Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis

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

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE206688 | GEO | 2022/11/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [Bisulfite-seq]

Project description:The evolutionally conserved COMPASS complexes are responsible for the catalyzation of H3K4 methylations. Recently, three types of COMPASS complexes which contains histone methyltransferases ATX1/2, ATX3, or ATX4/5 were identified in Arabidopsis. Here, we report the ATX proteins are essential for the survival of Arabidopsis. By RNA-seq and chromatin immunoprecipitation (ChIP-seq) analysis, we found ATX1/2-, ATX3-, and ATX4/5-containing COMPASS complex redundantly regulate gene expression and H3K4me3 modifications. In addition to the developmental-related genes, we found the expression of DNA methylation-related genes were also regulated by the COMPASS complexes. The transcript and H3K4me3 levels at the RdDM pathway genes (NRPE1, DCL3, IDN2, FDM2) and at the DNA demethylase encoding genes (ROS1, DML2, DML3) were down-regulated in atx1/2/4/5 mutants. Via bisulfate sequencing, we found the atx1/2/4/5 showed hypermethylation at CG and CHG contexts whereas the hypomethylation at CHH contexts. By comparing the differentially methylated regions (DMRs) in atx1/2/4/5 with that in ros1;dml2;dml3 (rdd) and in nrpe1, a large part of overlapping DMRs were identified. Based on these results and other findings, we propose that the hypermethylation in CG and CHG is partially caused by the down-regulation of ROS1/DML2/DML3, and the hypomethylation in CHH is mainly caused by the down-regulation of NRPE1. Furthermore, we revealed that the COMPASS complexes also play a redundant role in regulating the transcription of transposable elements (TEs). This study extends our knowledge about the function of COMPASS in plant development and illustrate the important roles for COMPASS complexes in the regulation of DNA methylation and TEs transcription.

2022-11-14 | GSE206683 | GEO

COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [ChIP-seq]

2022-11-14 | GSE206685 | GEO

COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [RNA-seq]

2022-11-14 | GSE206687 | GEO

Impact of human MLL/COMPASS and Polycomb complexes on the DNA methylome

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

2014-07-14 | GSE56539 | GEO

Extra-coding RNAs regulate neuronal DNA methylation dynamics

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-05-31 | E-GEOD-64988 | biostudies-arrayexpress

Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Pattern

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-29 | E-GEOD-51764 | biostudies-arrayexpress

Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility

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

2022-11-11 | GSE193397 | GEO

Extra-coding RNAs regulate neuronal DNA methylation dynamics

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

2016-05-31 | GSE64988 | GEO

DNA N6-adenine methylation in Arabidopsis thaliana

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

2018-04-16 | GSE81597 | GEO

DNA Topoisomerase 1M-NM-1 Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-07-08 | E-GEOD-50720 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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