Ponnaluri V K Chaithanya, Zhang Guoqiang, Estève Pierre-Olivier, Spracklin George, Sian Stephanie, Xu Shuang-Yong, Benoukraf Touati, Pradhan Sriharsa
New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
Genome Biol. 2017 Jun 28;18(1):122. doi: 10.1186/s13059-017-1247-6.
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.
开放染色质分析整合了来自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测序的方法更适用于天然状态或高细胞数量的样本。在此，我们描述了NicE-seq（切口酶辅助测序），用于对天然和甲醛固定细胞进行高分辨率开放染色质分析。NicE-seq以单核苷酸分辨率捕获并揭示开放染色质位点（OCS）和转录因子占据情况，在低测序负担下与DNase超敏位点和ATAC-seq位点一致。OCS与RNA聚合酶II占据情况和活性染色质标记相关，同时呈现出与CpG甲基化相反的模式。地西他滨介导的HCT116细胞低甲基化显示出更多的OCS。
