NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells.
NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells.
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NicE-viewSeq：一种用于检测固定细胞中可接近染色质的综合可视化和基因组学方法。
DOI：
10.1007/978-1-0716-2899-7_16
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Pradhan,Sriharsa
中科院分区：
文献类型：
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作者：
Estève,Pierre-Olivier;Vishnu,UdayakumarS;Chin,HangGyeong;Pradhan,Sriharsa
描述了一种新的全基因组可接近的染色质可视化，定量和测序方法，该方法允许在哺乳动物细胞中可接近的染色质的原位荧光可视化和测序。细胞通过甲醛交联固定，并使用改进的刻痕翻译方法进行处理，其中刻痕酶刻痕一条DNA链，DNA聚合酶结合生物素偶联dCTP， 5-甲基-dCTP，荧光素-12- datp或德克萨斯红-5- datp， dGTP和dTTP。这允许可访问的染色质DNA被标记为可视化和在头NGS文库制备。该技术允许细胞水平染色质可及性定量和染色质表观遗传信息的基因组分析，特别是可及性启动子、增强子、核小体定位、转录因子占用和其他染色体蛋白结合。
A novel genome-wide accessible chromatin visualization, quantitation, and sequencing method is described, which allows in situ fluorescence visualization and sequencing of the accessible chromatin in the mammalian cell. The cells are fixed by formaldehyde crosslinking, and processed using a modified nick translation method, where a nicking enzyme nicks one strand of DNA, and DNA polymerase incorporates biotin-conjugated dCTP, 5-methyl-dCTP, Fluorescein-12-dATP or Texas Red-5-dATP, dGTP, and dTTP. This allows accessible chromatin DNA to be labeled for visualization and on bead NGS library preparation. This technology allows cellular level chromatin accessibility quantification and genomic analysis of the epigenetic information in the chromatin, particularly accessible promoter, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding.