HiChew: a Tool for TAD Clustering in Embryogenesis

Nikolai S. Bykov, Olga M. Sigalova, Mikhail S. Gelfand, Aleksandra A. Galitsyna

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

The three-dimensional structure of the Drosophila chromatin has been shown to change at the early stages of embryogenesis from the state with no local structures to compartmentalized chromatin segregated into topologically associated domains (TADs). However, the dynamics of TAD formation and its association with the expression and epigenetics dynamics is not fully understood. As TAD calling and analysis of TAD dynamics have no standard, universally accepted solution, we have developed HiChew, a specialized tool for segmentation of Hi-C maps into TADs of a given expected size and subsequent clustering of TADs based on their dynamics during the embryogenesis. To validate the approach, we demonstrate that HiChew clusters correlate with genomic and epigenetic characteristics. Particularly, in accordance with previous findings, the maturation rate of TADs is positively correlated with the number of housekeeping genes per TAD and negatively correlated with the length of housekeeping genes. We also report a high positive correlation of the maturation rate of TADs with the growth rate of the associated ATAC-Seq signal.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 16th International Symposium, ISBRA 2020, Proceedings
EditorsZhipeng Cai, Ion Mandoiu, Giri Narasimhan, Pavel Skums, Xuan Guo
PublisherSpringer
Pages381-388
Number of pages8
ISBN (Print)9783030578206
DOIs
Publication statusPublished - 2020
Event16th International Symposium on Bioinformatics Research and Applications, ISBRA 2020 - Moscow, Russian Federation
Duration: 1 Dec 20204 Dec 2020

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume12304 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference16th International Symposium on Bioinformatics Research and Applications, ISBRA 2020
Country/TerritoryRussian Federation
CityMoscow
Period1/12/204/12/20

Keywords

  • Chromatin 3D structure
  • Clustering
  • Embryogenesis
  • Epigenetics
  • Housekeeping genes
  • TADs

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