PT  - JOURNAL ARTICLE
AU  - Chao Zeng
AU  - Masahiro Onoguchi
AU  - Michiaki Hamada
TI  - Association analysis of repetitive elements and R-loop formation across species
AID  - 10.1101/2020.11.09.374124
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.11.09.374124
4099  - http://biorxiv.org/content/early/2020/11/24/2020.11.09.374124.short
4100  - http://biorxiv.org/content/early/2020/11/24/2020.11.09.374124.full
AB  - 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 StatementThe authors have declared no competing interest.