Tissue-Specific In Vivo Biotin Chromatin Immunoprecipitation with Sequencing in Zebrafish and Chicken

STAR Protoc. 2020 Jul 31;1(2):100066. doi: 10.1016/j.xpro.2020.100066. eCollection 2020 Sep 18.

Abstract

Chromatin immunoprecipitation with sequencing (ChIP-seq) has been instrumental in understanding transcription factor (TF) binding during gene regulation. ChIP-seq requires specific antibodies against desired TFs, which are not available for numerous species. Here, we describe a tissue-specific biotin ChIP-seq protocol for zebrafish and chicken embryos which utilizes AVI tagging of TFs, permitting their biotinylation by a co-expressed nuclear biotin ligase. Subsequently, biotinylated factors can be precipitated with streptavidin beads, enabling the user to construct TF genome-wide binding landscapes like conventional ChIP-seq methods. For complete details on the use and execution of this protocol, please see Lukoseviciute et al. (2018) and Ling and Sauka-Spengler (2019).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biotin / chemistry*
  • Biotin / metabolism
  • Cells, Cultured
  • Chickens / genetics
  • Chromatin Immunoprecipitation / methods*
  • Organ Specificity / physiology
  • Sequence Analysis, DNA / methods*
  • Streptavidin / chemistry
  • Streptavidin / metabolism
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism
  • Zebrafish / genetics

Substances

  • Transcription Factors
  • Biotin
  • Streptavidin