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Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds [RNA-seq]

ABSTRACT: Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds [RNA-seq]

PROVIDER: PRJNA418578 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6294490.fastq.gz	Fastqsanger.gz
	SRR6294491.fastq.gz	Fastqsanger.gz
	SRR6294492.fastq.gz	Fastqsanger.gz
	SRR6294483.fastq.gz	Fastqsanger.gz
	SRR6294493.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds [RNA-seq]

Project description:We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. To further investigate the downstream targets of REF6 represented H3K27me3 demethylase, we performed RNA-seq using single, double mutant and triple mutant. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me3 demethylase, the binding targets of DNA binding domain deleted REF6 were identified in the triple mutant background in which REF6 and its two homologs were mutated. Meanwhile, the H3K27me3 marked regions in both wild type and triple mutant flowers were defined. By analyzing the differentially enriched H3K27me3 region and REF6 binding profile, we found that REF6 functions to determine the boundary of H3K27me3 regions. Comparison of binding profiles of REF6 in flowers and in seedlings (ref) revealed a tissue-specific binding manner. More importantly, we found that the indirect binding of REF6 is mediated by trans factors and this indirect binding is crucial for REF6 function, especially in reproductive organs in Arabidopsis. Our results provide novel molecular insights into REF6 functions.

2018-07-09 | GSE106943 | GEO

Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions in various Arabidopsis genetic backgrounds [ChIP-seq]

Project description:We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me3 demethylase, the binding targets of DNA binding domain deleted REF6 were identified in the triple mutant background in which REF6 and its two homologs were mutated. Meanwhile, the H3K27me3 marked regions in both wild type and triple mutant flowers were defined. By analyzing the differentially enriched H3K27me3 region and REF6 binding profile, we found that REF6 functions to determine the boundary of H3K27me3 regions. Comparison of binding profiles of REF6 in flowers and in seedlings (ref) revealed a tissue-specific binding manner. More importantly, we found that the indirect binding of REF6 is mediated by trans factors and this indirect binding is crucial for REF6 function, especially in reproductive organs in Arabidopsis. Our results provide novel molecular insights into REF6 functions.

2018-07-09 | GSE106942 | GEO

Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions in various Arabidopsis genetic backgrounds [ChIP-seq]

Project description:Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions in various Arabidopsis genetic backgrounds [ChIP-seq]

| PRJNA418657 | ENA

Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds

Project description:Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds

| PRJNA418497 | ENA

Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds

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

2018-07-09 | GSE106944 | GEO

DNA methylation prevents REF6 binding in Arabidopsis

Project description:RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing histone demethylase, directly recognizes the CTCTGYTY motif by its zinc-finger domains to demethylate H3K27me3 at specific loci in Arabidopsis genome. Here we show that the recognition of CTCTGYTY motif by REF6 is prevented by DNA methylation. REF6 prefers to bind DNA hypo-methylated regions in vivo. DNA cytosine-methylation decreases REF6 binding affinity in vitro, and the crystal structure of ZnF-clusters showed that REF6 prefers unmethylated DNA sequences. Furthermore, REF6 displayed ectopic binding on multiple new target loci in drm1 drm2 cmt2 cmt3 (ddcc) quadruple mutants, where non-CG methylation was largely diminished. Collectively, this study reveals a novel targeting crosstalk between an H3K27me3 demethylase and DNA methylation.

2019-05-01 | GSE111830 | GEO

Differential gene expression in ref6-1

2011-05-25 | GSE25444 | GEO

Differential gene expression in ref6-1

Project description:We demonstrate that REF6/JMJ12 (RELATIVE OF EARLY FLOWERING 6/Jumonji domain-containing protein 12) is an H3K27me3 and H3K27me2 demethylase. Plants overexpressing REF6/JMJ12 resemble mutants defective in H3K27me3-mediated gene silencing. Genetic interaction tests indicate that REF6/JMJ12 acts downstream of H3K27me3 methyltransferases. Moreover, loss of REF6/JMJ12 leads to ectopic and increased H3K27me3 and decreased mRNA expression of a large spectrum of genes involved in development and hormone responses to stimuli. Expression array to identify differentially expressed genes in ref6-1. For genome-wide expression analysis of ref6/jmj12, two replicates of Col and ref6/jmj12 samples (RNA from 10-day-old whole seedlings on MS plates in long day conditions at 23 degrees) were analyzed on an Affymetrix ATH1 chip by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer's protocols. Genes showing a 20.6-fold change with a q-value < 0.05 were considered as differentially expressed.

2011-05-25 | E-GEOD-25444 | biostudies-arrayexpress

The histone H3K27 demethylase REF6/JMJ12 Promotes thermomorphogenesis in Arabidopsis

Project description:Dynamic trimethylation of histone H3 at Lys27 (H3K27me3) affects gene expression and controls plant development and environmental responses. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6/JUMONJI DOMAIN-CONTAINING PROTEIN 12 (REF6/JMJ12) demethylates H3K27me3 by recognizing a specific DNA motif; however, little is known about how REF6 activates target gene expression after recognition, especially in environmental responses. In response to warm ambient temperature, plants undergo thermomorphogenesis, which involves accelerated growth, early flowering, and changes in morphology. Here we show that REF6 regulates thermomorphogenesis and cooperates with the transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) to synergistically activate thermo-responsive genes under warm ambient temperature. The ref6 loss-of-function mutants exhibited attenuated hypocotyl elongation at warm temperature, partially due to down-regulation of GIBBERELLIN 20-OXIDASE2 (GA20ox2) and BASIC HELIX-LOOP-HELIX 87 (bHLH87). REF6 enzymatic activity is necessary for warm ambient temperature responses. Together, our results provide direct evidence of an epigenetic modifier and a transcription factor working together to respond to the environment.

2021-12-31 | GSE181292 | GEO

The histone H3K27 demethylase REF6/JMJ12 Promotes thermomorphogenesis in Arabidopsis

Project description:The histone H3K27 demethylase REF6/JMJ12 Promotes thermomorphogenesis in Arabidopsis

| PRJNA751488 | ENA