between DNA sequences, which are closely juxtaposed in vivo. These interactions involve promoter regions, enhancers and other regulatory and structural elements of chromosomes and can reveal key details of the regulation of gene expression. 3C-seq is a variant of the method for the detection of interactions between one chosen genomic element (viewpoint) and the rest of the genome. We present r3Cseq, an R/Bioconductor package designed to perform 3C-seq data analysis in a number of different experimental designs. The package reads a common aligned read input format, provides data normalization, allows the visualization of candidate interaction regions and detects statistically significant chromatin interactions, thus greatly facilitating hypothesis generation and the interpretation of experimental results. We further demonstrate its use on a series of real-world applications.

PMID:
23671339
PMCID:
PMC3711450
DOI:
10.1093/nar/gkt373
[Indexed for MEDLINE]
Free PMC Article

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