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ZFIN ID: ZDB-PUB-111027-36
Integrated microarray and ChIP analysis identifies multiple Foxa2 dependent target genes in the notochord
Tamplin, O.J., Cox, B.J., and Rossant, J.
Date: 2011
Source: Developmental Biology   360(2): 415-25 (Journal)
Registered Authors: Tamplin, Owen
Keywords: noto, foxa2, enhancer, notochord, ChIP-seq, microarray
MeSH Terms:
  • Animals
  • Chromatin/metabolism*
  • Chromatin Immunoprecipitation
  • Enhancer Elements, Genetic
  • Hepatocyte Nuclear Factor 3-beta/genetics*
  • Hepatocyte Nuclear Factor 3-beta/metabolism
  • Homeodomain Proteins/genetics
  • Homeodomain Proteins/metabolism
  • Mice
  • Mutation
  • Notochord/embryology*
  • Notochord/metabolism
  • Protein Array Analysis
  • Zebrafish
PubMed: 22008794 Full text @ Dev. Biol.
The node and notochord are key tissues required for patterning of the vertebrate body plan. Understanding the gene regulatory network that drives their formation and function is therefore important. Foxa2 is a key transcription factor at the top of this genetic hierarchy and finding its targets will help us to better understand node and notochord development. We performed an extensive microarray-based gene expression screen using sorted embryonic notochord cells to identify early notochord-enriched genes. We validated their specificity to the node and notochord by whole mount in situ hybridization. This provides the largest available resource of notochord-expressed genes, and therefore candidate Foxa2 target genes in the notochord. Using existing Foxa2 ChIP-seq data from adult liver, we were able to identify a set of genes expressed in the notochord that had associated regions of Foxa2-bound chromatin. Given that Foxa2 is a pioneer transcription factor, we reasoned that these sites might represent notochord-specific enhancers. Candidate Foxa2-bound regions were tested for notochord specific enhancer function in a zebrafish reporter assay and 7 novel notochord enhancers were identified. Importantly, sequence conservation or predictive models could not have readily identified these regions. Mutation of putative Foxa2 binding elements in two of these novel enhancers abrogated reporter expression and confirmed their Foxa2 dependence. The combination of highly specific gene expression profiling and genome-wide ChIP analysis is a powerful means of understanding developmental pathways, even for small cell populations such as the notochord.