Literature DB >> 21327103

Chromosome conformation by crosslinking: polymer physics matters.

Jörg Langowski1.   

Abstract

The genetic information is encoded on double-stranded DNA, a long linear polymer chain. Among the central themes of Nucleus will be the advancement of our understanding of how those chains are folded so that they fit into the cell nucleus, and at the same time their information can be read off efficiently. In fact, a quantitative description of the structure of the folded genome is one of the most challenging problems in structural biology, and poses a much more formidable problem than-for instance-the folding of a protein. There are three main reasons for this: first, the genomic DNA is by orders of magnitude the largest biomolecule in the cell; second, it cannot be defined by a single spatial structure because of its flexibility; and third, even if the 'fold' of the genome were more or less defined in any one cell, variations among individual cells may be very large, for the same reasons of flexibility.

Entities:  

Keywords:  chromatin folding; chromosome conformation capture; deep sequencing; fractal globule; polymer chain models

Mesh:

Substances:

Year:  2010        PMID: 21327103      PMCID: PMC3035122          DOI: 10.4161/nucl.1.1.10837

Source DB:  PubMed          Journal:  Nucleus        ISSN: 1949-1034            Impact factor:   4.197


  11 in total

1.  Chromosome dynamics in the yeast interphase nucleus.

Authors:  P Heun; T Laroche; K Shimada; P Furrer; S M Gasser
Journal:  Science       Date:  2001-12-07       Impact factor: 47.728

Review 2.  Genome function and nuclear architecture: from gene expression to nanoscience.

Authors:  Timothy P O'Brien; Carol J Bult; Christoph Cremer; Michael Grunze; Barbara B Knowles; Jorg Langowski; James McNally; Thoru Pederson; Joan C Politz; Ana Pombo; Gunter Schmahl; Joachim P Spatz; Roel van Driel
Journal:  Genome Res       Date:  2003-05-12       Impact factor: 9.043

3.  Compartmentalization of interphase chromosomes observed in simulation and experiment.

Authors:  C Münkel; R Eils; S Dietzel; D Zink; C Mehring; G Wedemann; T Cremer; J Langowski
Journal:  J Mol Biol       Date:  1999-01-22       Impact factor: 5.469

4.  Interphase chromosomes undergo constrained diffusional motion in living cells.

Authors:  W F Marshall; A Straight; J F Marko; J Swedlow; A Dernburg; A Belmont; A W Murray; D A Agard; J W Sedat
Journal:  Curr Biol       Date:  1997-12-01       Impact factor: 10.834

5.  Capturing chromosome conformation.

Authors:  Job Dekker; Karsten Rippe; Martijn Dekker; Nancy Kleckner
Journal:  Science       Date:  2002-02-15       Impact factor: 47.728

6.  Spatially confined folding of chromatin in the interphase nucleus.

Authors:  Julio Mateos-Langerak; Manfred Bohn; Wim de Leeuw; Osdilly Giromus; Erik M M Manders; Pernette J Verschure; Mireille H G Indemans; Hinco J Gierman; Dieter W Heermann; Roel van Driel; Sandra Goetze
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-20       Impact factor: 11.205

7.  Global identification of yeast chromosome interactions using Genome conformation capture.

Authors:  C D M Rodley; F Bertels; B Jones; J M O'Sullivan
Journal:  Fungal Genet Biol       Date:  2009-07-21       Impact factor: 3.495

8.  Random loop model for long polymers.

Authors:  Manfred Bohn; Dieter W Heermann; Roel van Driel
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-11-27

9.  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

10.  Structure and dynamics of interphase chromosomes.

Authors:  Angelo Rosa; Ralf Everaers
Journal:  PLoS Comput Biol       Date:  2008-08-22       Impact factor: 4.475

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  4 in total

Review 1.  A decade of 3C technologies: insights into nuclear organization.

Authors:  Elzo de Wit; Wouter de Laat
Journal:  Genes Dev       Date:  2012-01-01       Impact factor: 11.361

Review 2.  The nucleus introduced.

Authors:  Thoru Pederson
Journal:  Cold Spring Harb Perspect Biol       Date:  2011-05-01       Impact factor: 10.005

3.  Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization.

Authors:  Marco Di Stefano; Jonas Paulsen; Tonje G Lien; Eivind Hovig; Cristian Micheletti
Journal:  Sci Rep       Date:  2016-10-27       Impact factor: 4.379

4.  Systematic characterization of the conformation and dynamics of budding yeast chromosome XII.

Authors:  Benjamin Albert; Julien Mathon; Ashutosh Shukla; Hicham Saad; Christophe Normand; Isabelle Léger-Silvestre; David Villa; Alain Kamgoue; Julien Mozziconacci; Hua Wong; Christophe Zimmer; Purnima Bhargava; Aurélien Bancaud; Olivier Gadal
Journal:  J Cell Biol       Date:  2013-07-22       Impact factor: 10.539

  4 in total

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