Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor

Wang, Kang; Wang, Honghong; Li, Conghui; Yin, Zhenggang; Xiao, Ran; Li, Qiuzi; Ying, Xiaofang; Wang, Wen; Huang, Jian; Chen, Liang; Fang, Pingping; Liang, Kaiwei

doi:10.1126/sciadv.abe3516

Cited by 55 publications

(63 citation statements)

References 50 publications

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“…We thus wondered if R-loop can also be detected with the CUT&Tag protocol using an R-loop specific S9.6 monoclonal antibody ( 79 ). In line with a recent report validating the utility of S9.6 CUT&Tag for mapping R loops ( 80 ), we achieved a high signal-to-noise ratio and determined R loops genome-wide in ESCs (Figure 5A ). Like G4, R-loop CUT&Tag peaks were also sensitive to Mung Bean nuclease treatment ( Supplementary Figure S3C ).…”

Section: Resultssupporting

confidence: 89%

Genome-wide mapping of G-quadruplex structures with CUT&Tag

Lyu

Shao

Yung

et al. 2021

Nucleic Acids Research

105

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Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect gene expression, DNA methylation, replication fork progression and genome stability. When and how G4 structures form and are resolved remains unclear. Here we report the use of Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping native G4 in mammalian cell lines at high resolution and low background. Mild native conditions used for the procedure retain more G4 structures and provide a higher signal-to-noise ratio than ChIP-based methods. We determine the G4 landscape of mouse embryonic stem cells (ESC), observing widespread G4 formation at active promoters, active and poised enhancers. We discover that the presence of G4 motifs and G4 structures distinguishes active and primed enhancers in mouse ESCs. Upon differentiation to neural progenitor cells (NPC), enhancer G4s are lost. Further, performing R-loop CUT&Tag, we demonstrate the genome-wide co-occurrence of single-stranded DNA, G4s and R loops at promoters and enhancers. We confirm that G4 structures exist independent of ongoing transcription, suggesting an intricate relationship between transcription and non-canonical DNA structures.

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Section: Resultssupporting

confidence: 89%

Genome-wide mapping of G-quadruplex structures with CUT&Tag

Lyu

Shao

Yung

et al. 2021

Nucleic Acids Research

105

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“…For cell types with R-loop mapping data available, we integrated and analyzed other genomics data that might help to distinguish bona fide R-loops from false positives, or interpret the molecular function of R-loops and R-loop regulators ( Supplementary Table S5 ). G4 ChIP-seq ( 69–71 ), RPA ChIP-seq ( 43 , 72 ), GRO-seq ( 13 , 73–76 ) and PRO-seq ( 24 , 77 ) data were searched and downloaded from GEO ( 78 ). All datasets were processed by following the original publications.…”

Section: Methodsmentioning

confidence: 99%

R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation

Lin

Zhong

Zhou

et al. 2021

Nucleic Acids Research

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R-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.

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“…These structures are very dynamic, and a subset of R-loops maintained after differentiation has been shown to be associated with repressive chromatin marks on silent pluripotency genes [ 31 ]. Meanwhile, several methods for their profiling have been developed in vivo [ 32 , 33 , 34 ]. Although many tools exist for analyzing other non-B DNA structures in silico, the options for R-loop analyses are limited.…”

Section: Discussionmentioning

confidence: 99%

R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences

Brázda

Havlík

Kolomazník

et al. 2021

IJMS

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R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA–DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as important in human diseases. Therefore, its prevalence and distribution in genomes are studied intensively. However, in silico tools for R-loop prediction are limited, and therefore, we have developed the R-loop tracker tool, which was implemented as a part of the DNA Analyser web server. This new tool is focused upon (1) prediction of R-loops in genomic DNA without length and sequence limitations; (2) integration of R-loop tracker results with other tools for nucleic acids analyses, including Genome Browser; (3) internal cross-evaluation of in silico results with experimental data, where available; (4) easy export and correlation analyses with other genome features and markers; and (5) enhanced visualization outputs. Our new R-loop tracker tool is freely accessible on the web pages of DNA Analyser tools, and its implementation on the web-based server allows effective analyses not only for DNA segments but also for full chromosomes and genomes.

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Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor

Cited by 55 publications

References 50 publications

Genome-wide mapping of G-quadruplex structures with CUT&Tag

Genome-wide mapping of G-quadruplex structures with CUT&Tag

R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation

R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences

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