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

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

PROVIDER: PRJNA684929 | 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
	SRR16343748_1.fastq.gz	Fastqsanger.gz

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

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: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 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.

2021-12-10 | GSE163117 | GEO

The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [RNA-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 associated interactions between chromatin and RNAs in rice.

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

| PRJNA684927 | ENA

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]

| PRJNA684930 | ENA

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]

| PRJNA684932 | 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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2014-08-21 | E-GEOD-59395 | biostudies-arrayexpress

The genomic landscape of cohesin-associated chromatin interactions

Project description:Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide scale. Here we performed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mouse limb. We identified 2,264 SMC1A interactions, of which 1,491 (65%) involved sites co-occupied by CTCF. SMC1A participates in tissue- specific enhancer-promoter interactions and interactions that demarcate regions of correlated regulatory output. In contrast to previous studies, we also identified interactions between promoters and distal sites that are maintained in multiple tissues, but are poised in embryonic stem cells and resolve to tissue-specific activated or repressed chromatin states in the mouse embryo. Our results reveal the diversity of cohesin- associated interactions in the genome and highlight their role in establishing the regulatory architecture of development. Smc1a ChIA-PET, RNA-seq, chromatin state maps (H3K27ac, H3K27me3, H3K4m2), and CTCF and Smc1a binding in mouse embryonic limb bud (E11.5)

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