HiC-TE: a computational pipeline for Hi-C data analysis to
study the role of repeat family interactions in the genome 3D
organization

J 2022

HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization

LEXA, Matej, Monika ČECHOVÁ, Son Hoang NGUYEN, Pavel JEDLIČKA, Viktor TOKAN et. al.

Základní údaje

Originální název

HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization

Autoři

LEXA, Matej (703 Slovensko, garant, domácí), Monika ČECHOVÁ (203 Česká republika, domácí), Son Hoang NGUYEN (704 Vietnam, domácí), Pavel JEDLIČKA (203 Česká republika), Viktor TOKAN (203 Česká republika), Zdeněk KUBÁT (203 Česká republika), Roman HOBZA (203 Česká republika) a Eduard KEJNOVSKÝ (203 Česká republika)

Vydání

BIOINFORMATICS, ENGLAND, OXFORD UNIV PRESS, 2022, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.800

Kód RIV

RIV/00216224:14330/22:00129122

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1093/bioinformatics/btac442

UT WoS

000824512000001

Klíčová slova anglicky

chromatin; transposable elements; Nextflow

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 11. 2024 12:03, doc. Ing. Matej Lexa, Ph.D.

Anotace

V originále

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.

Návaznosti

GA21-00580S, projekt VaV

Název: Jak rostlinné transposony přispívají ke "genomové krajině" a organizaci interfázního jádra (Akronym: transpozony)

Investor: Grantová agentura ČR, Jak rostlinné transposony přispívají ke "genomové krajině" a organizaci interfázních jáder

Citovat

LEXA, Matej, Monika ČECHOVÁ, Son Hoang NGUYEN, Pavel JEDLIČKA, Viktor TOKAN, Zdeněk KUBÁT, Roman HOBZA a 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, roč. 38, č. 16, s. 4030-4032. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btac442.

@article{1876219,
   author = {Lexa, Matej and Čechová, Monika and Nguyen, Son Hoang and Jedlička, Pavel and Tokan, Viktor and Kubát, Zdeněk and Hobza, Roman and Kejnovský, Eduard},
   article_location = {ENGLAND},
   article_number = {16},
   doi = {http://dx.doi.org/10.1093/bioinformatics/btac442},
   keywords = {chromatin; transposable elements; Nextflow},
   language = {eng},
   issn = {1367-4803},
   journal = {BIOINFORMATICS},
   title = {HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization},
   url = {https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btac442/6628581?redirectedFrom=fulltext&login=false},
   volume = {38},
   year = {2022}
}

TY  - JOUR
ID  - 1876219
AU  - Lexa, Matej - Čechová, Monika - Nguyen, Son Hoang - Jedlička, Pavel - Tokan, Viktor - Kubát, Zdeněk - Hobza, Roman - Kejnovský, Eduard
PY  - 2022
TI  - HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization
JF  - BIOINFORMATICS
VL  - 38
IS  - 16
SP  - 4030-4032
EP  - 4030-4032
PB  - OXFORD UNIV PRESS
SN  - 13674803
KW  - chromatin
KW  - transposable elements
KW  - Nextflow
UR  - https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btac442/6628581?redirectedFrom=fulltext&login=false
N2  - 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.
ER  -

LEXA, Matej, Monika ČECHOVÁ, Son Hoang NGUYEN, Pavel JEDLIČKA, Viktor TOKAN, Zdeněk KUBÁT, Roman HOBZA a 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. \textit{BIOINFORMATICS}. ENGLAND: OXFORD UNIV PRESS, 2022, roč.~38, č.~16, s.~4030-4032. ISSN~1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btac442.

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