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A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [RNA-Seq]

ABSTRACT: A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [RNA-Seq]

PROVIDER: PRJNA704827 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13782851.fastq.gz	Fastqsanger.gz
	SRR13782852.fastq.gz	Fastqsanger.gz
	SRR13782853.fastq.gz	Fastqsanger.gz
	SRR13782854.fastq.gz	Fastqsanger.gz
	SRR13782855.fastq.gz	Fastqsanger.gz

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A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [REF6-HA ChIP-seq]

Project description:We report transcriptome changes and genome-wide dynamics of H3K27me3 during seed germination in Arabidopdsis, and investigate the impact of REF6-mediated H3K27 demethylation on germination. Compared with transcriptome changes, we discover delayed H3K27me3 reprogramming closely associated with the embryo to vegetative cell fate switch. REF6-mediated H3K27 demethylation promotes germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state permissive to transcription. By analyzing REF6 genomic binding, we show that it is absent from mature embryo chromatin and gradually establishes occupancy during the course of germination to counteract increased PRC2 activity.

2022-09-28 | GSE167505 | GEO

A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [H3K27me3 ChIP-seq]

2022-09-28 | GSE167503 | GEO

A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [RNA-Seq]

2022-09-28 | GSE167502 | GEO

A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis

Project description:A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis

| PRJNA704823 | ENA

A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [REF6-HA ChIP-seq]

Project description:A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [REF6-HA ChIP-seq]

| PRJNA704831 | ENA

A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [H3K27me3 ChIP-seq]

Project description:A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [H3K27me3 ChIP-seq]

| PRJNA704828 | ENA

REF6 recognizes specific DNA sequence to regulate H3K27me3 demethylation and organ boundary formation

Project description:RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) counteracts Polycomb mediated gene silencing through demethylating histone H3 lysine 27 trimethylation (H3K27me3) in Arabidopsis. Genome-wide analysis has demonstrated that REF6 dependent H3K37me3 demethylation occurs on hundreds of genes. However, how these genes are selectively subjected to H3K27me3 demethylation remains elusive. Here we show that a tandem array of four Cys2-His2 zinc finger domains (C2H2-ZF) at REF6 C-terminus are essential for REF6 function. Mechanistically, we find that C2H2-ZF cluster can directly recognize a specific DNA sequence motif, and is essential for binding of REF6 to its targets. In addition, we demonstrate that CUP-SHAPED COTYLEDON 1 (CUC1) and CUC3 harbor such sequence motif and are direct targets of REF6; while their close homolog, CUC2, without such binding motif is not bound by REF6. Furthermore, REF6 is essential for proper H3K27me3 level at CUC1 locus, CUC1 activation and cotyledon separation. Collectively, our study reveals not only a novel mechanism of H3K27me3 demethylase genome targeting to counteract Polycomb silencing, but also a new function of H3K27me3 demethylation in organ boundary formation. All seeds, except for H3K9me2 ChIP-seq, were grown on 1/2MS plate at 23Â°C under long day condition. 12 day after germination (12DAG), whole seedling were harvested for ChIP-seq. anti-HA ChIP-seq were performed with three samples: Col (WT,Negtive control), REF6-HA(REF6p::REF6-HA ref6-1),REF6-ZnF-HA(REF6p::REF6-ZnF-HA ref6-1). anti-H3K27me3 ChIP-seq were performed with four samples: Col (WT), ref6-1 (mutant), REF6-HA(REF6p::REF6-HA ref6-1),REF6-ZnF-HA(REF6p::REF6-ZnF-HA ref6-1).For H3K9me2 ChIP-seq, plants were grown in soil at 23Â°C under long day condition. Aerial part of plants were harvested for ChIP-seq 28d after germination.

2016-03-22 | E-GEOD-65329 | biostudies-arrayexpress

Genome-wide comparison of H3K27me3 difference between ref6-1 and wild type Col

Project description:We demonstrate that REF6/JMJ12 (RELATIVE OF EARLY FLOWERING 6/Jumonji domain-containing protein 12) could demethylate H3K27me3. Loss of REF6/JMJ12 leads to ectopic and increased H3K27me3 of a large spectrum of genes involved in development and responses to stimuli. Examination of differences in H3K27me3 between ref6-1 and wild type Col.

2011-05-25 | E-GEOD-25446 | biostudies-arrayexpress

A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis

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

2022-09-30 | GSE167508 | GEO

REF6 recognizes specific DNA sequence to regulate H3K27me3 demethylation and organ boundary formation

2016-03-22 | GSE65329 | GEO