Abstract
Materials and methods To analyze chromosomal architecture between cell types, it is crucial to have a consistent way of analyzing Hi-C data and removal of experimental biases. To this end we developed a comprehensive method of Iterative Correction and Eigenvector decomposition (ICE). ICE maps Hi-C reads to the genome, filters mapped reads and obtains a Hi-C map of relative contact probabilities free of experimental biases. It then decomposes the maps into a set of genomic tracks characterizing high-order chromatin organization.
Highlights
The recently developed Hi-C method provides a comprehensive whole-genome picture of physical contacts between distal loci
Taken together, our results show that genome-wide chromatin interactions change upon differentiation of ES cells into IMR90, and suggest that sequence-dependent chromatin interactions in embryonic stem cells get overridden in a cell-type-specific manner
We show that upon differentiation regions change from an active to an inactive compartment, suggesting that change in chromatin interactions reflects cell-type-specific silencing of genomic regions
Summary
The recently developed Hi-C method provides a comprehensive whole-genome picture of physical contacts between distal loci. Analysis of these data has begun to reveal determinants of 3D genomic organization. The similarities and differences in chromosomal organization between cell-types remain unexplored
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