Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data
Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data
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改进的核小体定位算法 iNPS，可根据测序数据准确定位核小体
DOI：
10.1038/ncomms5909
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发表时间：
2014-09-01
影响因子：
16.6
通讯作者：
Han, Jing-Dong Jackie
中科院分区：
文献类型：
--
作者：
Chen, Weizhong;Liu, Yi;Han, Jing-Dong Jackie
全基因组核小体定位的准确确定可以为全球基因调控提供重要的见解。在这里，我们描述了一种改进的核小体定位算法-INPS-它的性能比广泛使用的NPS包要好得多。通过更精确地确定核小体边界，并根据局部MNase-SEQ信号合并或分离肩峰，INPS可以毫不含糊地检测到60%以上的核小体。检测到的核小体显示出更好的核小体‘宽度’和邻近的中心-中心距离分布，导致平均核小体轮廓的模式更清晰，相位更好，独立数据子集之间的一致性更高。INPS除了在根据形状对核小体进行分类以揭示其不同的生物学特性方面具有独特的优势外，还获得了比以前发表的方法更高的意义和更低的假阳性率。INPS在T细胞激活数据中的应用显示了更大的能力，以便于检测核小体重新定位，揭示激活过程中潜在的其他生物学特征。
Accurate determination of genome-wide nucleosome positioning can provide important insights into global gene regulation. Here, we describe the development of an improved nucleosome-positioning algorithm-iNPS-which achieves significantly better performance than the widely used NPS package. By determining nucleosome boundaries more precisely and merging or separating shoulder peaks based on local MNase-seq signals, iNPS can unambiguously detect 60% more nucleosomes. The detected nucleosomes display better nucleosome 'widths' and neighbouring centre-centre distance distributions, giving rise to sharper patterns and better phasing of average nucleosome profiles and higher consistency between independent data subsets. In addition to its unique advantage in classifying nucleosomes by shape to reveal their different biological properties, iNPS also achieves higher significance and lower false positive rates than previously published methods. The application of iNPS to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process.