@article {Zeng2020.11.09.374124, author = {Chao Zeng and Masahiro Onoguchi and Michiaki Hamada}, title = {Association analysis of repetitive elements and R-loop formation across species}, elocation-id = {2020.11.09.374124}, year = {2020}, doi = {10.1101/2020.11.09.374124}, publisher = {Cold Spring Harbor Laboratory}, 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.}, URL = {https://www.biorxiv.org/content/early/2020/11/10/2020.11.09.374124}, eprint = {https://www.biorxiv.org/content/early/2020/11/10/2020.11.09.374124.full.pdf}, journal = {bioRxiv} }