Genomics

Dataset Information

301

Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]


ABSTRACT: 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 combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis. Four biological replicates data of PIF3-binding sites were collected by comparing the parallel ChIP samples from transgenic seedlings overexpressing Myc-epitope-tagged PIF3 (35S:PIF3-5xMyc, P3M) in pif3-3 null mutant background and the wild-type (WT) control.

OTHER RELATED OMICS DATASETS IN: E-GEOD-39214

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Oleg Mayba   Yu Zhang  Peter H Quail 

PROVIDER: E-GEOD-39215 | ArrayExpress | 2013-02-01

SECONDARY ACCESSION(S): SRP014179GSE39215PRJNA170238

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

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.

Zhang Yu Y   Mayba Oleg O   Pfeiffer Anne A   Shi Hui H   Tepperman James M JM   Speed Terence P TP   Quail Peter H PH  

PLoS genetics 20130131 1


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 transc  ...[more]

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