Genome-wide profiling of SWI/SNF chromatin remodeler BRAHMA (BRM) and BRM Interacting Protein 1/2 (BRIP1/2) in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA597767 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10768982_1.fastq.gz | Fastqsanger.gz | |||
| SRR10768982_2.fastq.gz | Fastqsanger.gz | |||
| SRR10768983_1.fastq.gz | Fastqsanger.gz | |||
| SRR10768983_2.fastq.gz | Fastqsanger.gz | |||
| SRR10768984_1.fastq.gz | Fastqsanger.gz |
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Project description:SWI/SNF chromatin remodeling complexes control gene expression by regulating chromatin structure. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we show that BRAHMA Interacting Protein 1 (BRIP1) and BRIP2 in Arabidopsis thaliana are core subunits of plant SWI/SNF complexes. BRIP1 and 2 are two homolog proteins. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome strikingly similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and 2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and 2 physically interact with BRM-containing SWI/SNF complexes, and extensively co-localize with BRM at endogenous genes. Loss-of-brip1brip2 results in decreased BRM occupancy at almost all BRM target genes and substantially reduced subunits incorporation into the BRM-containing SWI/SNF complexes. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants, and uncovers the essential role of these subunits in regulating the integrity (assembly) of SWI/SNF complexes in plants.
2020-06-21 | GSE142621 | GEO
Project description:BRAHMA (BRM) is a conserved SWI/SNF-type chromatin remodeling ATPase implicated in many key nuclear events. Histone H3 Lysine 27 (H3K27) demethylases specifically remove the repressive histone mark, trimethylation of H3K27 (H3K27me3). Both proteins are thought to play active roles in regulating gene activities at the chromatin level, but their genome-wide coordination remains to be determined. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) is the first identified plant H3K27 demethylase. Here, genome-wide analyses revealed that REF6 targets to thousands of genes across the Arabidopsis genome and co-localizes with BRM at more than 1,000 genes, many of which are genes involved in response to various stimuli, especially plant hormones. Loss of REF6 activity results in decreased BRM occupancy at hundreds of BRM-REF6 co-targets, indicating that REF6 is required for the recruitment of BRM to chromatin. Further, REF6 targets to genomic loci that contains the CTCTGTTT motif in vivo
2016-03-31 | PXD003583 | Pride
Project description:BRAHMA (BRM) is a conserved SWI/SNF-type chromatin remodeling ATPase implicated in many key nuclear events. Histone H3 Lysine 27 (H3K27) demethylases specifically remove the repressive histone mark, trimethylation of H3K27 (H3K27me3). Both proteins are thought to play active roles in regulating gene activities at the chromatin level, but their genome-wide coordination remains to be determined. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) is the first identified plant H3K27 demethylase. Here, genome-wide analyses revealed that REF6 targets to thousands of genes across the Arabidopsis genome and co-localizes with BRM at more than 1,000 genes, many of which are genes involved in response to various stimuli, especially plant hormones. Loss of REF6 activity results in decreased BRM occupancy at hundreds of BRM-REF6 co-targets, indicating that REF6 is required for the recruitment of BRM to chromatin. Further, REF6 targets to genomic loci that contains the CTCTGTTT motif in vivo Examination of BRM occupancy in 14-day-old wt and ref6-1 seedlings. Examination of REF6 occupancy in 14-day-old wt and brm-1 seedlings. Examination of global RNA expression in 14-day-old wt, brm-1, ref6-1 and brm-1 ref6-1 seedlings. Examination of H3K27me3 profiles in 14-day-old wt, brm-1, ref6-1, and brm-1 ref6-1 seedlings.
2016-03-28 | E-GEOD-72735 | biostudies-arrayexpress
Project description:BRAHMA (BRM) is a conserved SWI/SNF-type chromatin remodeling ATPase implicated in many key nuclear events. Histone H3 Lysine 27 (H3K27) demethylases specifically remove the repressive histone mark, trimethylation of H3K27 (H3K27me3). Both proteins are thought to play active roles in regulating gene activities at the chromatin level, but their genome-wide coordination remains to be determined. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) is the first identified plant H3K27 demethylase. Here, genome-wide analyses revealed that REF6 targets to thousands of genes across the Arabidopsis genome and co-localizes with BRM at more than 1,000 genes, many of which are genes involved in response to various stimuli, especially plant hormones. Loss of REF6 activity results in decreased BRM occupancy at hundreds of BRM-REF6 co-targets, indicating that REF6 is required for the recruitment of BRM to chromatin. Further, REF6 targets to genomic loci that contains the CTCTGTTT motif in vivo through its C2H2 zinger finger domains. Consistently, the two proteins activate the expression of a set of common genes in plant cells. Thus, this work demonstrates a genome-wide coordination between an H3K27me3 demethylase and a chromatin remodelling protein. Examination of global RNA expression in 14-day-old wt, brm-1, ref6-1 and brm-1 ref6-1 seedlings. Three biological replicates for each one.
2016-03-28 | E-GEOD-72260 | biostudies-arrayexpress
Project description:Drosophila Piwi associates with PIWI-interacting RNAs (piRNAs) and represses transposons transcriptionally through heterochromatinization; however, this process is poorly understood. Here, we identify Brahma (Brm), the core adenosine triphosphatase of the SWI/SNF chromatin remodeling complex, as a new Piwi interactor, and show Brm involvement in activating transcription of Piwi-targeted transposons before silencing. Bioinformatic analyses indicated that Piwi, once bound to target RNAs, reduced the occupancies of SWI/SNF and RNA polymerase II (Pol II) on target loci, abrogating transcription. Artificial piRNA-driven targeting of Piwi to RNA transcripts enhanced repression of Brm-dependent reporters compared with Brm-independent reporters. This was dependent on Piwi cofactors, Gtsf1/Asterix (Gtsf1), Panoramix/Silencio (Panx), and Maelstrom (Mael), but not Eggless/dSetdb (Egg)–mediated H3K9me3 deposition. The lambdaN-box B–mediated tethering of Mael to reporters repressed Brm-dependent genes in the absence of Piwi, Panx, and Gtsf1. We propose that Piwi, via Mael, can rapidly suppress transcription of Brm-dependent genes to facilitate heterochromatin formation.
2020-12-13 | GSE108329 | GEO
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, brip1, brip2, brm-3, brm-1, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 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 4,000 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. Conclusions: Our study represents the first detailed analysis of brip1, brip2, brip1 brip2 transcriptomes, with biologic replicates, generated by RNA-seq technology.
2020-06-21 | GSE142622 | GEO
Project description:Synthesis and accumulation of seed storage proteins (SSPs) is an important aspect of the seed maturation program. Genes encoding SSPs are specifically and highly expressed in the seed during maturation. However, the mechanisms that repress the expression of these genes in leaf tissue are not well understood. To gain insight into the repression mechanisms, we have performed a transgenic screening for mutants that express SSPs in leaves. Here we show that mutations of BRAHMA (BRM), a SNF2 chromatin remodelling ATPase, cause the ectopic expression of a subset of SSPs and other embryogenesis related genes in leaf tissue. Consistent with the notion that such SNF2-like ATPases form protein complexes in vivo, we observed similar phenotypes for mutations of AtSWI3C, a BRM interacting partner, and BSH, a SNF5 homolog and essential SWI/SNF subunit. Further, we present chromatin immunoprecipitation evidence that BRM is recruited to the promoters of a number of embryogenesis genes including the 2S genes, which are expressed/elevated in brm leaves. Consistent with its role in nucleosome remodelling, BRM appears to control the chromatin structure of the At2S2 promoter. These results show that a BRM-containing chromatin remodelling ATPase complex is involved in the direct repression of SSPs in leaf tissue. A matrix comprising the signal intensity value of each gene per replicate hybridization and the averaged data of each gene generated from three replicate hybridizations of the wild type and mutant samples, respectively, is linked below as a supplementary file. Experiment Overall Design: Total RNA was isolated from three independent biological replicates of essp3 mutant and Wild type (Pro?CG:GUS)) respectively. Three ATH1 chips were used for the mutant and three for the wild type.
2009-02-07 | E-GEOD-11505 | biostudies-arrayexpress
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, brip1, brip2, brm-3, brm-1, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 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 4,000 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. Conclusions: Our study represents the first detailed analysis of brip1, brip2, brip1 brip2 transcriptomes, with biologic replicates, generated by RNA-seq technology.
2021-03-22 | GSE161516 | GEO
Project description:To understand how actions of the chromatin-remodeler BRAHMA (BRM) and Polycomb Group (PcG) proteins are coordinated during plant development, we performed a genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Increased H3K27me3 deposition at several hundred genes was observed in brm mutants and this increase was partially supressed upon removal of the CURLING LEAF (CLF) H3K27me3 methyltransferase. ChIP experiments demonstrated that BRM directly binds to a subset of genes and prevents the inappropriate association of PcG proteins at some of the loci. Together, these results indicate a crucial role of BRM in restricting the inappropriate activity of PcG protein complexes during plant development.
2015-03-09 | GSE53621 | GEO
Project description:Little is known of hematopoietic stem (HSC) and progenitor (HPC) cell self-renewal. The role of Brahma (BRM), a chromatin remodeler, in HSC/HPC function is unknown. Bone marrow (BM) from Brm-/- mice manifested increased numbers of long- and short-term HSCs, GMPs, and increased numbers and cycling of functional HPCs. Brm-/- HSC/HPC show demonstrated functional differences compared to wildtype HSC/HPC in vivo and ex vivo, due in part to increased intracellular valine in lineage negative BM. To determine changes in gene programs associated with loss of BRM, we performed RNA sequencing on Brm-/- LSK cells. Brm-/- LSK exhibited upregulated interferon response/cell cycle gene programs, suggesting important extrinsic effects on primitive HSC/HPC from more mature HPC due to the absence of BRM.
2021-11-08 | GSE183430 | GEO