Chromatin Immunoprecipitation Analysis of Xenopus Embryos
Chromatin immunoprecipitation (ChIP) is a powerful technique to study epigenetic regulation and transcription factor binding events in the nucleus. It is based on immune-affinity capture of epitopes that have been cross-linked to genomic DNA in vivo. A readout of the extent to which the epitope is associated with particular genomic regions can be obtained by quantitative PCR (ChIP-qPCR), microarray hybridization (ChIP-chip), or deep sequencing (ChIP-seq). ChIP can be used for molecular and quantitative analyses of histone modifications, transcription factors, and elongating RNA polymerase II at specific loci. It can also be applied to assess the cellular state of transcriptional activation or repression as a predictor of the cells’ capabilities and potential. Another possibility is to employ ChIP to characterize genomes, as histone modifications and binding events occur at specific and highly characteristic genomic elements and locations. This chapter provides a step-by-step protocol of ChIP using early Xenopus embryos and discusses potential pitfalls and other issues relevant for successful probing of protein–genome interactions by ChIP-qPCR and ChIP-seq.
- Design of Tag SNP Whole Genome Genotyping Arrays
- Expression of Recombinant Proteins with Uniform N-Termini
- Molecular Approaches for Delineating Marker Chromosomes
- Collection of Fertilized One-Cell Mouse Eggs for Microinjection
- Dideoxy Sequencing Reactions Using T7 Polymerase
- PRINS as an Efficient Tool for Aneuploidy Assessment in Human Oocytes and Preimplantation Embryos
- Folding-Promoting Agents in Recombinant Protein Production
- Molecular Analysis of Mitochondrial DNA Point Mutations by Polymerase Chain Reaction
- Functional Characterization of Insect Olfactory Receptor Neurons Through In Vivo Approaches
- Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases