GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE136843

Query DataSets for GSE136843

Status

Public on Sep 01, 2020

Title

Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PHYTOCHROME-INTERACTING FACTORS

Sample organism

Arabidopsis thaliana

Experiment type

Third-party reanalysis
Genome binding/occupancy profiling by high throughput sequencing

Summary

Light-environment signals, sensed by plant phytochrome (phy) photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown “trans factors” modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of co-localization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade, and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator, to regulate the expression of PIF-DTGs, through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF signaling hub.

Overall design

To examine the relative distributions of published DNA-binding sites of other transcription factors (TFs), with those of the PIF quartet proteins within the promoters of our 338 PIF-DTGs, we compared the published ChIP-defined binding regions for 25 Arabidopsis transcription factors (25 TFs) with those of four core PIFs. For this purpose, we used a BED file, kindly provided by K. Heyndrickx, K. Vandepoele and colleagues, containing the boundaries of genomic regions displaying significant binding of the TF specified. We located these binding regions within the promoters of our 338 PIF-DTGs, using the Integrative Genomics Viewer, and compared them to the binding peaks of all four PIFs. To quantify the extent and proximity of the binding sites of the ’25 TFs’ compared to those of the PIFs, across all PIF-DTG promoter regions, we first determined the overlap (if any) of the binding regions of each of the ’25 TFs’, with the mean of the PIF-bound summits. If the center of a PIF-bound region was located within a ’25-TF’ binding region, the binding was defined as ‘coincident’. The proximity was then defined as the distance between the coincident-TF and PIF binding centers, and was plotted using Mathematica (http://www.wolfram.com/mathematica/).
The re-analyzed sample information and data processing details are provided in the 'README.txt'.

Contributor(s)

Pfeiffer A, Tepperman JM, Zhang Y

Citation missing

Has this study been published? Please login to update or notify GEO.

Submission date

Sep 04, 2019

Last update date

Sep 01, 2020

Contact name

Yu Zhang

E-mail(s)

yuzhang@berkeley.edu

Phone

1-510-559-5889

Organization name

UC Berkeley

Department

Plant and Microbial Biology

Lab

Peter H. Quail

Street address

800 Buchanan Street

City

Albany

State/province

California

ZIP/Postal code

94710

Country

USA

Relations

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

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
GSE136843_25-TFs.bed.gz	547.3 Kb	(ftp)(http)	BED
GSE136843_G-box_motifs.bed.gz	99.1 Kb	(ftp)(http)	BED
GSE136843_PBE-box_motifs.bed.gz	409.4 Kb	(ftp)(http)	BED
GSE136843_PIF1-ChIP.wig.gz	28.1 Mb	(ftp)(http)	WIG
GSE136843_PIF1.bed.gz	24.8 Kb	(ftp)(http)	BED
GSE136843_PIF3-ChIP.wig.gz	29.6 Mb	(ftp)(http)	WIG
GSE136843_PIF3.bed.gz	8.8 Kb	(ftp)(http)	BED
GSE136843_PIF4-ChIP.wig.gz	25.3 Mb	(ftp)(http)	WIG
GSE136843_PIF4.bed.gz	22.0 Kb	(ftp)(http)	BED
GSE136843_PIF5-ChIP.wig.gz	22.9 Mb	(ftp)(http)	WIG
GSE136843_PIF5.bed.gz	16.8 Kb	(ftp)(http)	BED
GSE136843_readme.txt	4.8 Kb	(ftp)(http)	TXT
Processed data are available on Series record