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

Chao Zeng, Masahiro Onoguchi, Michiaki Hamada

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Although recent studies have revealed the genome-wide distribution of R-loops, our understanding of R-loop formation is still limited. Genomes are known to have a large number of repetitive elements. Emerging evidence suggests that these sequences may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. Results: We found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellite, long interspersed nuclear elements (LINEs), and DNA transposons 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 repeat retrotransposons (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. Conclusions: 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.

Original languageEnglish
Article number3
JournalMobile DNA
Volume12
Issue number1
DOIs
Publication statusPublished - 2021 Dec

Keywords

  • R-loop
  • Repetitive element
  • Transposable element

ASJC Scopus subject areas

  • Molecular Biology

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