DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice

Shafiq, Sarfraz; Chen, Chunli; Yang, Jing; Cheng, Lan; Ma, Fei; Widemann, Émilie; Sun, Qianwen

doi:10.1016/j.molp.2017.04.001

Cited by 48 publications

(26 citation statements)

References 66 publications

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“…R-loops in plants have recently gained increasing attention. They have been found to play a role in regulating flowering time (Sun et al 2013), root development (Shafiq et al 2017), gene splicing (Conn et al 2017), and genome instability (Yang et al 2017). The first global characterization of R-loops in Arabidopsis thaliana revealed a potential role in gene activation by repressing the expression of antisense lncRNA (Xu et al 2017).…”

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confidence: 99%

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

Fang¹,

Chen²,

Lin³

et al. 2019

Genome Res.

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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.

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confidence: 99%

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

Fang¹,

Chen²,

Lin³

et al. 2019

Genome Res.

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“…In plants, R-loops have been found to modulate the expression of the nuclear genes, thereby affecting plant development, such as flowering time regulation in Arabidopsis (Sun et al, 2013), and root development in rice (Shafiq et al, 2017). However, little is known about R-loop involvement in other biological processes in plants.…”

Section: Discussionmentioning

confidence: 99%

“…In plants, R-loops were first reported to repress the expression of the antisense long noncoding RNA COOLAIR to promote flowering in Arabidopsis thaliana (Sun et al, 2013). Recently, we revealed that the maintenance of nuclear inherent R-loops in rice (Oryza sativa) auxin-related genes by OsTOP1 is essential for root development (Shafiq et al, 2017) and uncovered the distinct R-loop profile in the Arabidopsis nuclear genome (Xu et al, 2017). However, we still have a limited understanding of the mechanisms of R-loop formation and resolution or their biological functions in plants, especially in DNA-containing organelles such as chloroplasts and mitochondria.…”

Section: Introductionmentioning

confidence: 99%

RNase H1 Cooperates with DNA Gyrases to Restrict R-Loops and Maintain Genome Integrity in Arabidopsis Chloroplasts

et al. 2017

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Maintaining organellar genome integrity is essential for eukaryotic cells, and many factors can threaten genome integrity. R-loops are DNA:RNA duplexes produced during transcription, with the nontemplated DNA forming a single-stranded region. R-loops function in the regulation of transcription, DNA replication, and DNA repair, but can also be susceptible to lesions that form double-stranded breaks and thus induce genome instability. From investigating the function of a plant chloroplast-localized R-loop removing enzyme AtRNH1C, we have found that it is responsible for plastid R-loop homeostasis, chloroplast genome instability, and development. Interactome analysis revealed that AtRNH1C associates with multiple chloroplast-localized DNA and RNA metabolism-related proteins, including the core DNA gyrases complex. The interaction between AtRNH1C and AtGyrases was critical for R-loop homeostasis in chloroplast and important to release the transcription-replication conflicts in the highly transcribed and replication originated cp-rDNA regions and thus to reduce the DNA damage. Our results reveal the plastid R-loop accumulation leads to chloroplast DNA instability and provide insight into the maintenance of genome integrity in chloroplasts, in which the evolutionarily conserved RNase H1 and DNA gyrase proteins are involved.

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“…Recently, it is been reported that the regulation of R-loop levels could impact antisense transcription at FLC locus in Arabidopsis [24]. Moreover, the misexpression of topoisomerase 1, a key R-loop regulator, could compromise the expression of auxin-related genes in rice [25]. In addition, there are three RNase H1s with different organelle localization and the chloroplast-localized RNase H1 is critical for maintaining chloroplast genome integrity in Arabidopsis [26].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Classification of the RNaseH-like domain-containing Proteins in Plants

Liu

Sun³

2019

Preprint

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Background R-loop is a nucleic acid structure containing an RNA-DNA hybrid and a displaced single-stranded DNA. Recently, accumulated evidences showed that R-loops occur frequently in various organisms’ genomes and have crucial physiological functions, including replication, transcription and DNA repair. RNaseH-like superfamily (RNHLS) domain-containing proteins, such as RNase H enzymes, RNase H1 and RNase H2, are important in restricting R-loop levels. However, little is known about other RNHLS proteins and their relationship and function on modulating R-loops, especially in plants.Results In this study we characterized 6193 RNHLS proteins from 13 representative plant species, and clustered them into 27 clusters, among which reverse transcriptases and exonucleases are the two largest groups. Moreover, we found there are 691 RNHLS proteins in Arabidopsis, and the catalytic alpha helix and beta sheet domain are conserved among them. Interestingly, each of the Arabidopsis RNHLS proteins is composed of RNHLS domains and other distinctive protein domains. we further found that RNHLS genes are highly expressed in diverse meristems and metabolic tissues. Various RNHLS genes expressed in different tissues grouped together indicate that they work both isolatedly and cooperatively.Conclusions In summary, we systematically analyzed RNHL proteins in plant and found that there are mainly 27 subclusters of them. Most of these proteins are implicated in DNA replication, RNA transcription and nucleic acid degradation. We characterized and classified the RNHLS proteins in plant, which affords new insights on investigation of novel regulatory mechanisms and functions in R-loop biology.

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DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice

Cited by 48 publications

References 66 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

RNase H1 Cooperates with DNA Gyrases to Restrict R-Loops and Maintain Genome Integrity in Arabidopsis Chloroplasts

Comprehensive Classification of the RNaseH-like domain-containing Proteins in Plants

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