ATAC-Seq、ChIP-Seq、Dnase-Seq、MNase-Seq、FAIRE-Seq整体的分析思路一致，找到富集区域，对富集区域进行功能分析。
• ChIP-Seq是揭示特定转录因子或蛋白复合物的结合区域，实际是研究DNA和蛋白质的相互作用，利用抗体将蛋白质和DNA一起富集，并对富集到的DNA进行测序。
• DNase-Seq、ATAC-Seq、FAIRE-Seq都是用来研究开放染色质区域。DNase-Seq是用的DNase I内切酶识别开放染色质区域，而ATAC-seq是用的Tn5转座酶，随后进行富集和扩增；FAIRE-Seq是先进行超声裂解，然后用酚-氯仿富集。
• MNase-Seq是用来鉴定核小体区域。

图片来源：https://cmb.i-learn.unito.it/mod/wiki/view.php?pageid=78

Figure 1. Overview of ChIP-seq, DNase-seq, ATAC-seq and MNase-seq experiments.

A genomic locus analyzed by complementary chromatin profiling experiments reveals different facets of chromatin structure; ChIP-seq reveals binding sites of specific transcription factors, DNase-seq and ATAC-seq reveal regions of open chromatin while MNase-seq identifies well-positioned nucleosomes. In ChIP-seq chromatin immunoprecipitation (ChIP) is used to extract DNA fragments that are bound to the target protein, either directly or via other proteins in a complex containing the target factor. In DNase-seq, chromatin is lightly digested by the DNase I endonuclease. Size selection is used to enrich for fragments that are produced in regions of chromatin where the DNA is highly sensitive to DNase I attack. ATAC-seq is an alternative to DNase-seq that uses an engineered Tn5 transposase to cleave DNA and to integrate primer DNA sequences into the cleaved genomic DNA. Micrococcal nuclease (MNase) is an endo-exo- nuclease that processively digests DNA until an obstruction such as a nucleosome is reached.[ ]