Genomics

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Genome-wide identification of PIF4-binding sites and direct-target genes of PIF4 transcriptional regulation in skotomorphogenesis


ABSTRACT: Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF4, 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 PIF4 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis. Three biological replicates data of PIF4-binding sites were collected by comparing the parallel ChIP samples from Myc-epitope-tagged-PIF4 (P1M) overexpressing transgenic seedlings and the wild-type (WT) control.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: james m tepperman  Yu Zhang   Peter H Quail   Hui Shi    

PROVIDER: E-GEOD-43284 | ArrayExpress | 2014-10-02

SECONDARY ACCESSION(S): SRP017774GSE43284PRJNA185278

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis.

Pfeiffer Anne A   Shi Hui H   Tepperman James M JM   Zhang Yu Y   Quail Peter H PH  

Molecular plant 20140813 11


A subfamily of four Phytochrome (phy)-Interacting bHLH transcription Factors (PIFs) collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by photoactivated phy molecules that induce degradation of the PIFs, thereby triggering the transcriptional changes that drive a transition to photomorphogenesis. The PIFs function both redundantly and partially differentially at the morphogenic level in this process. To identify the direct  ...[more]

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