Genomic methods in profiling DNA accessibility and factor localization
Genomic methods in profiling DNA accessibility and factor localization
复制标题
DOI：
10.1007/s10577-019-09619-9
复制
发表时间：
2019-11-27
影响因子：
2.6
通讯作者：
Hainer, Sarah J.
中科院分区：
文献类型：
--
作者：
Klein, David C.;Hainer, Sarah J.
下一代测序技术的最新进展和随之而来的成本降低导致了检测DNA可及性和染色质全基因组蛋白质定位的技术的爆炸。通常，染色质的可接近区域允许因子结合，因此是基因表达调控的热点;相反，被组蛋白高度占据的基因组区域不允许因子结合，并且不太可能是活性调控区域。鉴定差异可及性区域可用于揭示推定的基因调控区域，如增强子、启动子和绝缘子。此外，DNA结合蛋白，例如优先结合某些DNA序列的转录因子和形成核小体核心的组蛋白，在所有DNA模板化过程中发挥重要作用。因此，确定染色质结合蛋白的基因组定位在确定功能作用、对因子结合重要的序列基序和控制基因表达的调控网络中是必不可少的。在这篇综述中，我们讨论了用于确定DNA可及性和核小体定位的技术（DNase-seq，FAIRE-seq，MNase-seq和ATAC-seq）以及用于检测和功能表征染色质结合蛋白的技术（ChIP-seq，DamID和CUT&RUN）。这些方法已被优化到不同程度的分辨率，特异性和易用性。在这里，我们概述了这些技术的优点和缺点，他们的一般协议，并简要讨论他们的发展。总之，这些互补的方法提供了染色质结构和功能基因调控的无与伦比的观点。
Recent advancements in next-generation sequencing technologies and accompanying reductions in cost have led to an explosion of techniques to examine DNA accessibility and protein localization on chromatin genome-wide. Generally, accessible regions of chromatin are permissive for factor binding and are therefore hotspots for regulation of gene expression; conversely, genomic regions that are highly occupied by histone proteins are not permissive for factor binding and are less likely to be active regulatory regions. Identifying regions of differential accessibility can be useful to uncover putative gene regulatory regions, such as enhancers, promoters, and insulators. In addition, DNA-binding proteins, such as transcription factors that preferentially bind certain DNA sequences and histone proteins that form the core of the nucleosome, play essential roles in all DNA-templated processes. Determining the genomic localization of chromatin-bound proteins is therefore essential in determining functional roles, sequence motifs important for factor binding, and regulatory networks controlling gene expression. In this review, we discuss techniques for determining DNA accessibility and nucleosome positioning (DNase-seq, FAIRE-seq, MNase-seq, and ATAC-seq) and techniques for detecting and functionally characterizing chromatin-bound proteins (ChIP-seq, DamID, and CUT&RUN). These methods have been optimized to varying degrees of resolution, specificity, and ease of use. Here, we outline some advantages and disadvantages of these techniques, their general protocols, and a brief discussion of their development. Together, these complimentary approaches have provided an unparalleled view of chromatin architecture and functional gene regulation.