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WOX11 recruits a histone H3K27me3 demethylase to promote gene expression during shoot development in rice

ABSTRACT: WOX11 recruits a histone H3K27me3 demethylase to promote gene expression during shoot development in rice

PROVIDER: PRJNA412312 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6080100_1.fastq.gz	Fastqsanger.gz
	SRR6080100_2.fastq.gz	Fastqsanger.gz
	SRR6080095_1.fastq.gz	Fastqsanger.gz
	SRR6080095_2.fastq.gz	Fastqsanger.gz
	SRR6080096_1.fastq.gz	Fastqsanger.gz

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WOX11 recruits a histone H3K27me3 demethylase to promote gene expression during shoot development in rice

Project description:WUSCHEL-related homeobox (WOX) genes are key regulators of meristem activity and plant development, the chromatin mechanism of which to reprogram gene expression remains unclear. Histone H3K27me3 is a chromatin mark of developmentally repressed genes. How the repressive mark is removed from specific genes during plant development is largely unknown. Here, we show that WOX11 interacts with the H3K27me3 demethylase JMJ705 to activate gene expression during shoot development in rice. Genetic analysis indicates that WOX11 and JMJ705 cooperatively control shoot growth and commonly regulate the expression of a set of genes involved in meristem identity, chloroplast biogenesis, and energy metabolism in the shoot apex. Loss of WOX11 led to increased H3K27me3 and overexpression of JMJ705 decreased the methylation levels at a subset of common targets. JMJ705 is associated with most of the WOX11-binding sites found in the tested common targets in vivo, regardless of presence or absence of the JMJ705-binding motif. Furthermore, wox11 mutation reduced JMJ705-binding to many targets genome-wide. The results suggest that recruitment of JMJ705 to specific developmental pathway genes is promoted by DNA-binding transcription factors and that WOX11 functions to stimulate shoot growth through epigenetic reprogramming of genes involved in meristem development and energy-generating pathways.

2018-01-21 | GSE104306 | GEO

WOX11 recruits a histone H3K27me3 demethylase to promote gene expression during shoot development in rice.

| S-EPMC5861455 | biostudies-literature

The X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex specific manner

Project description:This SuperSeries is composed of the following subset Series: GSE39472: X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner [ChIP-Seq data] GSE39473: The X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex specific manner [Agilent array data] Refer to individual Series

2012-07-31 | E-GEOD-39222 | biostudies-arrayexpress

Transcriptome profiling of H3K27me3 demethylase deficient B cells

Project description:Transcriptome profiling of H3K27me3 demethylase deficient B cells

| PRJNA767650 | ENA

Accessible chromatin profiling of H3K27me3 demethylase deficient B cells

Project description:Accessible chromatin profiling of H3K27me3 demethylase deficient B cells

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H3K4me3 and H3K27me3 chromatin states in the Arabidopsis shoot phloem companion cells from INTACT reporter lines

Project description:We investigated the chromatin modifications H3K4me3 and H3K27me3 in the A. thaliana shoot phloem companion cells using INTACT reporter lines. Samples were collected in two biological replications.

2019-01-09 | E-MTAB-5737 | biostudies-arrayexpress

H3K36me3 Reader NPAC/GLYR1 Recruits H3K4 Demethylase LSD2/KDM1B to Modulate Active Gene Transcription

Project description:H3K36me3 Reader NPAC/GLYR1 Recruits H3K4 Demethylase LSD2/KDM1B to Modulate Active Gene Transcription

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Suppression of canonical TGF-β signaling enables GATA4 to interact with H3K27me3 demethylase JMJD3 to promote cardiomyogenesis

Project description:Direct reprogramming of fibroblasts into cardiomyocytes (CMs) represents a promising strategy to regenerate CMs lost after ischemic heart injury. Overexpression of GATA4, HAND2, MEF2C, TBX5, miR-1, and miR-133 (GHMT2m) along with transforming growth factor beta (TGFbeta) inhibition efficiently promotes reprogramming. However, the mechanisms by which TGFbeta; blockade promotes cardiac reprogramming remain unknown. Here, we identify interactions between the histone H3 lysine 27 trimethylation (H3K27me3), demethylase JMJD3, the SWI/SNF remodeling complex subunit BRG1, and cardiac transcription factors. Furthermore, canonical TGFbeta; signaling regulates the interaction between GATA4 and JMJD3. TGF-beta; activation impairs the ability of GATA4 to bind target genes and prevents demethylation of H3K27 at cardiac gene promoters during cardiac reprogramming. Finally, a mutation in GATA4 (V267M) exhibits reduced binding to JMJD3 and impaired cardiomyogenesis. Thus, we have identified an epigenetic mechanism wherein canonical TGFbeta; pathway activation impairs cardiac gene programming by interfering with GATA4-JMJD3 interactions.

2021-02-13 | GSE145290 | 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 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

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