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VAL1/2 recruit PKL to target sites in arabidopsis genome

ABSTRACT: VAL1/2 recruit PKL to target sites in arabidopsis genome

PROVIDER: PRJNA772752 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16487406_1.fastq.gz	Fastqsanger.gz
	SRR16487406_2.fastq.gz	Fastqsanger.gz
	SRR16487408_1.fastq.gz	Fastqsanger.gz
	SRR16487408_2.fastq.gz	Fastqsanger.gz
	SRR16487410_1.fastq.gz	Fastqsanger.gz

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VAL1/2 recruit PKL to target sites in arabidopsis genome

Project description:PICKLE (PKL), a Chromodomain Helicase DNA binding domain type 3-type (CHD3) chromatin remodeler, noted for an embryonic structure called pickle root in primary root tip in pkl mutant, has been studied for decades. we obtained a comprehensive genome occupancy of PKL by Chromatin immunoprecipitation-sequencing (ChIP-seq), and found PKL co-occupy with the major repressors of seed maturation program, VIVIPAROUS1/ABI3-LIKE1/2 (VAL1/2) in genome. Furthermore, PKL physically interacts with VAL1/2 in vivo and phenotype and transcriptome data indicated that PKL and VAL1/2 function in a common pathway. Moreover, ChIP-seq and ChIP-qPCR results showed that VAL1/2 are necessary for the recruitment of PKL to co-target genes

2023-05-10 | GSE186157 | GEO

VAL1 and 2 recruit SWN to targets

Project description:VAL1 and 2 recruit SWN to targets

2020-11-06 | GSE159499 | GEO

VAL1 and 2 recruit SWN to targets

Project description:VAL1 and 2 recruit SWN to targets

| PRJNA669062 | ENA

The Transcriptional Repressors VAL1 and VAL2 Recruit PRC2 for Genome-wide Polycomb Silencing in Arabidopsis

Project description:The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. We show that the val1 val2 double mutant possesses somatic embryonic phenotypes and a transcriptome strikingly similar to those of the swn clf double mutant, which lacks the PRC2 catalytic subunits SWINGER (SWN) and CURLY LEAF (CLF). We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. Genome-wide binding profiling demonstrated that they colocalize with SWN and CLF at PRC2 target loci. Loss of VAL1 and VAL2 significantly reduces SWN and CLF enrichment at PRC2 target loci and leads to a genome-wide redistribution of H3K27me3 that strongly affects transcription. Finally, we provide evidence that the VAL1/VAL2–RY regulatory system is largely independent of the TRB–Telobox and BPC1–GA/AZF1–Telobox modules for Polycomb silencing in plants. Taken together, our work demonstrates an extensive genome-wide interaction between VAL1/2 and PRC2 and provides mechanistic insights into the establishment of Polycomb silencing in plants.

2020-11-06 | GSE145387 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and val1 val2 pkl seedlings.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: RNA from 14-day-old seedlings of wild-type and pkl was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150). Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 5,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings. 14-day-old seedling of WT and val1 val2 pkl were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

2022-12-12 | GSE186156 | GEO

Transcriptomics analysis of developing wild type and val1 mutant Arabidopsis embryos

Project description:Developing Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL regulatory network. The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation. VAL1 functions as a repressor of seed metabolism, as val1 mutant seeds accumulated elevated levels of storage proteins compared to the wild type. Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length and a truncated form lacking the plant-homeodomain-like domain associated with epigenetic repression. None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUSCA3 appears to result in repression of a subset of seed maturation genes downstream of core LAFL regulators as 39% of transcripts in the FUSCA3 regulon were de-repressed in the val1 mutant. The LEC1 and LEC2 regulons also responded but to a lesser extent. Additional 832 transcripts that were not LAFL targets were de-repressed in val1 mutant embryos. These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression. 2 genotypes, 7 time points, 3 biological and 4 technical replicates

2016-02-19 | E-GEOD-74692 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and val1 val2 pkl seedlings.

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt and val1 val2 pkl seedlings.

| PRJNA772750 | ENA

The Transcriptional Repressors VAL1 and VAL2 Recruit PRC2 for Genome-wide Polycomb Silencing in Arabidopsis

Project description:The Transcriptional Repressors VAL1 and VAL2 Recruit PRC2 for Genome-wide Polycomb Silencing in Arabidopsis

| PRJNA607059 | ENA

Transcriptomics analysis of developing wild type and val1 mutant Arabidopsis embryos

2016-02-19 | GSE74692 | GEO

RNA-seq of WT, val1, val2, and val1 val2 14-day-old seedling in Arabidopsis

Project description:14-day-old seedling of WT, val1, val2, and val1val2 were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

2020-11-06 | GSE119715 | GEO

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