Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIP-seq]

ABSTRACT: 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIP-seq]

PROVIDER: PRJNA883711 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21685019_1.fastq.gz	Fastqsanger.gz
	SRR21685019_2.fastq.gz	Fastqsanger.gz
	SRR21685020_1.fastq.gz	Fastqsanger.gz
	SRR21685020_2.fastq.gz	Fastqsanger.gz
	SRR21685021_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice

Project description:3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice

| PRJNA883713 | ENA

3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIA-PET]

Project description:3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIA-PET]

| PRJNA883683 | ENA

3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIP-seq]

Project description:Repressive epigenetic modification histone H3 lysine 27 tri-methylation (H3K27me3) marks many agronomically important genes in plants. However, H3K27me3-associated three-dimensional (3D) genome architecture and its regulatory functions in rice flowering time remain unclear. In this study, we map H3K27me3-associated genome topology using long-read ChIA-PET and reveal extensive chromatin loops among H3K27me3-marked regions in different rice varieties and tissues. Multiple H3K27me3-associated chromatin loops usually tether together and further form repressive chromatin interacting domains (RIDs), which provide structural bases for the regulation of the co-modification and co-expression of interacting genes. Surprisingly, we identified extensive chromatin loops between the rice florigen genes Hd3a and RFT1, and frequent chromatin interactions between the positive flowering regulator Ehd1 on the chromosome 10 and Hd3a/ RFT1 loci on the chromosome 6. These results suggest that flowering genes might form a Ehd1-Hd3a/RFT1-centered spatial gene cluster in rice. We also demonstrate the flowering regulator protein complexes comprising Ghd7, Ghd8, and Hd1 could bind to the Ehd1-Hd3a/RFT1 spatial gene cluster. In addition, liquid-liquid phase separation of Ghd7 and Hd1, as well as the essentially synchronous expression of Ehd1 and Hd3a suggest that this spatial gene cluster acts as a regulatory hub to coordinately regulates the expression of Ehd1-Hd3a. This work uncovers the frame of integrated cis and trans molecular mechanism underlying transcriptional regulation of florigen genes in rice.

2022-09-28 | GSE214069 | GEO

3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIA-PET]

2022-09-28 | GSE214050 | GEO

Cis-trans

Project description:Cis-trans

| PRJEB1227 | ENA

3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice

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

2022-09-28 | GSE214073 | GEO

Cis-trans

Project description:Differential Expression analysis in Drosophila pseudoobscura to identify cis-trans regulation

2014-03-27 | E-MTAB-1424 | biostudies-arrayexpress

The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [ChIRP-seq]

Project description:We identified differentially expressed genes in flail mutants linked to the regulation of flowering through stranded RNA-seq. A genomic rescue fragment of FLAIL (pFLAIL:gFLAIL) introduced in flail mutants can complement expression defects and early flowering, consistent with trans-acting effects of the FLAILRNA. We determined the genomic binding regions of FLAIL by ChIRP-seq. FLAIL binding to chromatin regions promotes the expression of selected flowering repressors.

2022-02-12 | GSE186214 | GEO

The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [RNA-seq]

2022-01-10 | GSE186212 | GEO

Natural selection on cis and trans regulation in yeasts

Project description:Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans activating factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we investigate the global patterns of gene expression evolution in Saccharomyces cerivisiae. We report statistical methods useful in quantifying cis and trans regulation using next generation sequencing data. Using these methods, measured genome-wide allele-specific expression by deep sequencing to investigate the genetic architecture of gene regulatory variation between two strains of Saccharomyces cerevisiae. We find that expression polymorphism in yeast is common for both cis and trans regulation, though trans variation is more common. Our detailed analyses of the effects of functional constraint on expression variation as indicated by measures such as protein connectivity, gene essentiality, and the ratio of nonsynonymous substitutions to synonymous substitutions clearly reveal that both classes of variation are under purifying selection, but trans variation is more sensitive to selective constraint. Comparing interspecific expression divergence between S. cerevisiae and S. paradoxus to our intraspecific variation suggests that natural selection strongly influences the patterns of variation we observe. Further analyses revealed that cis divergence is more frequently mediated by positive Darwinian selection than trans divergence, which is compatible with neutral evolution. Study the gene expression patterns in two strains of yeast (BY and RM)

2010-04-02 | E-GEOD-20749 | biostudies-arrayexpress

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