Abstract:
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A series of recently developed chromatin conformation capture-based assays (3C, 4C, 5C and Hi-C) enabled the study of three-dimensional chromosomal structures and elucidated long-range genomic interactions between loci. However, current analysis pipelines of these data discard reads aligning to multiple locations (multi-reads) and, hence, underestimate inter-chromosomal interactions involving repetitive regions. We study this problem in depth and develop a hierarchical model for read allocation. Effective use of multi-reads leads to significant increase in the reproducibility of Hi-C data analysis and identifies novel promoter-enhancer interactions, most notably pertaining ZNF genes.
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