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Association analysis of repetitive elements and R-loop formation across species

Chao Zeng, Masahiro Onoguchi, Michiaki Hamada
doi: https://doi.org/10.1101/2020.11.09.374124
Chao Zeng
1AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
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  • For correspondence: chao.zeng@hamadalab.com mhamada@waseda.jp
Masahiro Onoguchi
1AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
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Michiaki Hamada
1AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
2Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo 169-8555, Japan
3Institute for Medical-oriented Structural Biology, Waseda University, 2-2, Wakamatsu-cho Shinjuku-ku, Tokyo 162-8480, Japan
4Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
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  • For correspondence: chao.zeng@hamadalab.com mhamada@waseda.jp
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ABSTRACT

Genomes are known to have a large number of repetitive elements. Emerging evidence suggests that these non-coding elements may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. In this study, we found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellites, long interspersed nuclear elements (LINEs), and DNAs were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeats (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 24, 2020.
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Association analysis of repetitive elements and R-loop formation across species
Chao Zeng, Masahiro Onoguchi, Michiaki Hamada
bioRxiv 2020.11.09.374124; doi: https://doi.org/10.1101/2020.11.09.374124
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Association analysis of repetitive elements and R-loop formation across species
Chao Zeng, Masahiro Onoguchi, Michiaki Hamada
bioRxiv 2020.11.09.374124; doi: https://doi.org/10.1101/2020.11.09.374124

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