Genomics

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Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes


ABSTRACT: Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers. Our study establishes the zebrafish as an excellent model for genome-wide study of a transcription factor in vivo. Zic3 ChIP of wild type and sqet33 transgenic

ORGANISM(S): Danio rerio  

SUBMITTER: Vibhor Kumar   Sinnakarupan Mathavan  Cecillia Winata 

PROVIDER: E-GEOD-41458 | ArrayExpress | 2014-02-27

SECONDARY ACCESSION(S): GSE41458SRP016053PRJNA177350

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish.

Winata Cecilia L CL   Kondrychyn Igor I   Kumar Vibhor V   Srinivasan Kandhadayar G KG   Orlov Yuriy Y   Ravishankar Ashwini A   Prabhakar Shyam S   Stanton Lawrence W LW   Korzh Vladimir V   Mathavan Sinnakaruppan S  

PLoS genetics 20131031 10


Zic3 regulates early embryonic patterning in vertebrates. Loss of Zic3 function is known to disrupt gastrulation, left-right patterning, and neurogenesis. However, molecular events downstream of this transcription factor are poorly characterized. Here we use the zebrafish as a model to study the developmental role of Zic3 in vivo, by applying a combination of two powerful genomics approaches--ChIP-seq and microarray. Besides confirming direct regulation of previously implicated Zic3 targets of t  ...[more]

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