title: Impact of chromatin structures on DNA processing for genomic analyses.
abstract: Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP) experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome.
authors.affiliation: Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, USA.
authors.forename: Leonid
authors.initials: L
authors.lastname: Teytelman
authors.forename: Bilge
authors.initials: B
authors.lastname: Ozaydin
authors.forename: Oliver
authors.initials: O
authors.lastname: Zill
authors.forename: Philippe
authors.initials: P
authors.lastname: Lefrançois
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Jasper
authors.initials: J
authors.lastname: Rine
authors.forename: Michael B
authors.initials: MB
authors.lastname: Eisen
mesh_terms: D001482:Base Composition; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry*; D047369:Chromatin Immunoprecipitation; D018983:DNA Footprinting; D004271:DNA, Fungal / Q000235:genetics*; D016681:Genome, Fungal; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D016615:Telomere; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D004271:DNA, Fungal; D014157:Transcription Factors
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