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Chapter 5: Chromatin Immunoprecipitation of Protein Complexes—References

Bellard M., Dretzen G., Giangrande A., and Ramain P. 1989. Nuclease digestion of transcriptionally active chromatin. Methods Enzymol. 170: 317–346.

Boyd K.E. and Farnham P.J. 1999. Coexamination of site-specific transcription factor binding and promoter activity in living cells. Mol. Cell. Biol. 19: 8393–8399.

Cao R., Wang L., Wang H., Xia L., Erdjument-Bromage H., Tempst P., Jones R.S., and Zhang Y. 2002. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298: 1039–1043.

Cawley S., Bekiranov S., Ng H.H., Kapranov P., Sekinger E.A., Kampa D., Piccolboni A., Sementchenko V., Cheng J., Williams A.J., Wheeler R., Wong B., Drenkow J., Yamanaka M., Patel S., Brubaker S., Tammana H., Helt G., Struhl K., and Gingeras T.R. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499–509.

Chua Y.L., Mott E., Brown A.P., MacLean D., and Gray J.C. 2004. Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. Plant J. 37: 789–800.

Church G.M. and Gilbert W. 1984. Genomic sequencing. Proc. Natl. Acad. Sci. 81: 1991–1995.

Cirillo L.A. and Zaret K.S. 2004. Preparation of defined mononucleosomes, dinucleosomes, and nucleosome arrays in vitro and analysis of transcription factor binding. Methods Enzymol. 375: 131–158.

Harlow E. and Lane D. 1988. Antibodies: A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

Litt M.D., Simpson M., Recillas-Targa F., Prioleau M.N., and Felsenfeld G. 2001. Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci. EMBO J. 20: 2224–2235.

Oberley M.J. and Farnham P.J. 2003. Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol. 371: 577–596.

Oberley M.J., Tsao J., Yau P., and Farnham P.J. 2004. High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol. 376: 315–334.

O'Neill L.P. and Turner B.M. 2003. Immunoprecipitation of native chromatin: NChIP. Methods 31: 76–82.

Orlando V. 2000. Mapping chromosomal proteins in vivo by formaldehyde-cross-linked-chromatin immunoprecipitation. Trends Biochem. Sci. 25: 99–104.

Orlando V., Strutt H., and Paro R. 1997. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11: 205–214.

Orlando V., Jane E.P., Chinwalla V., Harte P.J., and Paro R. 1998. Binding of trithorax and Polycomb proteins to the bithorax complex: Dynamic changes during early Drosophila embryogenesis. EMBO J. 17: 5141–5150.

Rychlik W. and Rhoads R.E. 1989. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in-vitro amplification of DNA. Nucleic Acids Res. 17: 8543–8551.

Sambrook J. and Russell D. 2001. Molecular cloning: A laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Strahl-Bolsinger S., Hecht A., Luo K., and Grunstein M. 1997. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11: 83–93.

Weinmann A.S., Bartley S.M., Zhang T., Zhang M.Q., and Farnham P.J. 2001. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol. Cell. Biol. 21: 6820–6832.

Weinmann A.S., Yan P.S., Oberley M.J., Huang T.H. and Farnham P.J. 2002. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 16: 235–244.

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