Heterogeneous fluid-like movements of chromatin and their implications to transcription

被引：18
作者：
Ashwin S.S. [1 ]
Maeshima K. [2 ,3 ]
Sasai M. [1 ]
机构：
[1] Department of Applied Physics, Nagoya University, Nagoya
[2] National Institute of Genetics, Mishima, 411-8540, Shizuoka
[3] Department of Genetics, SOKENDAI, Mishima, 411-8540, Shizuoka
来源：
Biophysical Reviews | 2020年 / 12卷 / 2期
基金：
日本学术振兴会;
关键词：
Cohesin; Liquid droplets; Live-cell imaging; Nucleosome; RNA polymerase II; Statistical analyses; Transcription factory;
D O I：
10.1007/s12551-020-00675-8
中图分类号：
学科分类号：
摘要：
Eukaryotic chromatin is a complex of genome DNA and associated proteins, and its structure and dynamics play a crucial role in regulating DNA functions. Chromatin takes rather irregular structures in the nucleus and exhibits heterogeneous sub-diffusive movements as polymers fluctuating in a fluid state. Using genome-wide single-nucleosome tracking data, heterogeneity of movements was statistically analyzed, which categorized chromatin into two types: slow chromatin that moves under structurally constrained environments and fast chromatin that moves with less constraints. Interactions of chromatin to various protein factors determine the motional constraints. For example, loss of the cohesin complex that bundles the chromatin chains reduces the motional constraints and increases the population of fast chromatin. Another example is the transcriptional machinery. While it was previously thought that the transcriptional activity is associated with more open and dynamic chromatin structure, recent studies suggested a more nuanced role of transcription in chromatin dynamics: dynamic association/dissociation of active RNA polymerase II (RNAPII) and other transcription factors and Mediators (TF-Meds) transiently bridges transcriptionally active DNA regions, which forms a loose network of chromatin and constrains chromatin movement, enhancing the slow chromatin population. This new view on the dynamical effects of transcription urges a reflection on the traditional model of transcription factories and invites the more recent models of condensates/phase-separated liquid droplets of RNAPII, transcription factors, and Mediators. The combined procedure of genome-wide single-nucleosome tracking and its statistical analysis would unveil heterogeneity in the chromatin movement, which should provide a key to understanding the relations among chromatin dynamics, structure, and function. © 2020, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature.
引用
收藏
页码：461 / 468
页数：7
相关论文
共 69 条
[11]  
Chen C., Lim H.H., Shi J., Tamura S., Maeshima M., Surana U., Et al., Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo, Mol Biol Cell, 27, pp. 3357-3368, (2016)
[12]  
Chen H., Levo M., Barinov L., Fujioka M., Jaynes J.B., Gregor T., Dynamic interplay between enhancer-promoter topology and gene activity, Nat Genet, 50, pp. 1296-1303, (2018)
[13]  
Cho W.K., Spille J.H., Hecht M., Lee C., Li C., Grube V., Cisse I.I., Mediator and RNA polymerase II clusters associate in transcription dependent condensates, Science, 361, pp. 412-415, (2018)
[14]  
Chong S., Dugast-Darzacq C., Liu Z., Dong P., Dailey G.M., Cattoglio C., Heckert A., Banala S., Lavis L., Darzacq X., Tjian R., Imaging dynamic and selective low-complexity domain interactions that control gene transcription, Science, 361, (2018)
[15]  
Chubb J.R., Boyle S., Perry P., Bickmore W.A., Chromatin motion is constrained by association with nuclear compartments in human cells, Curr Biol, 12, pp. 439-445, (2002)
[16]  
Dekker J., Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction, J Biol Chem, 283, pp. 34532-34540, (2008)
[17]  
Di Pierro M., Potoyan D.A., Wolynes P.G., Onuchic J.N., Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes, Proc Natl Acad Sci U S A, 115, pp. 7753-7758, (2018)
[18]  
Dion V., Kalck V., Seeber A., Schleker T., Gasser S.M., Cohesin and the nucleolus constrain the mobility of spontaneous repair foci, EMBO Rep, 14, pp. 984-991, (2013)
[19]  
Edelman L.B., Fraser P., Transcription factories: genetic programming in three dimensions, Curr Opin Genet Dev, 22, pp. 110-114, (2012)
[20]  
Eltsov M., Maclellan K.M., Maeshima K., Frangakis A.S., Dubochet J., Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ, Proc Natl Acad Sci U S A, 105, pp. 19732-19737, (2008)
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