Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.
Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.
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DOI：
10.1093/bib/bbw023
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发表时间：
2017-03-01
影响因子：
9.5
通讯作者：
Shirahige K
中科院分区：
文献类型：
--
作者：
Nakato R;Shirahige K
染色质免疫沉淀和测序(CHIP-SEQ)分析可以检测整个基因组中的蛋白质/DNA结合和组蛋白修饰位点。测序技术和分析的最新进展使我们能够同时比较数百个样本；这种大规模分析有可能揭示调控元件的高维相互关系水平，并注释新的功能基因组区域从头开始。由于许多实验考虑因素与芯片序列分析中方法的选择有关，因此实验的总体设计和质量管理至关重要。这篇综述提供了芯片序列分析的计算和样品制备的指导原则，强调了每一步最先进的程序的有效性和局限性。我们还讨论了单细胞分析的最新挑战，这将鼓励这一领域的新时代。
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field.