Chromatin immunoprecipitation,

Orlando, V. (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 3, 99-104. 

Das PM, Ramachandran K, vanWert J, Singal R. 2004. Chromatin immunoprecipitation assay. Biotechniques 37 961-969. 

The association between a histone tail modification and a particular functional state of chromatin, came with the demonstration that transcriptionally active chromatin fractions were enriched in acetylated histones, firstly by biochemical co-fractionationation ([8,9] and references therein) and then by Chromatin ImmunoPrecipitation, ChIP [10]. Subsequently, regions of transcriptionally silent constitutive and facultative heterochromatin, were shown, by immunofluorescence microscopy, to be under-acetylated [11,12]. This supported the idea that acetylation of the histone tails, with the associated loss of positive charge and reduction in DNA-binding constant, somehow caused chromatin to become more open (or less condensed ) and thereby more conducive to transcription. While this is likely to be an important contributory factor, it has now become clear that the... 

Finally, the deacetylation of histones in methylated gene regions may be selective with respect to the histone affected. Chromatin immunoprecipitation analysis of the histone acetylation status of proviral sequences targeted to defined genome loci in MEL cells showed that the in vitro methylated proviral sequences that were transcriptionally silent in vivo, were hypoacetylated only with respect to histone H3 in contrast, the acetylation status of histone H4 was comparable on the methylated and unmethylated provirus [78]. Moreover, the H3 acetylation status correlated closely with the location of methylated CpGs along the proviral sequence. 

Chromatin Immunoprecipitation as a Powerful Method to Study Chromatin... 

The combination of chromatin immunoprecipitation with DNA microarrays allows the genome-wide analysis of the distribution of an antigen. The immunoprecipitated DNA is quantitatively amplified, labeled and used to probe DNA microarrays. In principle ChIP-on-chip methods can be divided into two basic groups, depending on the content of the microarrays which are used (i) microarrays/promoter tiling arrays and (ii) genome tiling arrays. 

Immunoprecipitation can be used to study protein-DNA interactions (Kuo and Allis 1999). For instance, the basic chromatin immunoprecipitation technique is remarkably versatile and has now been used in a wide range of cell types, including budding yeast, fly, and human cells. This technique has been successfully employed to map the boundaries of specifically modified (e.g., acetylated) histones along target... 

Buck MJ, Lieb JD. ChIP-chip Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004 83(3) 349-360. 

Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 2002 16(2) 235-244. 

Weinmann AS, Farnham PJ. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 2002 26(1) 37 17. 

---