Association analysis of repetitive elements and R-loop formation across species
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:12 |
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| Enthalten in: |
Mobile DNA - 12(2021), 1 vom: 20. Jan., Seite 3 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Zeng, Chao [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Revised 11.02.2021 published: Electronic Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1186/s13100-021-00231-5 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM320350533 |
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| 500 | |a published: Electronic | ||
| 500 | |a Citation Status PubMed-not-MEDLINE | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a R-loop | |
| 650 | 4 | |a Repetitive element | |
| 650 | 4 | |a Transposable element | |
| 700 | 1 | |a Onoguchi, Masahiro |e verfasserin |4 aut | |
| 700 | 1 | |a Hamada, Michiaki |e verfasserin |4 aut | |
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