ChIP-Seq/ChIP-exo/HT-ChIP

ChIP-Seq/ChIP-exo/HT-ChIP

Chromatin immunoprecipitation sequencing (ChIP-Seq  or ChIP-exo ) or high-throughput chromatin immunoprecipitation (HT-ChIP ), is a well-established method to map specific protein-binding sites. In this method, DNA-protein complexes are crosslinked in vivo. Samples are then fragmented and treated with an exonuclease to trim unbound oligonucleotides. Protein-specific antibodies are used to immunoprecipitate the DNA-protein complex. The DNA is extracted and sequenced, giving high-resolution sequences of the protein-binding sites.

  • ChIP-Seq: Solomon M. J., Larsen P. L. and Varshavsky A. (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53: 937-947
  • ChIP-exo: Yen K., Vinayachandran V. and Pugh B. F. (2013) SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell 154: 1246-1256
  • HT-ChIP: Blecher-Gonen R., Barnett-Itzhaki Z., Jaitin D., Amann-Zalcenstein D., Lara-Astiaso D., et al. (2013) High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc 8: 539-554