Literature DB >> 32768408

Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields.

Andrews Akwasi Agbleke1, Assaf Amitai2, Jason D Buenrostro3, Aditi Chakrabarti4, Lingluo Chu5, Anders S Hansen6, Kristen M Koenig7, Ajay S Labade3, Sirui Liu8, Tadasu Nozaki5, Sergey Ovchinnikov9, Andrew Seeber10, Haitham A Shaban11, Jan-Hendrik Spille12, Andrew D Stephens13, Jun-Han Su5, Dushan Wadduwage14.   

Abstract

Nucleosomes package genomic DNA into chromatin. By regulating DNA access for transcription, replication, DNA repair, and epigenetic modification, chromatin forms the nexus of most nuclear processes. In addition, dynamic organization of chromatin underlies both regulation of gene expression and evolution of chromosomes into individualized sister objects, which can segregate cleanly to different daughter cells at anaphase. This collaborative review shines a spotlight on technologies that will be crucial to interrogate key questions in chromatin and chromosome biology including state-of-the-art microscopy techniques, tools to physically manipulate chromatin, single-cell methods to measure chromatin accessibility, computational imaging with neural networks and analytical tools to interpret chromatin structure and dynamics. In addition, this review provides perspectives on how these tools can be applied to specific research fields such as genome stability and developmental biology and to test concepts such as phase separation of chromatin.
Copyright © 2020 Elsevier Inc. All rights reserved.

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Year:  2020        PMID: 32768408      PMCID: PMC7888594          DOI: 10.1016/j.molcel.2020.07.003

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  225 in total

1.  Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.

Authors:  Brent D Brower-Toland; Corey L Smith; Richard C Yeh; John T Lis; Craig L Peterson; Michelle D Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-19       Impact factor: 11.205

2.  The lac repressor displays facilitated diffusion in living cells.

Authors:  Petter Hammar; Prune Leroy; Anel Mahmutovic; Erik G Marklund; Otto G Berg; Johan Elf
Journal:  Science       Date:  2012-06-22       Impact factor: 47.728

3.  A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation.

Authors:  Avinash Patel; Hyun O Lee; Louise Jawerth; Shovamayee Maharana; Marcus Jahnel; Marco Y Hein; Stoyno Stoynov; Julia Mahamid; Shambaditya Saha; Titus M Franzmann; Andrej Pozniakovski; Ina Poser; Nicola Maghelli; Loic A Royer; Martin Weigert; Eugene W Myers; Stephan Grill; David Drechsel; Anthony A Hyman; Simon Alberti
Journal:  Cell       Date:  2015-08-27       Impact factor: 41.582

4.  Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging.

Authors:  Tadasu Nozaki; Ryosuke Imai; Mai Tanbo; Ryosuke Nagashima; Sachiko Tamura; Tomomi Tani; Yasumasa Joti; Masaru Tomita; Kayo Hibino; Masato T Kanemaki; Kerstin S Wendt; Yasushi Okada; Takeharu Nagai; Kazuhiro Maeshima
Journal:  Mol Cell       Date:  2017-07-14       Impact factor: 17.970

5.  Superresolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact Caenorhabditis elegans tissue.

Authors:  Simone Köhler; Michal Wojcik; Ke Xu; Abby F Dernburg
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-30       Impact factor: 11.205

6.  Open and closed domains in the mouse genome are configured as 10-nm chromatin fibres.

Authors:  Eden Fussner; Mike Strauss; Ugljesa Djuric; Ren Li; Kashif Ahmed; Michael Hart; James Ellis; David P Bazett-Jones
Journal:  EMBO Rep       Date:  2012-11-06       Impact factor: 8.807

Review 7.  Biogenesis and function of nuclear bodies.

Authors:  Yuntao S Mao; Bin Zhang; David L Spector
Journal:  Trends Genet       Date:  2011-06-15       Impact factor: 11.639

8.  Direct imaging of DNA in living cells reveals the dynamics of chromosome formation.

Authors:  E M Manders; H Kimura; P R Cook
Journal:  J Cell Biol       Date:  1999-03-08       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

Review 10.  Evidence for and against Liquid-Liquid Phase Separation in the Nucleus.

Authors:  Peng A; Stephanie C Weber
Journal:  Noncoding RNA       Date:  2019-11-01
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  11 in total

Review 1.  Modifiers of CAG/CTG Repeat Instability: Insights from Mammalian Models.

Authors:  Vanessa C Wheeler; Vincent Dion
Journal:  J Huntingtons Dis       Date:  2021

Review 2.  Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures.

Authors:  Sreejith J Nair; Tom Suter; Susan Wang; Lu Yang; Feng Yang; Michael G Rosenfeld
Journal:  Trends Genet       Date:  2022-07-07       Impact factor: 11.821

Review 3.  The spatial organization of transcriptional control.

Authors:  Antonina Hafner; Alistair Boettiger
Journal:  Nat Rev Genet       Date:  2022-09-14       Impact factor: 59.581

4.  Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion.

Authors:  Roman Barth; Haitham A Shaban
Journal:  Nucleus       Date:  2022-12       Impact factor: 4.590

Review 5.  Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development.

Authors:  Rajarshi P Ghosh; Barbara J Meyer
Journal:  Annu Rev Cell Dev Biol       Date:  2021-07-06       Impact factor: 13.827

6.  Efficient cell chatting between embryo and uterus ensures embryo implantation†.

Authors:  Wenbo Deng; Haibin Wang
Journal:  Biol Reprod       Date:  2022-07-25       Impact factor: 4.161

Review 7.  Lactylation, a Novel Metabolic Reprogramming Code: Current Status and Prospects.

Authors:  An-Na Chen; Yan Luo; Yu-Han Yang; Jian-Tao Fu; Xiu-Mei Geng; Jun-Ping Shi; Jin Yang
Journal:  Front Immunol       Date:  2021-06-10       Impact factor: 7.561

Review 8.  Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription.

Authors:  Haitham A Shaban; Roman Barth; Kerstin Bystricky
Journal:  Genome Biol       Date:  2020-11-17       Impact factor: 13.583

Review 9.  Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin.

Authors:  Daniël P Melters; Yamini Dalal
Journal:  J Mol Biol       Date:  2020-11-20       Impact factor: 5.469

10.  Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion.

Authors:  Henrik D Pinholt; Søren S-R Bohr; Josephine F Iversen; Wouter Boomsma; Nikos S Hatzakis
Journal:  Proc Natl Acad Sci U S A       Date:  2021-08-03       Impact factor: 11.205

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