Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography

Nature Protocols

Volumn 3, Issue 3, 2008, Pages 398-409

  Brand, Marjorie ^a,b   Rampalli, Shravanti ^a   Chaturvedi, Chandra Prakash ^a   Dilworth, F Jeffrey ^a,b  

^a OTTAWA HOSPITAL RESEARCH INSTITUTE   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE; HYDROXYAPATITE; PROTEIN;

ANIMAL CELL; ARTICLE; CELL CULTURE; CELL NUCLEUS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMATOGRAPHY; CLINICAL PROTOCOL; CONTROLLED STUDY; DNA DETERMINATION; DNA MODIFICATION; EPIGENETICS; GENE LOCUS; GENOMICS; ISOLATION PROCEDURE; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOSOME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STEREOSPECIFICITY;

CHROMATIN IMMUNOPRECIPITATION; CHROMATOGRAPHY; DURAPATITE; EPIGENESIS, GENETIC; EPITOPES; NUCLEOSOMES; POLYMERASE CHAIN REACTION;

EID: 40649089223     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2008.8     Document Type: Article

References (22)

1. Hebbes, T.R., Thorne, A.W. & Crane-Robinson, C. A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J. 7, 1395-1402 (1988).
2. O'Neill, L.P. & Turner, B.M. Immunoprecipitation of native chromatin: NChIP. Methods 31, 76-82 (2003).
3. O'Neill, L.P., VerMilyea, M.D. & Turner, B.M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat. Genet. 38, 835-841 (2006).
4. Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853-862 (2005).
5. Dorbic, T. & Wittig, B. Isolation of oligonucleosomes from active chromatin using HMG17-specific monoclonal antibodies. Nucleic Acids Res. 14, 3363-3376 (1986).
6. Solomon, M.J., Larsen, P.L. & Varshavsky, A. Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene. Cell 53, 937-947 (1988).
7. Orlando, V., Strutt, H. & Paro, R. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11, 205-214 (1997).
8. Dhalluin, C. et al. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399, 491-496 (1999).
9. Santos-Rosa, H. et al. Methylation of histone H3 K4 mediates association of the isw1p ATPase with chromatin. Mol. Cell 12 1325-1332 (2003).
10. Wysocka, J. et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442, 86-90 (2006).
11. Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41-45 (2000).
12. Ruthenburg, A.J., Allis, C.D. & Wysocka, J. Methylation of lysine 4 on histone H3: Intricacy of writing and reading a single epigenetic mark. Mol. Cell 25, 15-30 (2007).
13. Vermeulen, M. et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58-69 (2007).
14. Bernardi, G. Chromatography of nucleic acids on hydroxyapatite. Nature 206, 779-783 (1965).
15. Thorne, A.W., Cary, P.D. & Crane-Robinson, C. Extraction and separation of core histone and non-histone chromosomal proteins. in Chromatin: A Practical Approach Vol. 9 (ed. Gould, H.) 35-57 (Oxford University Press, Oxford, 1998).
16. Rampalli, S. et al. p38 MAPK signaling regulates recruitment of Ash2L-containing methyltransferase complexes to specific genes during differentiation. Nat. Struct. Mol. Biol. 14, 1150-1156 (2007).
17. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).
18. Lee, T.I., Johnstone, S.E. & Young, R.A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 1, 729-748 (2006).
19. MikkeLsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007).
20. Hager, G.L. & Fragoso, G. Analysis of nucleosome positioning in mammalian cells. Methods Enzymol. 304, 626-638 (1999).
21. Lomvardas, S. & Thanos, D. Modifying gene expression programs by altering core promoter chromatin architecture. Cell 110, 261-271 (2002).
22. Sambrook, J. & Russell, D.W. Molecular Cloning: A Laboratory Manual (Cold Spring Laboratory Press, New York, 2001).