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

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R-loops are non-canonical three-stranded nucleic acid structures that are formed when the RNA hybridizes with the complementary DNA strand displacing the other strand free. The factors that influence the formation and genome-wide distribution of R-loops include several proteins involved in transcription, splicing, replication, recombination, DNA repair, and chromatin modifiers, etc. Additionally, R-loops tend to form at repetitive elements and skewed sequences (GC-skew and AT-skew). However, it is not clear if R-loops have any sequence bias in their genome-wide distribution among different species. Therefore, the authors of the current preprint looked into published datasets to understand the cis-regulatory elements associated with genome-wide R-loop distribution.

Key findings

1. The authors reanalyzed publicly available datasets generated in human cells (U2OS), fly (D. melanogaster embryos, S2 cells), and plants (seedling of A. thaliana) using different controls. They used R-loop (DRIP-seq) and nascent RNA profiles (GRO-seq) for the study. They observed that R-loops in plants tend to be longer (~998 nucleotides) than humans and fly (~414-618 nucleotides). Across the species, R-loops tend to enrich at gene promoters. Of note, plants harbor about 60% of the total R-loops at their promoters (and 0.2% at their introns). They also found a 70%, 24%, 39%, and 54% overlap between R-loops and transcribing regions in humans, fly embryos, S2 cells, and plants. However, when they analyzed further, flies tend to harbor R-loops more at intergenic regions (~90%) and possibly independent of transcription, suggesting the presence of trans R-loops.
2. The authors report some species-specific differences. They show that human and plant R-loops were marginally enriched at ribosomal DNA and underrepresented at short interspersed nuclear elements (SINEs). But more enriched at retrotransposons and satellite DNA. This is in contrary to the fly genome that has underrepresented R-loops at the satellite DNA (they also notice some difference in R-loop genome-wide distribution in the fly genome between embryos and S2 cells, possibly reflecting the developmental stages).
3. Overall, all the species analyzes showed a positive correlation between repetitive genetic elements and R-loop genome-wide distribution. In human cells, telomeres, centromeres, ribosomal DNA, and retrotransposons are enriched for R-loops. In the fly genome, Long interspersed nuclear elements (LINEs), Long terminal repeats (LTRs), and low complexity regions enriched for R-loops. However, in the plant genome, about half of the repeat families were enriched in R-loops; these include LINEs, LTRs, and low complexity regions, etc.

Perspective

Either a cause or consequence, R-loops seem to play a crucial role in developmental pathways, cancer progression, and neurodegenerative diseases. Thus, many researchers are drawn to understand their precise physiological role. While most of the work in R-loop biology looked at trans-acting factors, here, the authors investigated the association of cis-regulatory elements or sequence determinants of R-loop formation. The authors found strong correlations between R-loops and repetitive DNA sequences reinforcing earlier studies.

(Note: I only highlighted the key findings of the preprint without commenting on the methodology. Anyone is free to comment on the methodology, in case the preprint excites you.)

Acknowledgments: I am thankful to all the authors for their support, especially Chao Zeng for taking the time to comment on the preLight.

 

References:

1. https://doi.org/10.1093/nar/gkw1054
2. https://doi.org/10.1101/gr.158436.113
3. https://doi.org/10.1038/s41477-017-0004-x
4. https://doi.org/10.7554/elife.17548
5. https://doi.org/10.1038/s41467-017-00338-5
6. https://doi.org/10.1016/j.cub.2017.01.011

 

Tags: genomics, repetitive elements, rloops

doi: https://doi.org/10.1242/prelights.25813

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