Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications.
Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications.
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DOI：
10.1038/s41467-021-22284-z
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发表时间：
2021-03-30
影响因子：
16.6
通讯作者：
Zhao Y
中科院分区：
文献类型：
--
作者：
Chen F;Bai M;Cao X;Xue J;Zhao Y;Wu N;Wang L;Zhang D;Zhao Y
探索细胞纳米环境中不同生物分子的空间组织和相互关系，对阐明生命的基本过程具有重要意义。然而，它在方法上仍然具有挑战性。在此，我们报告了一种分子识别机制——细胞大分子拴链DNA行走索引（Cell-TALKING）来探测含有不同染色质修饰的纳米环境。作为一个例子，我们描述了围绕一个组蛋白翻译后修饰（PTM）的三种DNA修饰的纳米环境。固定细胞中的这些DNA修饰用各自的DNA条形码探针标记，然后用DNA行走探针拴在PTM位点上。Cell-TALKING可以连续产生行走探针附近任何条形码探针的切割记录。在裂解的条形码探针上产生新的3 ' -OH末端，诱导DNA扩增用于下游检测。结合荧光成像，我们鉴定了各种组合染色质修饰，并研究了它们在细胞周期中的动态变化。我们还探讨了不同癌细胞系和临床标本中的纳米环境。原则上，使用高通量测序代替荧光成像可以检测包含数十种生物分子（如转录因子）的复杂细胞纳米环境。研究细胞纳米环境中生物分子的空间组织和关系对于理解基本的生物过程是必要的，但在方法上具有挑战性。在这里，作者报告了细胞大分子拴系DNA行走索引（cell - talking）来探测组蛋白翻译后修饰周围DNA修饰的纳米环境，并探索了不同癌细胞系和临床标本的纳米环境。
Exploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3’-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors. Investigation of spatial organization and relationships of biomolecules in cellular nanoenvironments is necessary to understand essential biological processes, but methodologically challenging. Here, the authors report cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments of DNA modifications around histone post-translational modifications, and explore the nanoenvironments in different cancer cell lines and clinical specimens.
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DOI：
10.1038/nrm4043
发表时间：
2015-09
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Du J;Johnson LM;Jacobsen SE;Patel DJ
通讯作者：
Patel DJ
影响因子：
5.3
作者：
de Beer MA;Giepmans BNG
通讯作者：
Giepmans BNG
影响因子：
46.9
作者：
Fredriksson, S;Gullberg, M;Landegren, U
通讯作者：
Landegren, U
影响因子：
7.4
作者：
Chen, Feng;Fan, Chunhai;Zhao, Yongxi
通讯作者：
Zhao, Yongxi
影响因子：
15
作者：
Liu, Chang;Cui, Xiaolong;He, Chuan
通讯作者：
He, Chuan