Abstract
Imprinted genes are marked by parental allele specific DNA methylation and histone modifications which regulate their monoallelic expression. Chromatin immunoprecipitation (ChIP) is the technique of choice to characterize the histones associated with either maternal or paternal chromosomes. To study allele-specific chromatin composition at imprinted regions, the method has to be efficient to work on limiting amount of starting material, and specific enough to recognize one of the parental alleles. We optimized the commonly used ChIP technique for efficient recovery of one parental allele from small number of cells. We provide examples to show that this ChIP protocol can specifically distinguish between parental alleles in mouse embryo fibroblasts carrying maternal and paternal duplication of mouse distal Chr7 and also in normal mouse embryo fibroblasts carrying single nucleotide polymorphism at imprinted regions.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Ideraabdullah FY, Vigneau S, Bartolomei MS (2008) Genomic imprinting mechanisms in mammals. Mutat Res 647:77–85
Koerner MV, Barlow DP (2010) Genomic imprinting—an epigenetic gene-regulatory model. Curr Opin Genet Dev 20:164–170
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
Orlando V, Strutt H, Paro R (1997) Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11:205–214
Hebbes TR, Thorne AW, Crane-Robinson C (1988) A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J 7:1395–1402
McLaughlin KJ, Szabo P, Haegel H, Mann JR (1996) Mouse embryos with paternal duplication of an imprinted chromosome 7 region die at midgestation and lack placental spongiotrophoblast. Development 122:265–270
Singh P, Wu X, Lee DH et al (2011) Chromosome-wide analysis of parental allele-specific chromatin and DNA methylation. Mol Cell Biol 31:1757–1770
Singh P, Han L, Rivas GE et al (2010) Allele-specific H3K79 Di- versus trimethylation distinguishes opposite parental alleles at imprinted regions. Mol Cell Biol 30:2693–2707
Singh P, Cho J, Tsai SY, Rivas GE, Larson GP, Szabo PE (2010) Coordinated allele-specific histone acetylation at the differentially methylated regions of imprinted genes. Nucleic Acids Res 38:7974–7990
Lee DH, Singh P, Tsai SY et al (2010) CTCF-dependent chromatin bias constitutes transient epigenetic memory of the mother at the H19-Igf2 imprinting control region in prospermatogonia. PLoS Genet 6:e1001224
Gaillard C, Strauss F (1990) Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucleic Acids Res 18:378
Acknowledgments
We thank Jeff Mann for the MatDup.dist7 and PatDup.dist7 MEFs, Li Han for her work on the initial phases of this project, and Diana Tran for her comments on the manuscript. This work was supported by a Public Health Service grant (GM064378) from the National Institute of General Medicine to P.E.S.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Singh, P., Szabó, P.E. (2012). Chromatin Immunoprecipitation to Characterize the Epigenetic Profiles of Imprinted Domains. In: Engel, N. (eds) Genomic Imprinting. Methods in Molecular Biology, vol 925. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-011-3_10
Download citation
DOI: https://doi.org/10.1007/978-1-62703-011-3_10
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-010-6
Online ISBN: 978-1-62703-011-3
eBook Packages: Springer Protocols