Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA684932 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13248078_1.fastq.gz	Fastqsanger.gz
	SRR13248078_2.fastq.gz	Fastqsanger.gz
	SRR13248079_1.fastq.gz	Fastqsanger.gz
	SRR13248079_2.fastq.gz	Fastqsanger.gz
	SRR16343787_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

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.

2021-12-10 | GSE163118 | GEO

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

2021-12-10 | GSE163116 | GEO

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 associated interactions between chromatin and RNAs in rice [ATAC-seq]

2021-12-10 | GSE163117 | GEO

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.

2021-12-10 | GSE163115 | GEO

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 associated interactions between chromatin and RNAs in rice [ChRD-PET]

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]

| PRJNA684931 | ENA

Repeat RNAs associate with replication forks and post-replicative DNA

Project description:Repeat RNAs associate with replication forks and post-replicative DNA

| PRJNA579364 | ENA

Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14

Project description:Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.

2023-02-22 | MSV000091349 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data