PUBLICATION

Functional Assessment of Disease-Associated Regulatory Variants In Vivo Using a Versatile Dual Colour Transgenesis Strategy in Zebrafish

Authors
Bhatia, S., Gordon, C.T., Foster, R.G., Melin, L., Abadie, V., Baujat, G., Vazquez, M.P., Amiel, J., Lyonnet, S., Heyningen, V.V., Kleinjan, D.A.
ID
ZDB-PUB-150602-2
Date
2015
Source
PLoS Genetics   11: e1005193 (Journal)
Registered Authors
Bhatia, Shipra, Gordon, Chris, Lyonnet, Stanislas
Keywords
Zebrafish, Embryos, Hypothalamus, Morpholino, Gene expression, Transcription factors, Enhancer elements, Point mutation
MeSH Terms
  • Animals
  • Eye Proteins/genetics
  • Eye Proteins/metabolism
  • Green Fluorescent Proteins/genetics
  • Green Fluorescent Proteins/metabolism
  • Hedgehog Proteins/genetics
  • Hedgehog Proteins/metabolism
  • Homeodomain Proteins/genetics
  • Homeodomain Proteins/metabolism
  • Interferon Regulatory Factors/genetics
  • Interferon Regulatory Factors/metabolism
  • PAX6 Transcription Factor
  • Paired Box Transcription Factors/genetics
  • Paired Box Transcription Factors/metabolism
  • Pierre Robin Syndrome/genetics*
  • Protein Binding
  • Regulatory Elements, Transcriptional*
  • Repressor Proteins/genetics
  • Repressor Proteins/metabolism
  • Transgenes*
  • Zebrafish
  • Zebrafish Proteins/genetics
  • Zebrafish Proteins/metabolism
PubMed
26030420 Full text @ PLoS Genet.
Abstract
Disruption of gene regulation by sequence variation in non-coding regions of the genome is now recognised as a significant cause of human disease and disease susceptibility. Sequence variants in cis-regulatory elements (CREs), the primary determinants of spatio-temporal gene regulation, can alter transcription factor binding sites. While technological advances have led to easy identification of disease-associated CRE variants, robust methods for discerning functional CRE variants from background variation are lacking. Here we describe an efficient dual-colour reporter transgenesis approach in zebrafish, simultaneously allowing detailed in vivo comparison of spatio-temporal differences in regulatory activity between putative CRE variants and assessment of altered transcription factor binding potential of the variant. We validate the method on known disease-associated elements regulating SHH, PAX6 and IRF6 and subsequently characterise novel, ultra-long-range SOX9 enhancers implicated in the craniofacial abnormality Pierre Robin Sequence. The method provides a highly cost-effective, fast and robust approach for simultaneously unravelling in a single assay whether, where and when in embryonic development a disease-associated CRE-variant is affecting its regulatory function.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping