Chromatin immunoprecipitation in early Xenopus laevis embryos

Dev Dyn. 2009 Jun;238(6):1422-32. doi: 10.1002/dvdy.21931.


Chromatin immunoprecipitation (ChIP) is a powerful method for analyzing the interaction of regulatory proteins with genomic loci, but has been difficult to apply to studies on early embryos due to the limiting amount of genomic material in these samples. Here, we present a comprehensive technique for performing ChIP on blastula and gastrula stage Xenopus embryos. We also describe methods for optimizing crosslinking and chromatin shearing, verifying antibody specificity, maximizing PCR sensitivity, and quantifying PCR results, allowing for the use of as few as 50 early blastula stage embryos (approximately 5x10(4) cells) per experimental condition. Finally, we demonstrate the predicted binding of endogenous beta-catenin to the nodal-related 6 promoter, binding of tagged Fast-1/FoxH1 to the goosecoid promoter, and binding of tagged Tcf3 to the siamois and nodal-related 6 promoters as examples of the potential application of ChIP to embryological investigations. Developmental Dynamics 238:1422-1432, 2009. (c) 2009 Wiley-Liss, Inc.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Chromatin Immunoprecipitation*
  • Forkhead Transcription Factors / genetics
  • Forkhead Transcription Factors / metabolism
  • Goosecoid Protein / genetics
  • Goosecoid Protein / metabolism
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism
  • Nodal Protein / genetics
  • Nodal Protein / metabolism
  • Polymerase Chain Reaction / methods*
  • Promoter Regions, Genetic
  • TCF Transcription Factors / genetics
  • TCF Transcription Factors / metabolism
  • Transcription Factor 7-Like 1 Protein
  • Xenopus Proteins / genetics
  • Xenopus Proteins / metabolism
  • Xenopus laevis* / embryology
  • Xenopus laevis* / genetics
  • beta Catenin / genetics
  • beta Catenin / metabolism


  • FOXH1 protein, Xenopus
  • Forkhead Transcription Factors
  • Goosecoid Protein
  • Homeodomain Proteins
  • Nodal Protein
  • SIA1 protein, Xenopus
  • TCF Transcription Factors
  • Transcription Factor 7-Like 1 Protein
  • Xenopus Proteins
  • beta Catenin