The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications.

Publisher Summary Chromatin immunoprecipitation (IP) experiments use antibodies to immunoprecipitate a protein of interest and associated DNA from a solubilized chromatin preparation. Specialized antibodies can be used to enrich for DNA associated with histones that exhibit specific post-translational modifications. A considerable number of antibodies that recognize histones acetylated, methylated, or phosphorylated at specific residues are developed, and many are commercially available. Chromatin IP experiments typically assess whether a particular gene, gene promoter, or genomic region is enriched in the IP sample relative to a whole cell extract (WCE) control. For example, quantitative polymerase chain reaction (PCR) using pre-selected primer pairs can be used to compare the representation of specific DNA species in the IP and WCE. Although several regions can be queried simultaneously, these conventional studies are limited to a subset of genes or regions chosen by the investigator. Methods for analysis of histone modifications genome-wide in yeast are developed and applied toward a limited subset of site-specific acetylation and methylation marks. Furthermore, the development of microarrays able to query regulatory regions of the human genome should allow for global analyses of histone modifications in higher organisms.

[1]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[2]  L. Wodicka,et al.  Genome-wide expression monitoring in Saccharomyces cerevisiae , 1997, Nature Biotechnology.

[3]  T. Hughes,et al.  Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. , 2000, Science.

[4]  G. Church,et al.  Systematic determination of genetic network architecture , 1999, Nature Genetics.

[5]  S. Schreiber,et al.  Development and validation of a T7 based linear amplification for genomic DNA , 2003, BMC Genomics.

[6]  J. Rowley,et al.  A method for the rapid sequence-independent amplification of microdissected chromosomal material. , 1992, Genomics.

[7]  David Botstein,et al.  Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association , 2001, Nature Genetics.

[8]  D. Botstein,et al.  Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF , 2001, Nature.

[9]  M. Grunstein,et al.  Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. , 1999, Methods in enzymology.

[10]  Tim Hui-Ming Huang,et al.  Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. , 2002, Genes & development.

[11]  A. Gasch.  Yeast genomic expression studies using DNA microarrays. , 2002, Methods in enzymology.

[12]  C. Allis,et al.  In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. , 1999, Methods.

[13]  Michael Snyder,et al.  ChIP-chip: a genomic approach for identifying transcription factor binding sites. , 2002, Methods in enzymology.

[14]  T. Volkert,et al.  E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. , 2002, Genes & development.

[15]  Alexander Varshavsky,et al.  Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene , 1988, Cell.

[16]  S. Schreiber,et al.  Genomewide studies of histone deacetylase function in yeast. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Ioannis Xenarios,et al.  Microarray Deacetylation Maps Determine Genome-Wide Functions for Yeast Histone Deacetylases , 2002, Cell.

[18]  Arkady B. Khodursky,et al.  Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[19]  J. Broach,et al.  Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. , 1993, Genes & development.

[20]  R. Paro,et al.  Analysis of chromatin structure by in vivo formaldehyde cross-linking. , 1997, Methods.

[21]  David Botstein,et al.  The Stanford Microarray Database: data access and quality assessment tools , 2003, Nucleic Acids Res..

[22]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[23]  Anthony C. Bishop,et al.  Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response , 2001, Proceedings of the National Academy of Sciences of the United States of America.