Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
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ABSTRACT:
PROVIDER: PRJNA438658 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6847720_1.fastq.gz | Fastqsanger.gz | |||
| SRR6847720_2.fastq.gz | Fastqsanger.gz | |||
| SRR6847721_1.fastq.gz | Fastqsanger.gz | |||
| SRR6847721_2.fastq.gz | Fastqsanger.gz | |||
| SRR6847722_1.fastq.gz | Fastqsanger.gz |
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Project description:We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expressionand epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-looppeak levels was dependent on the positions of R-loops within gene structures (hereafter named 'genic position'). Both antisenseonly (ASO)-R-loops and sense/antisense(S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peaklevels corresponded positively with transcript levels of overlapping genes. In contrast, sense only (SO)-R-loops were generallyspread over the coding regions, and their peak levels corresponded inversely to transcript levels of overlapping genes. Inaddition, integrative analyses of R-loop data with existing RNA-seq, chromatin-immunoprecipitation (ChIP-seq), deoxyribonucleaseI-seq (DNase-seq) and whole-genome bisulfite sequencing (BS-seq) data revealed interrelationships and intricate connectionsamong R-loops, gene expression and epigenetic signatures. Experimental validation provided evidence that the demethylationof both DNA and histone marks can influence R-loop peak levels on a genome-wide scale. This is the first study in plants thatreveals novel functional aspects of R-loops, their interrelations with epigenetic methylation, and roles in transcriptionalregulation.
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Project description:We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expression and epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-loop peak levels was dependent on the positions of R-loops within gene structures (hereafter named "genic position"). Both antisense only (ASO)-R-loops and sense/antisense (S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peak levels corresponded positively with transcript levels of overlapping genes. In contrast, sense only (SO)-R-loops were generally spread over the coding regions, and their peak levels corresponded inversely to transcript levels of overlapping genes. In addition, integrative analyses of R-loop data with existing RNA-seq, chromatin immunoprecipitation sequencing (ChIP-seq), DNase I hypersensitive sites sequencing (DNase-seq), and whole-genome bisulfite sequencing (WGBS or BS-seq) data revealed interrelationships and intricate connections among R-loops, gene expression, and epigenetic signatures. Experimental validation provided evidence that the demethylation of both DNA and histone marks can influence R-loop peak levels on a genome-wide scale. This is the first study in plants that reveals novel functional aspects of R-loops, their interrelations with epigenetic methylation, and roles in transcriptional regulation.
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Project description:Cold is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in plants. R-loops can function in a series of biological processes, including normal development and stress responses, in plants. However, how R-loops function in cold responses is still largely unknown in plants, especially in cold sensitive rice. Herein, we conducted DRIP-seq in combination with other newly generated omics data (RNA-seq, DNase-seq, ChIP-seq and MNase-seq) in rice with or without cold treatment. We found that cold treatment caused R-loop dynamics across the genome, indicating that R-loops are cold sensitive non-B DNA structures. Moreover, cold biased R-loops had high GC content and novel motifs the binding of distinct TFs as compared to CK biased R-loops, indicative of occurrence of differential biological implications of R-loop dynamics in response to cold stress. More importantly, we for the first time to provide evidence showing that, in addition to the direct involvement of R-loops in the regulation of cold-responsive gene transcription, R-loops can indirectly modulate transcription of subsets of cold-responsive genes through R-loop overlapping TF-centered or cis-regulatory element related regulatory networks and lncRNAs in rice. Thus, our study for the first time provides evidence showing functions of R-loop dynamics in rice cold responses. It also provides some potential R-loop loci for genetic and epigenetic manipulation towards breeding of enhanced cold tolerance rice varieties.
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Project description:DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure functioning in various biological processes in mammals. G4 ChIP-seq assay, In this study, we developed a robust BG4-DNA ChIP-seq for global identification of DNA G4 in rice..We found that G4s harbored some functional motifs for binding of certain trans-factors, were co-localized with R-loops and DHSs in the rice genome. Importantly, G4s exhibited differential effects on DNA methylation between TE and non-TE genes in rice. Especially, G4 intensity-dependent enrichment occurred between DNA 5mC and 6mA.These DNA-related features suggest potential regulatory roles of G4 in rice. Thus, our study will pave the way for prompting intensive characterization towards identifying novel functions of G4 in plants, especially for agronomic important crops.
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