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bioRxiv · 10.1101/2021.12.18.473300

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

Lexa, M.·Cechova, M.·Nguyen, S. H.·Jedlicka, P.·Tokan, V.·Kubat, Z.·Hobza, R.·Kejnovsky, E.
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Abstract

The role of repetitive DNA in the 3D organization of the interphase nucleus in plant cells is a subject of intensive study. High-throughput chromosome conformation capture (Hi-C) is a sequencing-based method detecting the proximity of DNA segments in nuclei. We combined Hi-C data, plant reference genome data and tools for the characterization of genomic repeats to build a Nextflow pipeline identifying and quantifying the contacts of specific repeats revealing the preferential homotypic interactions of ribosomal DNA, DNA transposons and some LTR retrotransposon families. We provide a novel way to analyze the organization of repetitive elements in the 3D nucleus.

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Lexa, M., Cechova, M., Nguyen, S. H., Jedlicka, P., Tokan, V., Kubat, Z., Hobza, R., Kejnovsky, E.. 2021-12-21. HiC-TE: a computational pipeline for Hi-C data analysis shows a possible role of repeat family interactions in the genome 3D organization. https://doi.org/10.1101/2021.12.18.473300

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