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The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice.

ABSTRACT: The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice.

PROVIDER: PRJNA684927 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13248068_1.fastq.gz	Fastqsanger.gz
	SRR13248068_2.fastq.gz	Fastqsanger.gz
	SRR13248069_1.fastq.gz	Fastqsanger.gz
	SRR13248069_2.fastq.gz	Fastqsanger.gz
	SRR13248071_1.fastq.gz	Fastqsanger.gz

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The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice [ATAC-seq]

Project description:High-order rice chromatin contains numerous interactions among DNA, RNA and protein to regulate critical biological processes in various aspects of rice life. We developed an effective method for mapping histone-mediated chromatin associated RNA-DNA interactions, followed by paired-end-tag sequencing (ChRD-PET) in rice. With H3K4me3 ChRD-PET, H3 ChRD-PET and RNase H treated H3K4me3 ChRD-PET, we present a highly comprehensive map of RNA and chromatin interactions around promoters in rice MH63. Through integrating ChIA-PET (published data), ChRD-PET and ssDRIP-seq data analysis, we demonstrated the function of RNAs-chromatin interactions in different level. We also conducted ATAC-seq and integrative analysis uncovered the relationship of epigenetic modifications and ChRD-PET interactions. Our findings firstly revealed the map and features of RNAs-chromatin interactions in rice.

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The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [RNA-seq]

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Project description:High-order rice chromatin contains numerous interactions among DNA, RNA and protein to regulate critical biological processes in various aspects of rice life. We developed an effective method for mapping histone-mediated chromatin associated RNA-DNA interactions, followed by paired-end-tag sequencing (ChRD-PET) in rice. With H3K4me3-mediated ChRD-PET, H3 ChRD-PET and RNase H treated H3K4me3-mediated ChRD-PET data, we present a highly comprehensive map of RNA and chromatin interactions in rice MH63. Through integrating ChIA-PET (published data) , ChRD-PET and ssDRIP-seq data analysis, we demonstrated the function of RNAs-chromatin interactions in different level. We also conducted ATAC-seq and integrative analysis uncovered the relationship of epigenetic modification and ChRD-PET interactions. Our findings revealed the map and features of RNAs-chromatin interactions in rice.

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The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [ssDRIP-seq]

Project description:The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [ssDRIP-seq]

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The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [RNA-seq]

Project description:The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [RNA-seq]

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Project description:The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice [ChRD-PET]

| PRJNA684929 | ENA

The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice [ATAC-seq]

Project description:The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice [ATAC-seq]

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The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice.

Project description:This SuperSeries is composed of the SubSeries listed below.

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H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation [Illumina BeadArray]

Project description:Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription through interactions with effector proteins that include initiation factor TFIID. We demonstrate that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53 targets. Further analyses show that (i) H3K4me3 enhances p53-dependent transcription by stimulating preinitiation complex (PIC) formation; (ii) H3K4me3, through TAF3 interactions, can act either independently or cooperatively with the TATA box to direct PIC formation and transcription; and (iii) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of p53 in response to genotoxic stress. Our findings indicate a mechanism by which H3K4me3 directs PIC assembly for the rapid induction of specific p53 target genes. Total RNAs from control or TAF3 knockdown cells before and after doxorubicin treatment were subjected to Illumina microarray analyses.

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