A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis

Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4, and 5) are critically necessary to maintaining this developmental state and that light activation of phy induces a...

Full description

Saved in:
Bibliographic Details
Published in:PLoS genetics 2013-01, Vol.9 (1), p.e1003244-e1003244
Main Authors: Zhang, Yu, Mayba, Oleg, Pfeiffer, Anne, Shi, Hui, Tepperman, James M, Speed, Terence P, Quail, Peter H
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Arabidopsis - growth & development
Arabidopsis - metabolism
Arabidopsis Proteins - genetics
Arabidopsis Proteins - metabolism
Arabidopsis thaliana
BASIC BIOLOGICAL SCIENCES
Basic Helix-Loop-Helix Transcription Factors - genetics
Basic Helix-Loop-Helix Transcription Factors - metabolism
Binding sites
Biology
Deoxyribonucleic acid
DNA
DNA transcription
DNA-Binding Proteins
G-Box Binding Factors - genetics
gene expression
Gene Expression Regulation, Plant
gene regulation
Genes
Genetic aspects
Genetic transcription
Health aspects
Light
Morphogenesis
Morphogenesis - genetics
Nucleotide Motifs - genetics
Physiological aspects
Phytochrome - genetics
Phytochrome - metabolism
Plant genetics
Proteins
seedlings
Seedlings - genetics
Seedlings - growth & development
Sequence Analysis, RNA
sequence motif analysis
Signal Transduction - genetics
transcription factors
transcriptional control
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4, and 5) are critically necessary to maintaining this developmental state and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using integrated ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, exerted by sequence-specific binding to G-box (CACGTG) or PBE-box (CACATG) motifs in the target promoters genome-wide. In addition, expression analysis of selected genes in this set, in all triple pif-mutant combinations, provides evidence that the PIF quartet members collaborate to generate an expression pattern that is the product of a mosaic of differential transcriptional responsiveness of individual genes to the different PIFs and of differential regulatory activity of individual PIFs toward the different genes. Together with prior evidence that all four PIFs can bind to G-boxes, the data suggest that this collective activity may be exerted via shared occupancy of binding sites in target promoters.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1003244