NicE-seq: high resolution open chromatin profiling.
NicE-seq: high resolution open chromatin profiling.
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DOI：
10.1186/s13059-017-1247-6
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发表时间：
2017-06-28
期刊：
影响因子：
12.3
通讯作者：
Pradhan S
中科院分区：
文献类型：
--
作者：
Ponnaluri VKC;Zhang G;Estève PO;Spracklin G;Sian S;Xu SY;Benoukraf T;Pradhan S
开放染色质图谱整合了不同调控元件的信息，以揭示转录活跃的基因组。基于Tn5转座酶和DNase I测序的方法更倾向于天然或高细胞数量。在这里，我们描述了NICE-SEQ(缺口酶辅助测序)，用于在天然细胞和甲醛固定细胞上进行高分辨率开放染色质分析。NICE-SEQ捕获并揭示了单核苷酸分辨率下的开放染色质位点(OCS)和转录因子占有率，与DNA酶超敏和ATAC-SEQ位点一致，测序负担较低。OCS与RNA聚合酶II的占有率和活性染色质标记相关，同时显示出与CpG甲基化相反的模式。地西他滨介导的HCT116低甲基化表现出更多的OCS。本文的在线版本(doi：10.1186/s13059-017-1247-6)包含补充材料，授权用户可以使用。
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin profiling on both native and formaldehyde-fixed cells. NicE-seq captures and reveals open chromatin sites (OCSs) and transcription factor occupancy at single nucleotide resolution, coincident with DNase hypersensitive and ATAC-seq sites at a low sequencing burden. OCSs correlate with RNA polymerase II occupancy and active chromatin marks, while displaying a contrasting pattern to CpG methylation. Decitabine-mediated hypomethylation of HCT116 displays higher numbers of OCSs. The online version of this article (doi:10.1186/s13059-017-1247-6) contains supplementary material, which is available to authorized users.