Impact of chromatin structures on DNA processing for genomic analyses.
Impact of chromatin structures on DNA processing for genomic analyses.
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DOI：
10.1371/journal.pone.0006700
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发表时间：
2009-08-20
期刊：
影响因子：
3.7
通讯作者：
Eisen MB
中科院分区：
文献类型：
--
作者：
Teytelman L;Ozaydin B;Zill O;Lefrançois P;Snyder M;Rine J;Eisen MB
染色质对DNA的重组、修复、复制和进化有影响。在此我们报道，染色质结构也会以扭曲染色质免疫沉淀（ChIP）实验结果的方式影响实验室中的DNA操作。我们最初在酿酒酵母（Saccharomyces cerevisiae）的HMR位点发现了这种效应，在该位点我们发现，相对于常染色质，沉默的染色质难以被剪切。利用来自ChIP - Seq研究的输入样本，我们在酵母基因组的异染色质部分检测到了类似的偏差。我们还在端粒、蛋白质结合位点和基因处观察到了显著的与染色质相关的效应，这反映在输入 - Seq覆盖度的变化上。对候选区域的实验测试表明，染色质在一些位点影响剪切，并且染色质还可能导致制备样本中DNA水平的富集或减少，这与剪切效应无关。我们的结果表明，依赖于染色质免疫沉淀的分析将因包装成不同染色质结构的区域之间的内在差异而产生偏差——这种偏差到目前为止在很大程度上被忽视了。这些结果确定了这种偏差在全基因组范围内的普遍性，并表明这种偏差可用于检测基因组中染色质结构的差异。
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.
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