Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Oryza sativa Indica Group

PROVIDER: GSE213227 | GEO | 2022/09/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq]

Project description:Plants are extremely sensitive to and can re-output rhythm by light signals during photoperiod cues. The circadian transcriptome and epigenetically modified rice genome exhibited distinct circadian behavioural outputs under three light signals during the photoperiod.By comparing and analysing the output circadian genes under different light signals, we detected that constant light (LL) shortens the day-night cycle, while constant night (DD) suppresses the oscillation amplitude. The circadian changing lncRNAs at the genome-wide level that were temporally correlated with oscillating genes at proximal loci and accompanied by synchronised circadian oscillations of H3K9ac modifications. We used the Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to profile the open chromatin regions and transcription factor (TF) footprints in rice at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20). The regulation of circadian gene expression occurs, not through temporal regulation of chromatin opening but through time-dependent binding of transcription factors in cis-regulatory elements. We mapped the 4D genome architecture of rice by employing BL-Hi-C, to capture oscillating chromatin interactions at ZT8 and ZT20. Circadian genes within the same peak phases of expression were preferentially coordinated transcription with non-circadian genes. Circadian genes at the ZT8 circadian phase tended to be enriched in ZT8-speific spatial clusters to orchestrate gene expression. Our findings contribute significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways in rice.

2022-09-15 | GSE213226 | GEO

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [RNA-Seq]

2022-09-15 | GSE213093 | GEO

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C]

2022-09-15 | GSE213090 | GEO

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq]

2022-09-15 | GSE213089 | GEO

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice

| PRJNA879786 | ENA

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq]

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ChIP-Seq]

| PRJNA879791 | ENA

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [RNA-Seq]

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [RNA-Seq]

| PRJNA879083 | ENA

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C]

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [Hi-C]

| PRJNA879086 | ENA

Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq]

Project description:Systematic analysis of circadian gene expression mediated by epigenetic modification and 3D genome organization in Rice [ATAC-Seq]

| PRJNA879081 | ENA

Tracking Epigenetic Modification-Mediated Genome Organization

Project description:Spatiotemporal control of chromatin structure and dynamics at sub-kilobase to megabase scales is essential for genome function. Epigenetic modification plays important roles in transcriptional regulation. How histone marks regulate genome organization at different scales remain unclear. Here we introduce an EpiGo (Epigenetic perturbation induced Genome organization) system to modify hundreds of genomic loci with H3K9me3 spanning megabases on human chromosome 19 and simultaneously track their changes of genome organization. EpiGo-mediated H3K9me3 spreads more extensively in transcriptionally inactive regions than active regions. H3K9 trimethylation of active regions trigger local chromatin compaction without substantial gene silencing. H3K9 trimethylated loci or regions associate with HP1a condensates and adjacent loci with H3K9me3 coalesce over time. H3K9 trimethylation of inactive regions reshape local genome compartmentalization. These results reveal that H3K9me3 mediates local chromatin compaction or genome compartmentalization upon distinct transcriptional states.

2020-11-04 | GSE137469 | GEO

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