Literature DB >> 27692923

Genomic Energy Landscapes.

Bin Zhang1, Peter G Wolynes2.   

Abstract

Energy landscape theory, developed in the context of protein folding, provides, to our knowledge, a new perspective on chromosome architecture. We review what has been learned concerning the topology and structure of both the interphase and mitotic chromosomes from effective energy landscapes constructed using Hi-C data. Energy landscape thinking raises new questions about the nonequilibrium dynamics of the chromosome and gene regulation.
Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2016        PMID: 27692923      PMCID: PMC5300775          DOI: 10.1016/j.bpj.2016.08.046

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  68 in total

1.  The fractal globule as a model of chromatin architecture in the cell.

Authors:  Leonid A Mirny
Journal:  Chromosome Res       Date:  2011-01       Impact factor: 5.239

2.  Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles.

Authors:  Patrick Weinkam; Ekaterina V Pletneva; Harry B Gray; Jay R Winkler; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-30       Impact factor: 11.205

Review 3.  Micromechanical studies of mitotic chromosomes.

Authors:  John F Marko
Journal:  Chromosome Res       Date:  2008       Impact factor: 5.239

4.  Characterization of the Drosophila melanogaster genome at the nuclear lamina.

Authors:  Helen Pickersgill; Bernike Kalverda; Elzo de Wit; Wendy Talhout; Maarten Fornerod; Bas van Steensel
Journal:  Nat Genet       Date:  2006-07-30       Impact factor: 38.330

5.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

6.  Entropy gives rise to topologically associating domains.

Authors:  Paula A Vasquez; Caitlin Hult; David Adalsteinsson; Josh Lawrimore; Mark G Forest; Kerry Bloom
Journal:  Nucleic Acids Res       Date:  2016-06-02       Impact factor: 16.971

7.  Learning To Fold Proteins Using Energy Landscape Theory.

Authors:  N P Schafer; B L Kim; W Zheng; P G Wolynes
Journal:  Isr J Chem       Date:  2014-08       Impact factor: 3.333

8.  Formation of Chromosomal Domains by Loop Extrusion.

Authors:  Geoffrey Fudenberg; Maxim Imakaev; Carolyn Lu; Anton Goloborodko; Nezar Abdennur; Leonid A Mirny
Journal:  Cell Rep       Date:  2016-05-19       Impact factor: 9.423

9.  Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations.

Authors:  Hiroo Kenzaki; Shoji Takada
Journal:  PLoS Comput Biol       Date:  2015-08-11       Impact factor: 4.475

10.  Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.

Authors:  Fabrizio Benedetti; Julien Dorier; Yannis Burnier; Andrzej Stasiak
Journal:  Nucleic Acids Res       Date:  2013-12-23       Impact factor: 16.971

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  16 in total

1.  Learning the Formation Mechanism of Domain-Level Chromatin States with Epigenomics Data.

Authors:  Wen Jun Xie; Bin Zhang
Journal:  Biophys J       Date:  2019-04-11       Impact factor: 4.033

2.  Conformational state switching and pathways of chromosome dynamics in cell cycle.

Authors:  Xiakun Chu; Jin Wang
Journal:  Appl Phys Rev       Date:  2020-09       Impact factor: 19.162

Review 3.  Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.

Authors:  Dario Meluzzi; Gaurav Arya
Journal:  Methods       Date:  2019-08-27       Impact factor: 3.608

4.  Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus.

Authors:  Ankit Agrawal; Nirmalendu Ganai; Surajit Sengupta; Gautam I Menon
Journal:  Biophys J       Date:  2019-11-22       Impact factor: 4.033

5.  Theory of Active Chromatin Remodeling.

Authors:  Zhongling Jiang; Bin Zhang
Journal:  Phys Rev Lett       Date:  2019-11-15       Impact factor: 9.161

Review 6.  Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units.

Authors:  Jie Liang; Alan Perez-Rathke
Journal:  Curr Opin Struct Biol       Date:  2021-08-14       Impact factor: 6.809

7.  Thermodynamic energetics underlying genomic instability and whole-genome doubling in cancer.

Authors:  Francoise Remacle; Thomas G Graeber; R D Levine
Journal:  Proc Natl Acad Sci U S A       Date:  2020-07-21       Impact factor: 11.205

8.  Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins.

Authors:  Andrew P Latham; Bin Zhang
Journal:  J Chem Theory Comput       Date:  2019-12-13       Impact factor: 6.006

9.  De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.

Authors:  Michele Di Pierro; Ryan R Cheng; Erez Lieberman Aiden; Peter G Wolynes; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-31       Impact factor: 11.205

10.  Multiscale modeling of genome organization with maximum entropy optimization.

Authors:  Xingcheng Lin; Yifeng Qi; Andrew P Latham; Bin Zhang
Journal:  J Chem Phys       Date:  2021-07-07       Impact factor: 3.488

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