Abstract：
:The 3D organization of chromatin within the nucleus enables dynamic regulation and cell type-specific transcription of the genome. This is true at multiple levels of resolution: on a large scale, with chromosomes occupying distinct volumes (chromosome territories); at the level of individual chromatin fibers, which are organized into compartmentalized domains (e.g., Topologically Associating Domains-TADs), and at the level of short-range chromatin interactions between functional elements of the genome (e.g., enhancer-promoter loops).The widespread availability of Chromosome Conformation Capture (3C)-based high-throughput techniques has been instrumental in advancing our knowledge of chromatin nuclear organization. In particular, Hi-C has the potential to achieve the most comprehensive characterization of chromatin 3D interactions, as it is theoretically able to detect any pair of restriction fragments connected as a result of ligation by proximity.This chapter will illustrate how to compare the chromatin interactome in different experimental conditions, starting from pre-computed Hi-C contact matrices, how to visualize the results, and how to correlate the observed variations in chromatin interaction strength with changes in gene expression.
journal_name
Methods Mol Bioljournal_title
Methods in molecular biology (Clifton, N.J.)authors
Nicoletti Cdoi
10.1007/978-1-0716-1390-0_4keywords:
["3D chromatin structure","Bioinformatics","Differential chromatin interactions","Hi-C data"]subject
Has Abstractpub_date
2022-01-01 00:00:00pages
61-95eissn
1064-3745issn
1940-6029journal_volume
2301pub_type
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