ZFIN ID: ZDB-PUB-131204-12
Genome wide analysis reveals zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish
Winata, C.L., Kondrychyn, I., Kumar, V., Srinivasan, K.G., Orlov, Y., Ravishankar, A., Prabhakar, S., Stanton, L.W., Korzh, V., and Mathavan, S.
Date: 2013
Source: PLoS Genetics 9(10): e1003852 (Journal)
Registered Authors: Kondrychyn, Igor, Korzh, Vladimir, Mathavan, S., Winata, Cecilia Lanny
Keywords: Embryos, Gene regulation, Sequence motif analysis, Gene expression, Microarrays, Zebrafish, Wnt signaling cascade, Recombinant proteins
Microarrays: GEO:GSE41458
MeSH Terms:
  • Animals
  • Binding Sites
  • Body Patterning/genetics*
  • Gene Expression Regulation, Developmental
  • Genomics
  • Homeodomain Proteins/genetics*
  • Homeodomain Proteins/metabolism
  • Regulatory Elements, Transcriptional/genetics*
  • Regulatory Sequences, Nucleic Acid/genetics*
  • Transcription Factors/genetics*
  • Transcription Factors/metabolism
  • Wnt Signaling Pathway/genetics
  • Zebrafish/genetics
  • Zebrafish/growth & development
  • Zebrafish Proteins/genetics*
  • Zebrafish Proteins/metabolism
PubMed: 24204288 Full text @ PLoS Genet.
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ABSTRACT

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 the Nodal and canonical Wnt pathways, analysis of gastrula stage embryos uncovered a number of novel candidate target genes, among which were members of the non-canonical Wnt pathway and the neural pre-pattern genes. A similar analysis in zic3-expressing cells obtained by FACS at segmentation stage revealed a dramatic shift in Zic3 binding site locations and identified an entirely distinct set of target genes associated with later developmental functions such as neural development. We demonstrate cis-regulation of several of these target genes by Zic3 using in vivo enhancer assay. Analysis of Zic3 binding sites revealed a distribution biased towards distal intergenic regions, indicative of a long distance regulatory mechanism; some of these binding sites are highly conserved during evolution and act as functional enhancers. This demonstrated that Zic3 regulation of developmental genes is achieved predominantly through long distance regulatory mechanism and revealed that developmental transitions could be accompanied by dramatic changes in regulatory landscape.

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