Extensive Chromatin Fragmentation Improves Enrichment of Protein Binding Sites in Chromatin Immunoprecipitation Experiments

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Extensive Chromatin Fragmentation Improves Enrichment of Protein Binding Sites in Chromatin Immunoprecipitation Experiments

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Title: Extensive Chromatin Fragmentation Improves Enrichment of Protein Binding Sites in Chromatin Immunoprecipitation Experiments
Author: Fan, Xiaochun; Lamarre-Vincent, Nathan; Wang, Jian; Struhl, Kevin

Note: Order does not necessarily reflect citation order of authors.

Citation: Fan, Xiaochun, Nathan Lamarre-Vincent, Qian Wang, and Kevin Struhl. 2008. Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucleic Acids Research 36(19): e125.
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Abstract: Extensive sonication of formaldehyde-crosslinked chromatin can generate DNA fragments averaging 200 bp in length (range 75–300 bp). Fragmentation is largely random with respect to genomic region and nucleosome position. ChIP experiments employing such extensively fragmented samples show 2- to 4-fold increased enrichment of protein binding sites over control genomic regions, when compared to samples sonicated to a more conventional size range (300–500 bp). The basis of improved fold enrichments is that immunoprecipitation of protein-bound regions is unaffected by fragment size, whereas immunoprecipitation of control genomic regions decreases progressively along with reduced fragment size due to fewer nonspecific binding sites. The use of extensively sonicated samples improves mapping of protein binding sites, and it extends the dynamic range for quantitative measurements of histone density. We show that many yeast promoter regions are virtually devoid of histones.
Published Version: doi:10.1093/nar/gkn535
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577354/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:8255740

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