R-loop: an emerging regulator of chromatin dynamics

Al-Hadid, Qais; Yang, Yanzhong

doi:10.1093/abbs/gmw052

Cited by 39 publications

(33 citation statements)

References 103 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5A). A previous study showed that R-loops with the H3K9me2 mark can repress FMR1 gene expression (Colak et al 2014), and this scenario aligns well with the results from other studies (Al-Hadid and Yang 2016;Sanz et al 2016;García-Benítez et al 2017;García-Pichardo et al 2017), which found that epigenetic marks are linked to R-loop formation. We validated this finding experimentally in methylation-deficient mutants using dot blot and western blotting ( Fig.…”

Section: The Coordination Of R-loops and Histone Markssupporting

confidence: 90%

“…Because the technology to partially deplete R-loops on a genome-wide scale is not yet available, we could not verify the causal effects of R-loops on epigenetic modifications on a large scale, although we indeed provided multiple lines of computational evidence to support this. In addition, two other studies have shown that R-loops have effects on histone modifications (Castellano-Pozo et al 2013;Al-Hadid and Yang 2016).…”

Section: The Coordination Of R-loops and Histone Marksmentioning

confidence: 98%

See 1 more Smart Citation

Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice

Fang¹,

Chen²,

Lin³

et al. 2019

Genome Res.

View full text Add to dashboard Cite

We thank the Bioinformatics Center, Nanjing Agricultural University for providing computing facilities for data processing and analyses. This research was partially supported by the China Scholarship Council (grant no. 201706850071), which awarded a fellowship to Y.F. Author contributions: W.Z. conceived and designed the study; W.Z. developed the DRIP-seq methodology and generated DRIPseq and NBS-seq data sets. Y.F. analyzed the data; P.Z. analyzed the 6mA data. L.C. prepared all transgenic rice lines and conducted G4-ChIP-qPCR and histone-related western blotting experiments. K.L. grew the material and performed the 6mA and 5mC dot blotting assays. Y.L.F. prepared the genomic DNA and conducted the G4-ChIP experiments. J.S. proofread the manuscript. X.P. performed the qPCR and dot blotting assays. C.C. assisted in the NBS-seq library sequencing and provided 6mA-related cas9 rice transgenic lines. X.W. helped with DNA fragmentation. Z.S. helped with rice callus preparation. Y.W. and H.W. supervised the data analysis. W.Z., Y.F., and H.W. interpreted the results. W.Z. and H.W. wrote the paper. All authors read and approved the final version of the manuscript.

show abstract

Section: The Coordination Of R-loops and Histone Markssupporting

confidence: 90%

Section: The Coordination Of R-loops and Histone Marksmentioning

confidence: 98%

Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice

Fang¹,

Chen²,

Lin³

et al. 2019

Genome Res.

View full text Add to dashboard Cite

show abstract

“…In fact, not only an R-loop per se but also a stalled RNA polymerase machinery may impede DNA replication and lead to further R-loop accumulation ( García-Muse and Aguilera, 2016 ). Moreover, R-loops have been shown to trigger chromatin modifications, mainly including chromatin condensation ( Castellano-Pozo et al, 2013 ; Al-Hadid and Yang, 2016 ; García-Pichardo et al, 2017 ; Figure 2 ), and this event seems to be a key requisite for compromising genome stability ( García-Pichardo et al, 2017 ).…”

Section: R-loops As Sources Of Genome Instabilitymentioning

confidence: 99%

Sensing R-Loop-Associated DNA Damage to Safeguard Genome Stability

Rinaldi

Pizzul

Longhese

et al. 2021

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

DNA transcription and replication are two essential physiological processes that can turn into a threat for genome integrity when they compete for the same DNA substrate. During transcription, the nascent RNA strongly binds the template DNA strand, leading to the formation of a peculiar RNA–DNA hybrid structure that displaces the non-template single-stranded DNA. This three-stranded nucleic acid transition is called R-loop. Although a programed formation of R-loops plays important physiological functions, these structures can turn into sources of DNA damage and genome instability when their homeostasis is altered. Indeed, both R-loop level and distribution in the genome are tightly controlled, and the list of factors involved in these regulatory mechanisms is continuously growing. Over the last years, our knowledge of R-loop homeostasis regulation (formation, stabilization, and resolution) has definitely increased. However, how R-loops affect genome stability and how the cellular response to their unscheduled formation is orchestrated are still not fully understood. In this review, we will report and discuss recent findings about these questions and we will focus on the role of ATM- and Rad3-related (ATR) and Ataxia–telangiectasia-mutated (ATM) kinases in the activation of an R-loop-dependent DNA damage response.

show abstract

“…Similarly, in yeast and mammalian cells R-loop association with chromatin modification and non-coding RNA mediates termination of transcription (44)(45)(46)(47). Indeed, R-loop and chromatin modification might be a widespread association (48)(49)(50), since the hybrids can be found throughout some protein-coding genes, rather than being limited to promoters and terminators (51,52).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome

Briggs

Hamilton

Crouch

et al. 2018

Preprint

View full text Add to dashboard Cite

R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere homeostasis, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked transsplicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localisation was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the intergenic regions of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination, most T. brucei R-loops act in a novel role, promoting RNA Pol II movement or mRNA processing. Finally, we show there is little evidence for correlation between R-loop localisation and mapped sites of DNA replication initiation.

show abstract

R-loop: an emerging regulator of chromatin dynamics

Cited by 39 publications

References 103 publications

Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice

Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice

Sensing R-Loop-Associated DNA Damage to Safeguard Genome Stability

Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome

Contact Info

Product

Resources

About