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
- O'Geen H., Henry I. M., Bhakta M. S., Meckler J. F. and Segal D. J. (2015) A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res 43: 3389-3404
- Ramos M. P., Wijetunga N. A., McLellan A. S., Suzuki M. and Greally J. M. (2015) DNA demethylation by 5-aza-2'-deoxycytidine is imprinted, targeted to euchromatin, and has limited transcriptional consequences. Epigenetics Chromatin 8: 11
- Han P., Li W., Lin C. H., Yang J., Shang C., et al. (2014) A long noncoding RNA protects the heart from pathological hypertrophy. Nature 514: 102-106
- Brind'Amour J., Liu S., Hudson M., Chen C., Karimi M. M., et al. (2015) An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nat Commun 6: 6033
- Frank C. L., Liu F., Wijayatunge R., Song L., Biegler M. T., et al. (2015) Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. Nat Neurosci 18: 647-656