Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments.

ABSTRACT:

Background

Understanding the role of various factors in 3D genome organization is essential to determine their impact on shaping large-scale chromatin units such as euchromatin (A) and heterochromatin (B) compartments. At this level, chromatin compaction is extensively modulated when transcription and epigenetic profiles change upon cell differentiation and response to various external impacts. However, detailed analysis of chromatin contact patterns within and between compartments is complicated because of a lack of suitable computational methods.

Results

We developed a tool, Pentad, to perform calculation, visualisation and quantitative analysis of the average chromatin compartment from the Hi-C matrices in cis, trans, and specified genomic distances. As we demonstrated by

SUBMITTER: Magnitov MD 

PROVIDER: S-EPMC8976968 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature