Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is the preferred approach to map histone modifications and identify cis-regulatory DNA elements throughout the genome. Multiple methods have been described to increase the efficiency of library preparation and to reduce hands-on time as well as costs. This review describes detailed steps to perform cell fixation, chromatin shearing, immunoprecipitation, and sequencing library preparation for a batch of 48–96 samples with small cell numbers. The protocol implements a semiautomated platform to reduce technical variability and improve signal-to-noise ratio as well as reduce hands-on time, thus allowing large-scale epigenetic studies of clinical samples with limited cell numbers.
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Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jorgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Muller F, Forrest ARR, Carninci P, Rehli M, Sandelin A (2014) An atlas of active enhancers across human cell types and tissues. Nature 507(7493):455–461. https://doi.org/10.1038/nature12787
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A 107(50):21931–21936. https://doi.org/10.1073/pnas.1016071107
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473(7345):43–49. https://doi.org/10.1038/nature09906
Roadmap Epigenomics C, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M (2015) Integrative analysis of 111 reference human epigenomes. Nature 518(7539):317–330. https://doi.org/10.1038/nature14248
Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13(12):840–852. https://doi.org/10.1038/nrg3306
Dahl JA, Collas P (2008) A rapid micro chromatin immunoprecipitation assay (microChIP). Nat Protoc 3(6):1032–1045. https://doi.org/10.1038/nprot.2008.68
van Galen P, Viny AD, Ram O, Ryan RJ, Cotton MJ, Donohue L, Sievers C, Drier Y, Liau BB, Gillespie SM, Carroll KM, Cross MB, Levine RL, Bernstein BE (2016) A multiplexed system for quantitative comparisons of chromatin landscapes. Mol Cell 61(1):170–180. https://doi.org/10.1016/j.molcel.2015.11.003
Engel I, Seumois G, Chavez L, Samaniego-Castruita D, White B, Chawla A, Mock D, Vijayanand P, Kronenberg M (2016) Innate-like functions of natural killer T cell subsets result from highly divergent gene programs. Nat Immunol 17(6):728–739. https://doi.org/10.1038/ni.3437
Seumois G, Chavez L, Gerasimova A, Lienhard M, Omran N, Kalinke L, Vedanayagam M, Ganesan AP, Chawla A, Djukanovic R, Ansel KM, Peters B, Rao A, Vijayanand P (2014) Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility. Nat Immunol 15(8):777–788. https://doi.org/10.1038/ni.2937
Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P (2016) 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells. Nat Commun 7:13426
Schmidl C, Rendeiro AF, Sheffield NC, Bock C (2015) ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods 12(10):963–965. https://doi.org/10.1038/nmeth.3542
Pchelintsev NA, Adams PD, Nelson DM (2016) Critical parameters for efficient sonication and improved chromatin immunoprecipitation of high molecular weight proteins. PLoS One 11(1):e0148023. https://doi.org/10.1371/journal.pone.0148023
Acknowledgments
We thank the Vijayanand lab members for technical help and constructive discussions and Dr. Sharron Squazzo from Diagenode for technical assistance with the Bioruptor Pico and SX-8G IP-Star Compact machine and protocols. This work was supported by NIH grants (P.V.): NIH R24 AI108564, NIH U19 AI118626, NIH R01 HL114093, NIH R01 AI121426 and NIH S10 OD016262S10.
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Youhanna Jankeel, D., Cayford, J., Schmiedel, B.J., Vijayanand, P., Seumois, G. (2018). An Integrated and Semiautomated Microscaled Approach to Profile Cis-Regulatory Elements by Histone Modification ChIP-Seq for Large-Scale Epigenetic Studies. In: Reinhardt, R. (eds) Type 2 Immunity. Methods in Molecular Biology, vol 1799. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-7896-0_22
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DOI: https://doi.org/10.1007/978-1-4939-7896-0_22
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