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Chromatin Loops Associated with Active Genes and Heterochromatin Shape Rice Genome Architecture for Transcriptional Regulation

ABSTRACT: Chromatin Loops Associated with Active Genes and Heterochromatin Shape Rice Genome Architecture for Transcriptional Regulation

PROVIDER: PRJNA542905 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9054440_1.fastq.gz	Fastqsanger.gz
	SRR9054440_2.fastq.gz	Fastqsanger.gz
	SRR9054441_1.fastq.gz	Fastqsanger.gz
	SRR9054441_2.fastq.gz	Fastqsanger.gz
	SRR9054442_1.fastq.gz	Fastqsanger.gz

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Chromatin Loops Associated with Active Genes and Heterochromatin Shape Rice Genome Architecture for Transcriptional Regulation

Project description:We systematically analyze the basic features of chromatin interaction mediated by RNAP2, H3K4me3 and H3K9me2. All interactions further aggregated into higher-order clusters and modular interacting domains with distinct genomic and transcriptional properties. Together, our strategy provides hierarchical and modular 3D genome architecture for transcription regulation in rice.

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Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation.

Project description:Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- and RNA polymerase II (RNAPII)-associated promoter-promoter interactions and H3K9me2-marked heterochromatin interactions at nucleotide/gene resolution in rice. The chromatin architecture is separated into different independent spatial interacting modules with distinct transcriptional potential and covers approximately 82% of the genome. Compared to inactive modules, active modules possess the majority of active loop genes with higher density and contribute to most of the transcriptional activity in rice. In addition, promoter-promoter interacting genes tend to be transcribed cooperatively. In contrast, the heterochromatin-mediated loops form relative stable structure domains in chromatin configuration. Furthermore, we examine the impact of genetic variation on chromatin interactions and transcription and identify a spatial correlation between the genetic regulation of eQTLs and e-traits. Thus, our results reveal hierarchical and modular 3D genome architecture for transcriptional regulation in rice.

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Project description:The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displaced DNA coding strand. However R-loops may also possess beneficial effects as their widespread formation has been detected over CpG island promoters in human genes. Furthermore we have previously shown that R-loops are particularly enriched over G-rich terminator elements. These facilitate RNA polymerase II (Pol II) pausing prior to efficient termination. Here we reveal an unanticipated link between R-loops and RNA interference (RNAi)-dependent H3K9me2 formation over pause site termination regions of mammalian protein coding genes. We show that R-loops induce antisense transcription over these pause elements which in turn lead to the generation of double-strand RNA (dsRNA) and recruitment of Dicer, Ago1, Ago2, and G9a histone lysine methyltransferase (HKMT). Consequently an H3K9me2 repressive mark is formed and Heterochromatin Protein 1γ (HP1γ) is recruited, that reinforces Pol II pausing prior to efficient transcriptional termination. We predict that R-loops promote a chromatin architecture that defines the termination region for a substantial subset of mammalian genes. PolIIS2ph ChIP-seq and input in untreated condition and treated with BIX and RNaseH1 overexpression in HeLa cells. The 4 samples have been multiplexed, pooled and sequenced on 3 lanes of Illumina HiSeq2000.

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Large domains of heterochromatin direct the formation of short mitotic chromosome loops

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