LEXA, Matej, Monika ČECHOVÁ, Son Hoang NGUYEN, Pavel JEDLIČKA, Viktor TOKAN, Zdeněk KUBÁT, Roman HOBZA and Eduard KEJNOVSKÝ. HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization. BIOINFORMATICS. ENGLAND: OXFORD UNIV PRESS, 2022, vol. 38, No 16, p. 4030-4032. ISSN 1367-4803. doi:10.1093/bioinformatics/btac442.
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Basic information
Original name HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization
Authors LEXA, Matej (703 Slovakia, guarantor, belonging to the institution), Monika ČECHOVÁ (203 Czech Republic, belonging to the institution), Son Hoang NGUYEN (704 Viet Nam, belonging to the institution), Pavel JEDLIČKA (203 Czech Republic), Viktor TOKAN (203 Czech Republic), Zdeněk KUBÁT (203 Czech Republic), Roman HOBZA (203 Czech Republic) and Eduard KEJNOVSKÝ (203 Czech Republic).
Edition BIOINFORMATICS, ENGLAND, OXFORD UNIV PRESS, 2022, 1367-4803.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 6.931 in 2021
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1093/bioinformatics/btac442
UT WoS 000824512000001
Keywords in English chromatin; transposable elements; Nextflow
Changed by Changed by: Ing. Matej Lexa, Ph.D., učo 31298. Changed: 6/9/2022 20:34.
Abstract
Motivation The role of repetitive DNA in the 3D organization of the interphase nucleus is a subject of intensive study. In studies of 3D nucleus organization, mutual contacts of various loci can be identified by Hi-C sequencing. Typical analyses use binning of read pairs by location to reduce noise. We use binning by repeat families instead to make similar conclusions about repeat regions. Results To achieve this, we combined Hi-C data, reference genome data and tools for repeat analysis into a Nextflow pipeline identifying and quantifying the contacts of specific repeat families. As an output, our pipeline produces heatmaps showing contact frequency and circular diagrams visualizing repeat contact localization. Using our pipeline with tomato data, we revealed the preferential homotypic interactions of ribosomal DNA, centromeric satellites and some LTR retrotransposon families and, as expected, little contact between organellar and nuclear DNA elements. While the pipeline can be applied to any eukaryotic genome, results in plants provide better coverage, since the built-in TE-greedy-nester software only detects tandems and LTR retrotransposons. Other repeats can be fed via GFF3 files. This pipeline represents a novel and reproducible way to analyze the role of repetitive elements in the 3D organization of genomes. Availability https://gitlab.fi.muni.cz/lexa/hic-te/ Supplementary information Supplementary data are available at Bioinformatics online.
Links
GA21-00580S, research and development projectName: Jak rostlinné transposony přispívají ke "genomové krajině" a organizaci interfázního jádra (Acronym: transpozony)
Investor: Czech Science Foundation
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