Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.
Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.
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DOI：
10.1371/journal.pone.0069853
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Hubbard TJ
中科院分区：
文献类型：
--
作者：
Koohy H;Down TA;Hubbard TJ
DNA酶I是一种以强烈依赖于其染色质环境的速率切割双链体DNA的酶。结合高通量测序（HTS）技术，它可以用来推断开放染色质区域的全基因组景观。使用这种技术，系统地鉴定每种细胞类型的数十万个DNA酶I超敏位点（DHS）是可能的，这反过来又有助于精确地描绘基因组调控区室。然而，迄今为止，对影响这一数据的可能偏差的调查相对较少。我们报告了一个显着程度的序列偏好跨越网站的DNA酶I在一些已发表的数据集。目前使用的两种主要方案各自显示出不同的模式，但对于给定的方案，序列特异性的模式似乎是相当一致的。这些模式与在其他类型的HTS数据集中看到的偏差有很大不同，并且在某些情况下，最受约束的位置位于测序片段之外，这意味着这种约束必须与消化过程有关，而不是与文库制备或测序期间发生的事件有关。DNA酶I是一种序列特异性酶，其特异性可能取决于实验条件。现有的用于鉴定开放染色质区域的管道没有考虑这种序列特异性。在解释DNase I结果时必须小心，特别是在查看读数的精确位置时。未来的研究可能能够通过补偿序列偏差来提高染色质状态测量的灵敏度和精确度。
DNase I is an enzyme which cuts duplex DNA at a rate that depends strongly upon its chromatin environment. In combination with high-throughput sequencing (HTS) technology, it can be used to infer genome-wide landscapes of open chromatin regions. Using this technology, systematic identification of hundreds of thousands of DNase I hypersensitive sites (DHS) per cell type has been possible, and this in turn has helped to precisely delineate genomic regulatory compartments. However, to date there has been relatively little investigation into possible biases affecting this data. We report a significant degree of sequence preference spanning sites cut by DNase I in a number of published data sets. The two major protocols in current use each show a different pattern, but for a given protocol the pattern of sequence specificity seems to be quite consistent. The patterns are substantially different from biases seen in other types of HTS data sets, and in some cases the most constrained position lies outside the sequenced fragment, implying that this constraint must relate to the digestion process rather than events occurring during library preparation or sequencing. DNase I is a sequence-specific enzyme, with a specificity that may depend on experimental conditions. This sequence specificity is not taken into account by existing pipelines for identifying open chromatin regions. Care must be taken when interpreting DNase I results, especially when looking at the precise locations of the reads. Future studies may be able to improve the sensitivity and precision of chromatin state measurement by compensating for sequence bias.
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