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Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [RNA-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. Transcriptomic profiles of the wild-type (WT), pif3 monogenic mutant, pif1pif4pif5 (pif145) triple mutant, and pif1pif3pif4pif5 (pifq) quadruple mutant were collected from biological triplicates using 3'-end-captured directional RNA-seq analysis.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Yu Zhang 

PROVIDER: E-GEOD-39214 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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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