Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.
Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.
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通用 NicE-Seq：一种简单快速的固定细胞染色质检测方法。
DOI：
10.1007/978-1-0716-2899-7_3
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Pradhan,Sriharsa
中科院分区：
文献类型：
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作者：
Chin,HangGyeong;Vishnu,UdayakumarS;Sun,Zhiyi;Ponnaluri,VKChaithanya;Zhang,Guoqiang;Xu,Shuang-Yong;Benoukraf,Touati;Cejas,Paloma;Spracklin,George;Estève,Pierre-Olivier;Long,HenryW;Pradhan,Sriharsa
全基因组可接近的染色质测序和鉴定能够破译染色质编码的表观遗传信息，揭示可接近的启动子、增强子、核小体定位、转录因子占用和其他染色体蛋白质结合。起始生物材料通常采用甲醛交联固定。在这里，我们描述了使用改进的缺口翻译方法从少量甲醛交联细胞中制备可访问的染色质文库，其中缺口酶切割一条DNA链，DNA聚合酶结合生物素偶联的dATP， dCTP和甲基-dCTP。一旦DNA被标记，它可以被分离用于NGS文库的准备。我们将这种方法称为通用NicE-seq （nick酶辅助测序）。我们还演示了一种单管方法，可以直接从低细胞数量制备NGS文库，而无需纯化DNA。此外，我们在FFPE组织切片样本上展示了通用的NicE-seq。
Genome-wide accessible chromatin sequencing and identification has enabled deciphering the epigenetic information encoded in chromatin, revealing accessible promoters, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding. The starting biological materials are often fixed using formaldehyde crosslinking. Here, we describe accessible chromatin library preparation from low numbers of formaldehyde-crosslinked cells using a modified nick translation method, where a nicking enzyme nicks one strand of DNA and DNA polymerase incorporates biotin-conjugated dATP, dCTP, and methyl-dCTP. Once the DNA is labeled, it can be isolated for NGS library preparation. We termed this method as universal NicE-seq (nicking enzyme-assisted sequencing). We also demonstrate a single tube method that enables direct NGS library preparation from low cell numbers without DNA purification. Furthermore, we demonstrated universal NicE-seq on FFPE tissue section sample.