Transcriptomics

Dataset Information

21

Induction of ERDNp63a via Tamoxifen in primary keratinocytes


ABSTRACT: Genome-wide identification of bona fide targets of transcription factors in mammalian cells is still a challenge. We present a novel integrated computational and experimental approach to identify direct targets of a transcription factor. This consists in measuring time-course (dynamic) gene expression profiles upon perturbation of the transcription factor under study, and in applying a novel reverse-engineering” algorithm (TSNI) to rank genes according to their probability of being direct targets. Using primary keratinocytes as a model system, we identified novel transcriptional target genes of Trp63, a crucial regulator of skin development. TSNI-predicted Trp63 target genes were validated by Trp63 knockdown and by ChIP-chip to identify Trp63-bound regions in vivo. Our study revealed that short sampling times, in the order of minutes, are needed to capture the dynamics of gene expression in mammalian cells. We show that Trp63 transiently regulates a subset of its direct targets, thus highlighting the importance of considering temporal dynamics when identifying transcriptional targets. Using this approach, we uncovered a previously unsuspected transient regulation of the AP-1 complex by Trp63, through direct regulation of a subset of AP-1 components. The integrated experimental and computational approach described here is readily applicable to other transcription factors in mammalian systems and is complementary to genome-wide identification of transcription factor binding sites. Keywords: time course, p63, keratinocytes Overall design: Primary keratinocytes were infected with a retrovirus carryng the DNp63alpha isform fused to the Estrogene receptor domain Upon induction with Tamoxifen, cells were collected every 20 minutes up to 4 hours.

INSTRUMENT(S): [Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array

ORGANISM(S): Mus musculus  

SUBMITTER: Diego di Bernardo  

PROVIDER: GSE10562 | GEO | 2008-03-01

SECONDARY ACCESSION(S): PRJNA108951

REPOSITORIES: GEO

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