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

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

PROVIDER: PRJNA438658 | ENA |

REPOSITORIES: ENA

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

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.

2019-03-07 | GSE111944 | GEO

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

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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Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize

Project description:Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize We report an integrated genome-wide analysis of DNA methylation, histone modifications, smRNAs and mRNA transcriptional activity, using maize as a model. We surveyed the epigenomes of the maize inbred line B73 in shoot and root tissue by Illumina/Solexa 1G parallel sequencing after digesting genomic DNA with a methylation-sensitive restriction enzyme and after conducting chromatin immunoprecipitations (ChIP) using antibodies that target specific histone modifications (H3K4me3, H3K9ac, H3K27me3, H3K36me3, respectively). Additionally, we profiled RNA pools (micro RNA (miRNA), siRNA and mRNA) using the same sequencing strategy. Keywords: Epigenetics, mRNA transcription and small RNAs H3K4me3, H3K9ac, H3K27me3, H3K36me3, DNA methylation and mRNA, small RNA profiled from shoots and roots of 14 day-old maize B73 seedlings

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Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize

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Three-dimensional analysis of regulatory features reveals functional enhancer-associated loops

Project description:To gain insight into the relationship between chromatin structure and gene expression, we conducted a Tethered Chromatin Capture (TCC) analysis using MCF7 breast cancer and PANC1 pancreatic cancer cells. We applied a novel Hi-C analysis algorithm and identified hundreds of thousands of Interacting Loci Pairs (ILPs) in each of the two cell types. We classified ILPs according to location with respect to gene structure, gene expression, different histone modifications, DNase hypersensitivity, and RNA polymerase II and CTCF binding, identifying distinct classes of ILPs. Interestingly, we found that only 5% of the ILPs involved promoter regions, with even fewer promoter-enhancer loops. We find that genes associated with promoter-enhancer loops have cell type-specific functional annotations. We then tested the impact of pharmacological inhibition of histone acetylation on genes having promoter-enhancer ILPs in PANC1 cells. We found that genes with promoter-enhancer ILPs show reduced expression in response to drug treatment, suggesting that the chromatin loops we identified are functional.

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Genome-wide maps of R-loops in Arabidopsis

Project description:Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops, and demonstrate its high efficiency, low bias, and strand-specificity when profiling the R-loops in Arabidopsis. Using this single-strand DNA ligation based library construction technique, we find that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews. R-loops are prevalent in regions with multiple chromatin modifications, and are negatively correlated with CG DNA hypermethylation. R-loops are strongly enriched in gene promoters and gene bodies, highly associated with noncoding RNA and repetitive genomic regions, and correlated with activated and repressed gene loci. In summary, our analysis reveals that R-loop is a common feature of the Arabidopsis genome, and suggests diverse roles for R-loops in genome organization and gene regulation, thereby providing novel insights into plant nuclear genome formation and function.

2017-05-31 | GSE95765 | GEO

Absolute quantification of proteins and histone modifications in Drosophila embryos reveals stoichiometric relationships in chromatin regulation

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R-loops act as a master regulatory switch modulating transcription of cold-responsive genes in rice

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.

2023-09-26 | GSE217841 | GEO

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