ChIP-Seq/ChIP-exo/HT-ChIP

ChIP-Seq/ChIP-exo/HT-ChIP

ChIP-Seq is a well-established method to map specific protein-binding sites. It has given rise to a vast number of derivatives, such as AHT-ChIP-Seq¹, BisChIP-Seq², CAST-ChIP³, ChIP-BMS⁴, ChIP-BS-seq⁵, ChIPmentation⁶, Drop-ChIP⁷, Mint-ChIP⁸, PAT–ChIP⁹, reChIP-seq¹⁰, scChIP-seq¹¹, and X-ChIP¹². Sequential ChIP-seq (reChIP) can also show the association of different proteins on the chromatin¹³.

In this method, DNA-protein complexes are crosslinked in vivo. Next, samples are 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, purified, and sequenced, giving high-resolution sequences of the protein-binding sites.

Pros:

• Base-pair resolution of protein-binding sites
• Can map specific regulatory factors or proteins
• Exonuclease use eliminates contamination by unbound DNA¹⁴

Cons:

• Nonspecific antibodies can dilute the pool of DNA-protein complexes of interest
• Target protein must be known and be able to raise an antibody

• 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
• 1. Aldridge S., Watt S., Quail M. A., et al. AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation. Genome Biol. 2013;14:R124
• 2. Statham A. L., Robinson M. D., Song J. Z., Coolen M. W., Stirzaker C. and Clark S. J. Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res. 2012;22:1120-1127
• 3. Schauer T., Schwalie P. C., Handley A., Margulies C. E., Flicek P. and Ladurner A. G. CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system. Cell Rep. 2013;5:271-282
• 4. Li Y. and Tollefsbol T. O. Combined chromatin immunoprecipitation and bisulfite methylation sequencing analysis. Methods Mol Biol. 2011;791:239-251
• 5. Brinkman A. B., Gu H., Bartels S. J., et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012;22:1128-1138
• 6. Schmidl C., Rendeiro A. F., Sheffield N. C. and Bock C. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015;12:963-965
• 7. Rotem A., Ram O., Shoresh N., et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015;33:1165-1172
• 8. van Galen P., Viny A. D., Ram O., et al. A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Mol Cell. 2016;61:170-180
• 9. Fanelli M., Amatori S., Barozzi I. and Minucci S. Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue. Nat Protoc. 2011;6:1905-1919
• 10. Truax A. D. and Greer S. F. ChIP and Re-ChIP assays: investigating interactions between regulatory proteins, histone modifications, and the DNA sequences to which they bind. Methods Mol Biol. 2012;809:175-188
• 11. Rotem A., Ram O., Shoresh N., et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015;33:1165-1172
• 12. Skene P. J., Hernandez A. E., Groudine M. and Henikoff S. The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. Elife. 2014;3:e02042
• 13. Elsasser S. J., Noh K. M., Diaz N., Allis C. D. and Banaszynski L. A. Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature. 2015;522:240-244
• 14. Zentner G. E. and Henikoff S. Surveying the epigenomic landscape, one base at a time. Genome Biol. 2012;13:250

1. Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109

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