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Series GSE108450 Query DataSets for GSE108450
Status Public on Jan 05, 2018
Title The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Genome variation profiling by high throughput sequencing
Summary Plants adapt to changes in their environment by regulating transcription and chromatin organization. The histone H2A variant H2A.Z and the SWI2/SNF2 ATPase BRAHMA have overlapping roles in positively and negatively regulating environmentally responsive genes in Arabidopsis, but the extent of this overlap was uncharacterized. Both have been associated with various changes in nucleosome positioning and stability in different contexts, but their specific roles in transcriptional regulation and chromatin organization need further characterization. We show that H2A.Z and BRM act both cooperatively and antagonistically to contribute directly to transcriptional repression and activation of genes involved in development and response to environmental stimuli. We identified 8 classes of genes that show distinct relationships between H2A.Z and BRM and their roles in transcription. We found that H2A.Z contributes to a range of different nucleosome properties, while BRM stabilizes nucleosomes where it binds and destabilizes and/or repositions flanking nucleosomes. H2A.Z and BRM contribute to +1 nucleosome destabilization, especially where they coordinately regulate transcription. While profiling nucleosomes in arp6 mutants, we discovered that large deletions had accumulated in the arp6 genome. We also found that at genes regulated by both BRM and H2A.Z, both factors overlap with the binding sites of light-regulated transcription factors PIF4, PIF5, and FRS9, and that some of the FRS9 binding sites are dependent on H2A.Z and BRM for accessibility. Collectively, we comprehensively characterized the antagonistic and cooperative contributions of H2A.Z and BRM to transcriptional regulation, and illuminated their interrelated roles in chromatin organization. The variability observed in their individual functions implies that both BRM and H2A.Z have more context-specific roles within diverse chromatin environments than previously assumed.
 
Overall design We performed MNase-seq, H2A.Z ChIP-seq, and RNA-seq on 4-5 leaf developmentally-staged, shoot Arabidopsis material from WT, arp6-1, and brm-1. RNA-seq and MNase-seq were also performed on arp6-1;brm-1 mutants. Two biological replicates were generated for H2A.Z ChIP-seq experiments and MNase-seq, and three biological replicates were performed for RNA-seq experiments. The genome of arp6 mutants was also sequenced to identify genomic deletions.
 
Contributor(s) Torres ES, Deal RB
Citation(s) 30742338
Submission date Dec 22, 2017
Last update date Jun 01, 2020
Contact name Roger B Deal
E-mail(s) roger.deal@emory.edu
Phone 404-727-8087
Organization name Emory University
Department Biology
Street address 1510 Clifton Rd NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platforms (2)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (33)
GSM2898288 WT H2A.Z ChIP - rep1
GSM2898289 WT H2A.Z ChIP - rep2
GSM2898290 WT Input - rep1
Relations
BioProject PRJNA427312
SRA SRP127400

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE108450_A1_Z_histone.bed.gz 42.9 Kb (ftp)(http) BED
GSE108450_A2_Z_histone.bed.gz 51.5 Kb (ftp)(http) BED
GSE108450_B1_Z_histone.bed.gz 202.4 Kb (ftp)(http) BED
GSE108450_B2_Z_histone.bed.gz 183.3 Kb (ftp)(http) BED
GSE108450_WT1_Z_histone.bed.gz 127.3 Kb (ftp)(http) BED
GSE108450_WT2_Z_histone.bed.gz 198.3 Kb (ftp)(http) BED
GSE108450_WT_30M.nucleosomes.bw 41.9 Mb (ftp)(http) BW
GSE108450_WT_vs_arp6.edgeR.txt.gz 701.0 Kb (ftp)(http) TXT
GSE108450_WT_vs_arp6brm.edgeR.txt.gz 730.0 Kb (ftp)(http) TXT
GSE108450_WT_vs_brm.edgeR.txt.gz 717.4 Kb (ftp)(http) TXT
GSE108450_arp6_30M.nucleosomes.bw 41.2 Mb (ftp)(http) BW
GSE108450_arp6_CNVnator_deletions.bed.gz 10.5 Kb (ftp)(http) BED
GSE108450_arp6brm_30M.nucleosomes.bw 39.8 Mb (ftp)(http) BW
GSE108450_brm_30M.nucleosomes.bw 39.4 Mb (ftp)(http) BW
GSE108450_data_arp6_bam_30M-data_WT_bam_30M.positions.integrative.xls.gz 68.9 Mb (ftp)(http) XLS
GSE108450_data_arp6brm_bam_30M-data_WT_bam_30M.positions.integrative.xls.gz 68.9 Mb (ftp)(http) XLS
GSE108450_data_brm_bam_30M-data_WT_bam_30M.positions.integrative.xls.gz 69.1 Mb (ftp)(http) XLS
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