Abstract
Many of the key cellular processes including establishing the cell’s identity are governed by chromatin proteins. Mapping their binding on the level of a single cell would give us important insights into a new dimension of cellular heterogeneity. However, ChIP-seq, the main method to study protein–DNA interaction in the chromatin context, has proven very challenging to scale down. ChIPmentation is a modification of ChIP-seq, in which the Tn5 transposase is used to introduce sequencing adapters in one step. This allows to significantly reduce the required input material. ChIPmentation is a robust and versatile approach and even though it has not yet achieved single-cell resolution, we believe that it is a very promising starting point for further downscaling.
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References
Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
Helin K, Minucci S (2017) The role of chromatin-associated proteins in cancer. Annu Rev Cancer Biol 1:355–377
Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT (2018) The human transcription factors. Cell 172:650–665
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837
Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502
Mikkelsen TS, Ku M, Jaffe DB et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553
Solomon MJ, Larsen PL, 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
Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48:240–248
Farnham PJ (2009) Insights from genomic profiling of transcription factors. Nat Rev Genet 10:605–616
Brind’Amour J, Liu S, Hudson M, Chen C, Karimi MM, Lorincz MC (2015) An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nat Commun 6:6033. https://doi.org/10.1038/ncomms7033
Dahl JA, Jung I, Aanes H et al (2016) Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature 537:548–552
Lara-Astiaso D, Weiner A, Lorenzo-Vivas E et al (2014) Immunogenetics. Chromatin state dynamics during blood formation. Science 345:943–949
Adli M, Zhu J, Bernstein BE (2010) Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat Methods 7:615–618
Shankaranarayanan P, Mendoza-Parra M-A, Walia M, Wang L, Li N, Trindade LM, Gronemeyer H (2011) Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nat Methods 8:565–567
O’Neill LP, VerMilyea MD, Turner BM (2006) Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat Genet 38:835–841
Zwart W, Koornstra R, Wesseling J, Rutgers E, Linn S, Carroll JS (2013) A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples. BMC Genomics 14:232
Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE (2015) Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol 33:1165–1172
Skene PJ, Henikoff S (2017) An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6:e21856
Hainer SJ, Boskovic A, Rando OJ, Fazzio TG (2018) Profiling of pluripotency factors in individual stem cells and early embryos. bioRxiv 286351
Schmid M, Durussel T, Laemmli UK (2004) ChIC and ChEC; genomic mapping of chromatin proteins. Mol Cell 16:147–157
Schmidl C, Rendeiro AF, Sheffield NC, Bock C (2015) ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods 12:963–965
Stadhouders R, Vidal E, Serra F et al (2018) Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat Genet 50:238–249
Rodríguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, THN H, Ozadam H, Dekker J, Duboule D (2017) The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev 31:2264–2281
Akay A, Di Domenico T, Suen KM et al (2017) The helicase Aquarius/EMB-4 is required to overcome intronic barriers to allow nuclear RNAi pathways to heritably silence transcription. Dev Cell 42:241–255.e6
Bolte C, Flood HM, Ren X, Jagannathan S, Barski A, Kalin TV, Kalinichenko VV (2017) FOXF1 transcription factor promotes lung regeneration after partial pneumonectomy. Sci Rep 7:10690
Akhtar J, More P, Kulkarni A, Marini F, Kaiser W (2018) TAF-ChIP: An ultra-low input approach for genome wide chromatin immunoprecipitation assay. bioRxiv
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360
Zhang Y, Liu T, Meyer CA et al (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9:R137
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Kunowska, N., Chen, X. (2019). ChIPmentation for Low-Input Profiling of In Vivo Protein–DNA Interactions. In: Proserpio, V. (eds) Single Cell Methods. Methods in Molecular Biology, vol 1979. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9240-9_17
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DOI: https://doi.org/10.1007/978-1-4939-9240-9_17
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