Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

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

Json Xml
altmetric image

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]

Similar Datasets

Genomics Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]
2013-02-01 | E-GEOD-39215 | biostudies-arrayexpress
Transcriptomics Transcriptome-wide analysis of gene expression in dark-grown WT and pif mutant seedlings
2014-10-02 | E-GEOD-42665 | biostudies-arrayexpress
Unknown Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]
2013-02-01 | GSE39215 | GEO
Unknown Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [RNA-Seq]
2013-02-01 | GSE39214 | GEO
Genomics Genome-wide identification of PIF1-binding sites and direct-target genes of PIF1 transcriptional regulation in skotomorphogenesis
2014-10-02 | E-GEOD-43283 | biostudies-arrayexpress
Genomics Genome-wide identification of PIF4-binding sites and direct-target genes of PIF4 transcriptional regulation in skotomorphogenesis
2014-10-02 | E-GEOD-43284 | biostudies-arrayexpress
Transcriptomics Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis
2013-02-01 | E-GEOD-39217 | biostudies-arrayexpress
Unknown Genome-wide identification of PIF4-binding sites and direct-target genes of PIF4 transcriptional regulation in skotomorphogenesis
2014-10-02 | GSE43284 | GEO
Unknown Genome-wide identification of PIF1-binding sites and direct-target genes of PIF1 transcriptional regulation in skotomorphogenesis
2014-10-02 | GSE43283 | GEO
Unknown Gene expression in pif1pif3pif4pif5 mutant under dark or red light conditions
2009-11-01 | GSE17159 | GEO