Abstract
ChIP-seq is a powerful technique that allows the detection of chromatin localization for proteins and epigenetic modifications. However, conventional ChIP-seq usually requires millions of cells. This becomes a daunting task for applications in which only limited experimental materials are available. For example, during mammalian embryo development, the epigenomes undergo drastic reprogramming which endows a fertilized egg with the potential to develop into the whole body. Low-input ChIP-seq methods would be instrumental to help decipher molecular mechanisms underlying such epigenetic reprogramming. Here we describe an optimized ChIP-seq method—STAR (Small-scale TELP-Assisted Rapid) ChIP-seq—that allows the detection of histone modifications using only a few hundred cells. This method is proven to be robust in epigenomic profiling in both embryos and cultured cells.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837. https://doi.org/10.1016/j.cell.2007.05.009
Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502. https://doi.org/10.1126/science.1141319
Xu Q, Xie W (2017) Epigenome in early mammalian development: inheritance, reprogramming and establishment. Trends Cell Biol. https://doi.org/10.1016/j.tcb.2017.10.008
Zoghbi HY, Beaudet AL (2016) Epigenetics and human disease. Cold Spring Harb Perspect Biol 8:a019497. https://doi.org/10.1101/cshperspect.a019497
Zhang B, Zheng H, Huang B et al (2016) Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. Nature 537:553–557. https://doi.org/10.1038/nature19361
Solter D, Knowles BB (1975) Immunosurgery of mouse blastocyst. Proc Natl Acad Sci U S A 72:5099–5102. https://doi.org/10.1073/pnas.72.12.5099
Boroviak T, Loos R, Bertone P et al (2014) The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification. Nat Cell Biol 16:513–525. https://doi.org/10.1038/ncb2965
Gilfillan GD, Hughes T, Sheng Y et al (2012) Limitations and possibilities of low cell number ChIP-seq. BMC Genomics 13:645. https://doi.org/10.1186/1471-2164-13-645
O’Neill LP, Turner BM (2003) Immunoprecipitation of native chromatin: NChIP. Methods 31:76–82. https://doi.org/10.1016/s1046-2023(03)00090-2
Peng X, Wu J, Brunmeir R et al (2015) TELP, a sensitive and versatile library construction method for next-generation sequencing. Nucleic Acids Res 43:e35. https://doi.org/10.1093/nar/gku818
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Zhang, B., Peng, X., Xu, F., Xie, W. (2021). Tracking Histone Modifications in Embryos and Low-Input Samples Using Ultrasensitive STAR ChIP-Seq. In: Ancelin, K., Borensztein, M. (eds) Epigenetic Reprogramming During Mouse Embryogenesis. Methods in Molecular Biology, vol 2214. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0958-3_16
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0958-3_16
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0957-6
Online ISBN: 978-1-0716-0958-3
eBook Packages: Springer Protocols