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Series GSE149686

Query DataSets for GSE149686

Status

Public on Feb 14, 2023

Title

Warm temperature-triggered developmental reprogramming requires VIL1-mediated, genome-wide H3K27me3 accumulation in Arabidopsis

Organism

Arabidopsis thaliana

Experiment type

Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing

Summary

Through RNA-seq and ChIP-seq we show that VIL1 mediates warm ambient temperature responses.

Overall design

We grew Col-0 (WT) and vil1-1 mutant at two different temperatures (22C and 27C) and compared the transcriptome. RNA-seq analysis shows that vil1 fails to downregulate high ambient temperature suppressed genes. H3K27me3 ChIP-seq showed high temperature-mediated accumulation of H3K27me3 compromised in vil1. We also found that vil1 suppresses constitutive thermo-morphogenic transcriptome of arp6. RNA-seq analysis revealed that constitutive heat responsive transcriptome of arp6 reverted back to the wild-type levels in arp6vil1. This observation suggests an antagonistic relationship between VIL1 and ARP6. H2A.Z ChIP-seq showed that unlike wild type, vil1 fails to evict H2A.Z at high ambient temperature from high temperature responsive genes.

Web link

http://10.1242/dev.201343

Contributor(s)

Kim J, Bordiya Y, Zhao B, Sung S

Citation(s)

Submission date

May 01, 2020

Last update date

May 16, 2023

Contact name

Sibum Sung

E-mail(s)

sbsung@austin.utexas.edu

Organization name

University of Texas at Austin

Street address

NMS 5.110, Stop A5000

City

Austin

State/province

TX

ZIP/Postal code

78712

Country

USA

Platforms (1)

Illumina NextSeq 500 (Arabidopsis thaliana)

Samples (42)

More...

GSM4508971	Col-0 22°C RNA-seq (replicate 1)
GSM4508972	Col-0 22°C RNA-seq (replicate 2)
GSM4508973	Col-0 27°C RNA-seq (replicate 1)

GSM4508974	Col-0 27°C RNA-seq (replicate 2)
GSM4508975	vil1-1 22°C RNA-seq (replicate 1)
GSM4508976	vil1-1 22°C RNA-seq (replicate 2)
GSM4508977	vil1-1 27°C RNA-seq (replicate 1)
GSM4508978	vil1-1 27°C RNA-seq (replicate 2)
GSM4508979	arp6 22°C RNA-seq (replicate 1)
GSM4508980	arp6 22°C RNA-seq (replicate 2)
GSM4508981	arp6vil1 22°C RNA-seq (replicate 1)
GSM4508982	arp6vil1 22°C RNA-seq (replicate 2)
GSM4508983	Col-0 22°C H2AZ ChIP-seq input
GSM4508984	Col-0 22°C H2AZ ChIP-seq IP (replicate 1)
GSM4508985	Col-0 22°C H2AZ ChIP-seq IP (replicate 2)
GSM4508986	Col-0 27°C H2AZ ChIP-seq input
GSM4508987	Col-0 27°C H2AZ ChIP-seq IP (replicate 1)
GSM4508988	Col-0 27°C H2AZ ChIP-seq IP (replicate 2)
GSM4508989	vil1-1 22°C H2AZ ChIP-seq input
GSM4508990	vil1-1 22°C H2AZ ChIP-seq IP (replicate 1)
GSM4508991	vil1-1 22°C H2AZ ChIP-seq IP (replicate 2)
GSM4508992	vil1-1 27°C H2AZ ChIP-seq input
GSM4508993	vil1-1 27°C H2AZ ChIP-seq IP (replicate 1)
GSM4508994	vil1-1 27°C H2AZ ChIP-seq IP (replicate 2)
GSM4508995	arp6 22°C H2AZ ChIP-seq input
GSM4508996	arp6 22°C H2AZ ChIP-seq IP (replicate 1)
GSM4508997	arp6 22°C H2AZ ChIP-seq IP (replicate 2)
GSM4508998	arp6vil1 22°C H2AZ ChIP-seq input
GSM4508999	arp6vil1 22°C H2AZ ChIP-seq IP (replicate 1)
GSM4509000	arp6vil1 22°C H2AZ ChIP-seq IP (replicate 2)
GSM5566252	Col-0 22°C H3K27me3 ChIP-seq input
GSM5566253	Col-0 22°C H3K27me3 ChIP-seq IP (replicate 1)
GSM5566254	Col-0 22°C H3K27me3 ChIP-seq IP (replicate 2)
GSM5566255	Col-0 27°C H3K27me3 ChIP-seq input
GSM5566256	Col-0 27°C H3K27me3 ChIP-seq IP (replicate 1)
GSM5566257	Col-0 27°C H3K27me3 ChIP-seq IP (replicate 2)
GSM5566258	vil1 22°C H3K27me3 ChIP-seq input
GSM5566259	vil1 22°C H3K27me3 ChIP-seq IP (replicate 1)
GSM5566260	vil1 22°C H3K27me3 ChIP-seq IP (replicate 2)
GSM5566261	vil1 27°C H3K27me3 ChIP-seq input
GSM5566262	vil1 27°C H3K27me3 ChIP-seq IP (replicate 1)
GSM5566263	vil1 27°C H3K27me3 ChIP-seq IP (replicate 2)

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE149686_Col-0_22C_IP.bw	45.7 Mb	(ftp)(http)	BW
GSE149686_Col-0_22C_Input.bw	58.3 Mb	(ftp)(http)	BW
GSE149686_Col-0_27C_IP.bw	45.4 Mb	(ftp)(http)	BW
GSE149686_Col-0_27C_Input.bw	49.8 Mb	(ftp)(http)	BW
GSE149686_H2AZCol_Inp_22.bw	48.7 Mb	(ftp)(http)	BW
GSE149686_H2AZCol_Inp_27.bw	48.3 Mb	(ftp)(http)	BW
GSE149686_H2AZ_IP_Col22.bw	57.0 Mb	(ftp)(http)	BW
GSE149686_H2AZ_IP_Col27.bw	57.8 Mb	(ftp)(http)	BW
GSE149686_H2AZ_IP_Vil22.bw	57.7 Mb	(ftp)(http)	BW
GSE149686_H2AZ_IP_Vil27.bw	58.1 Mb	(ftp)(http)	BW
GSE149686_H2AZvil1_Inp_22.bw	49.2 Mb	(ftp)(http)	BW
GSE149686_H2AZvil1_Inp_27.bw	48.5 Mb	(ftp)(http)	BW
GSE149686_RPKM_normalized_gene_count.xlsx	6.0 Mb	(ftp)(http)	XLSX
GSE149686_arp6_H2AZ_IP.bw	59.2 Mb	(ftp)(http)	BW
GSE149686_arp6_input.bw	52.4 Mb	(ftp)(http)	BW
GSE149686_arp6vil1_H2AZ_IP.bw	60.5 Mb	(ftp)(http)	BW
GSE149686_arp6vil1_input.bw	48.7 Mb	(ftp)(http)	BW
GSE149686_vil1_22C_IP.bw	45.6 Mb	(ftp)(http)	BW
GSE149686_vil1_22C_Input.bw	53.6 Mb	(ftp)(http)	BW
GSE149686_vil1_27C_IP.bw	42.7 Mb	(ftp)(http)	BW
GSE149686_vil1_27C_Input.bw	49.8 Mb	(ftp)(http)	BW
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