Literature DB >> 32976797

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

Tom Misteli1.   

Abstract

Genomes have complex three-dimensional architectures. The recent convergence of genetic, biochemical, biophysical, and cell biological methods has uncovered several fundamental principles of genome organization. They highlight that genome function is a major driver of genome architecture and that structural features of chromatin act as modulators, rather than binary determinants, of genome activity. The interplay of these principles in the context of self-organization can account for the emergence of structural chromatin features, the diversity and single-cell heterogeneity of nuclear architecture in cell types and tissues, and explains evolutionarily conserved functional features of genomes, including plasticity and robustness. Published by Elsevier Inc.

Entities:  

Keywords:  chromatin; dynamics; gene expression; genome organization; nuclear architecture; phase separation; self-organization

Year:  2020        PMID: 32976797      PMCID: PMC7541718          DOI: 10.1016/j.cell.2020.09.014

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  140 in total

1.  High mobility of proteins in the mammalian cell nucleus.

Authors:  R D Phair; T Misteli
Journal:  Nature       Date:  2000-04-06       Impact factor: 49.962

Review 2.  The nature of robustness in development.

Authors:  H F Nijhout
Journal:  Bioessays       Date:  2002-06       Impact factor: 4.345

3.  Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins.

Authors:  Robert D Phair; Paola Scaffidi; Cem Elbi; Jaromíra Vecerová; Anup Dey; Keiko Ozato; David T Brown; Gordon Hager; Michael Bustin; Tom Misteli
Journal:  Mol Cell Biol       Date:  2004-07       Impact factor: 4.272

4.  DNA loop extrusion by human cohesin.

Authors:  Iain F Davidson; Benedikt Bauer; Daniela Goetz; Wen Tang; Gordana Wutz; Jan-Michael Peters
Journal:  Science       Date:  2019-11-21       Impact factor: 47.728

5.  Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements.

Authors:  Bo Gu; Tomek Swigut; Andrew Spencley; Matthew R Bauer; Mingyu Chung; Tobias Meyer; Joanna Wysocka
Journal:  Science       Date:  2018-01-25       Impact factor: 47.728

6.  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

7.  Polymer physics predicts the effects of structural variants on chromatin architecture.

Authors:  Simona Bianco; Darío G Lupiáñez; Andrea M Chiariello; Carlo Annunziatella; Katerina Kraft; Robert Schöpflin; Lars Wittler; Guillaume Andrey; Martin Vingron; Ana Pombo; Stefan Mundlos; Mario Nicodemi
Journal:  Nat Genet       Date:  2018-04-16       Impact factor: 38.330

8.  Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence.

Authors:  Lindsay S Shopland; Christopher R Lynch; Kevin A Peterson; Kathleen Thornton; Nick Kepper; Johann von Hase; Stefan Stein; Sarah Vincent; Kelly R Molloy; Gregor Kreth; Christoph Cremer; Carol J Bult; Timothy P O'Brien
Journal:  J Cell Biol       Date:  2006-07-03       Impact factor: 10.539

9.  Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.

Authors:  Yang Eric Guo; John C Manteiga; Jonathan E Henninger; Benjamin R Sabari; Alessandra Dall'Agnese; Nancy M Hannett; Jan-Hendrik Spille; Lena K Afeyan; Alicia V Zamudio; Krishna Shrinivas; Brian J Abraham; Ann Boija; Tim-Michael Decker; Jenna K Rimel; Charli B Fant; Tong Ihn Lee; Ibrahim I Cisse; Phillip A Sharp; Dylan J Taatjes; Richard A Young
Journal:  Nature       Date:  2019-08-07       Impact factor: 49.962

10.  Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation.

Authors:  Anqi Wang; Janhavi A Kolhe; Nate Gioacchini; Imke Baade; William M Brieher; Craig L Peterson; Brian C Freeman
Journal:  Dev Cell       Date:  2020-01-02       Impact factor: 12.270

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  66 in total

Review 1.  In search of lost time: Enhancers as modulators of timing in lymphocyte development and differentiation.

Authors:  Jonathan M Chu; Nicholas A Pease; Hao Yuan Kueh
Journal:  Immunol Rev       Date:  2021-03-18       Impact factor: 12.988

Review 2.  Integrative approaches in genome structure analysis.

Authors:  Lorenzo Boninsegna; Asli Yildirim; Yuxiang Zhan; Frank Alber
Journal:  Structure       Date:  2021-12-27       Impact factor: 5.006

Review 3.  Cis-Regulatory Control of Mammalian Sex Determination.

Authors:  Meshi Ridnik; Stefan Schoenfelder; Nitzan Gonen
Journal:  Sex Dev       Date:  2021-10-28       Impact factor: 1.824

4.  The interplay of chromatin phase separation and lamina interactions in nuclear organization.

Authors:  Rabia Laghmach; Michele Di Pierro; Davit A Potoyan
Journal:  Biophys J       Date:  2021-10-13       Impact factor: 4.033

5.  Assessing Specific Networks of Chromatin Interactions with HiChIP.

Authors:  Dafne Campigli Di Giammartino; Alexander Polyzos; Effie Apostolou
Journal:  Methods Mol Biol       Date:  2022

Review 6.  Regulation of Chromatin Organization in Cell Stemness: The Emerging Role of Long Non-coding RNAs.

Authors:  Hesam Dehghani
Journal:  Stem Cell Rev Rep       Date:  2021-06-28       Impact factor: 5.739

Review 7.  Phase separation in transcription factor dynamics and chromatin organization.

Authors:  Kaustubh Wagh; David A Garcia; Arpita Upadhyaya
Journal:  Curr Opin Struct Biol       Date:  2021-07-22       Impact factor: 6.809

8.  CRISPR-Cas-Mediated Tethering Recruits the Yeast HMR Mating-Type Locus to the Nuclear Periphery but Fails to Silence Gene Expression.

Authors:  Emily R Cliff; Robin L Kirkpatrick; Daniel Cunningham-Bryant; Brianna Fernandez; Joseph L Harman; Jesse G Zalatan
Journal:  ACS Synth Biol       Date:  2021-11-01       Impact factor: 5.110

9.  The hierarchical packing of euchromatin domains can be described as multiplicative cascades.

Authors:  Amra Noa; Hui-Shun Kuan; Vera Aschmann; Vasily Zaburdaev; Lennart Hilbert
Journal:  PLoS Comput Biol       Date:  2021-05-05       Impact factor: 4.475

Review 10.  Transcriptionally Active Chromatin-Lessons Learned from the Chicken Erythrocyte Chromatin Fractionation.

Authors:  Tasnim H Beacon; James R Davie
Journal:  Cells       Date:  2021-05-30       Impact factor: 6.600

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