Literature DB >> 36180596

New insights into genome folding by loop extrusion from inducible degron technologies.

Elzo de Wit1,2, Elphège P Nora3,4.   

Abstract

Chromatin folds into dynamic loops that often span hundreds of kilobases and physically wire distant loci together for gene regulation. These loops are continuously created, extended and positioned by structural maintenance of chromosomes (SMC) protein complexes, such as condensin and cohesin, and their regulators, including CTCF, in a highly dynamic process known as loop extrusion. Genetic loss of extrusion factors is lethal, complicating their study. Inducible protein degradation technologies enable the depletion of loop extrusion factors within hours, leading to the rapid reconfiguration of chromatin folding. Here, we review how these technologies have changed our understanding of genome organization, upsetting long-held beliefs on its role in transcription. Finally, we examine recent models that attempt to reconcile observations after chronic versus acute perturbations, and discuss future developments in this rapidly developing field of research.
© 2022. Springer Nature Limited.

Entities:  

Year:  2022        PMID: 36180596     DOI: 10.1038/s41576-022-00530-4

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   59.581


  161 in total

Review 1.  Chromosome territories--a functional nuclear landscape.

Authors:  Thomas Cremer; Marion Cremer; Steffen Dietzel; Stefan Müller; Irina Solovei; Stanislav Fakan
Journal:  Curr Opin Cell Biol       Date:  2006-05-09       Impact factor: 8.382

Review 2.  Mechanisms and Functions of Chromosome Compartmentalization.

Authors:  Erica M Hildebrand; Job Dekker
Journal:  Trends Biochem Sci       Date:  2020-02-18       Impact factor: 13.807

3.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

Review 4.  The Self-Organizing Genome: Principles of Genome Architecture and Function.

Authors:  Tom Misteli
Journal:  Cell       Date:  2020-09-24       Impact factor: 41.582

5.  A pathway for mitotic chromosome formation.

Authors:  Johan H Gibcus; Kumiko Samejima; Anton Goloborodko; Itaru Samejima; Natalia Naumova; Johannes Nuebler; Masato T Kanemaki; Linfeng Xie; James R Paulson; William C Earnshaw; Leonid A Mirny; Job Dekker
Journal:  Science       Date:  2018-01-18       Impact factor: 47.728

Review 6.  Organizational principles of 3D genome architecture.

Authors:  M Jordan Rowley; Victor G Corces
Journal:  Nat Rev Genet       Date:  2018-12       Impact factor: 53.242

7.  Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells.

Authors:  Bogdan Bintu; Leslie J Mateo; Jun-Han Su; Nicholas A Sinnott-Armstrong; Mirae Parker; Seon Kinrot; Kei Yamaya; Alistair N Boettiger; Xiaowei Zhuang
Journal:  Science       Date:  2018-10-26       Impact factor: 47.728

8.  Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.

Authors:  Tsung-Han S Hsieh; Assaf Weiner; Bryan Lajoie; Job Dekker; Nir Friedman; Oliver J Rando
Journal:  Cell       Date:  2015-06-25       Impact factor: 41.582

9.  Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.

Authors:  Alistair N Boettiger; Bogdan Bintu; Jeffrey R Moffitt; Siyuan Wang; Brian J Beliveau; Geoffrey Fudenberg; Maxim Imakaev; Leonid A Mirny; Chao-ting Wu; Xiaowei Zhuang
Journal:  Nature       Date:  2016-01-13       Impact factor: 49.962

Review 10.  Gene functioning and storage within a folded genome.

Authors:  Sergey V Razin; Sergey V Ulianov
Journal:  Cell Mol Biol Lett       Date:  2017-08-29       Impact factor: 5.787

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