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ATAC-Seq、ChIP-Seq、Dnase-Seq、MNase-Seq、FAIRE-Seq整體的分析思路一致，找到富集區(qū)域，對富集區(qū)域進行功能分析。
? ChIP-Seq是揭示特定轉錄因子或蛋白復合物的結合區(qū)域，實際是研究DNA和蛋白質的相互作用，利用抗體將蛋白質和DNA一起富集，并對富集到的DNA進行測序。
? DNase-Seq、ATAC-Seq、FAIRE-Seq都是用來研究開放染色質區(qū)域。DNase-Seq是用的DNase I內(nèi)切酶識別開放染色質區(qū)域，而ATAC-seq是用的Tn5轉座酶，隨后進行富集和擴增；FAIRE-Seq是先進行超聲裂解，然后用酚-氯仿富集。
? MNase-Seq是用來鑒定核小體區(qū)域。

圖片來源：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.[ ]