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高速原子力显微镜成像揭示了黏连蛋白-NIPBL 介导的 DNA 捕获和环挤出动力学。

High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL.

机构信息

Physics Department, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA.

Department of BioSciences, Rice University, Houston, Texas, USA.

出版信息

J Biol Chem. 2023 Nov;299(11):105296. doi: 10.1016/j.jbc.2023.105296. Epub 2023 Sep 28.

Abstract

3D chromatin organization plays a critical role in regulating gene expression, DNA replication, recombination, and repair. While initially discovered for its role in sister chromatid cohesion, emerging evidence suggests that the cohesin complex (SMC1, SMC3, RAD21, and SA1/SA2), facilitated by NIPBL, mediates topologically associating domains and chromatin loops through DNA loop extrusion. However, information on how conformational changes of cohesin-NIPBL drive its loading onto DNA, initiation, and growth of DNA loops is still lacking. In this study, high-speed atomic force microscopy imaging reveals that cohesin-NIPBL captures DNA through arm extension, assisted by feet (shorter protrusions), and followed by transfer of DNA to its lower compartment (SMC heads, RAD21, SA1, and NIPBL). While binding at the lower compartment, arm extension leads to the capture of a second DNA segment and the initiation of a DNA loop that is independent of ATP hydrolysis. The feet are likely contributed by the C-terminal domains of SA1 and NIPBL and can transiently bind to DNA to facilitate the loading of the cohesin complex onto DNA. Furthermore, high-speed atomic force microscopy imaging reveals distinct forward and reverse DNA loop extrusion steps by cohesin-NIPBL. These results advance our understanding of cohesin by establishing direct experimental evidence for a multistep DNA-binding mechanism mediated by dynamic protein conformational changes.

摘要

三维染色质组织在调节基因表达、DNA 复制、重组和修复中起着关键作用。虽然最初发现其在姐妹染色单体黏合中发挥作用,但新出现的证据表明,黏合复合物(SMC1、SMC3、RAD21 和 SA1/SA2)通过 NIPBL 介导拓扑关联域和染色质环,通过 DNA 环挤出。然而,关于黏合蛋白-NIPBL 的构象变化如何驱动其加载到 DNA 上、DNA 环的起始和生长的信息仍然缺乏。在这项研究中,高速原子力显微镜成像显示,黏合蛋白-NIPBL 通过臂延伸捕获 DNA,由脚(较短的突起)辅助,并随后将 DNA 转移到其下部隔室(SMC 头部、RAD21、SA1 和 NIPBL)。在结合到下部隔室时,臂延伸导致捕获第二个 DNA 片段并启动独立于 ATP 水解的 DNA 环。脚可能由 SA1 和 NIPBL 的 C 端结构域贡献,并且可以暂时结合 DNA 以促进黏合复合物加载到 DNA 上。此外,高速原子力显微镜成像揭示了黏合蛋白-NIPBL 通过独特的正向和反向 DNA 环挤出步骤。这些结果通过建立由动态蛋白构象变化介导的多步 DNA 结合机制的直接实验证据,推进了我们对黏合蛋白的理解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/34bf/10656236/e26ed15a7bd7/gr1.jpg

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