Literature DB >> 16362820

Organization of interphase chromatin.

Rachel A Horowitz-Scherer1, Christopher L Woodcock.   

Abstract

The organization of interphase chromatin spans many topics, ranging in scale from the molecular level to the whole nucleus, and its study requires a concomitant range of experimental approaches. In this review, we examine these approaches, the results they have generated, and the interfaces between them. The greatest challenge appears to be the integration of information on whole nuclei obtained by light microscopy with data on nucleosome-nucleosome interactions and chromatin higher-order structures, obtained in vitro using biophysical characterization, atomic force microscopy, and electron microscopy. We consider strategies that may assist in the integration process, and we review emerging technologies that promise to reduce the "resolution gap."

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Year:  2005        PMID: 16362820     DOI: 10.1007/s00412-005-0035-3

Source DB:  PubMed          Journal:  Chromosoma        ISSN: 0009-5915            Impact factor:   4.316


  130 in total

1.  Genome-wide location and function of DNA binding proteins.

Authors:  B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

2.  The glucocorticoid receptor: rapid exchange with regulatory sites in living cells.

Authors:  J G McNally; W G Müller; D Walker; R Wolford; G L Hager
Journal:  Science       Date:  2000-02-18       Impact factor: 47.728

3.  Looping and interaction between hypersensitive sites in the active beta-globin locus.

Authors:  Bas Tolhuis; Robert Jan Palstra; Erik Splinter; Frank Grosveld; Wouter de Laat
Journal:  Mol Cell       Date:  2002-12       Impact factor: 17.970

Review 4.  Chromatin fibers, one-at-a-time.

Authors:  Jordanka Zlatanova; Sanford H Leuba
Journal:  J Mol Biol       Date:  2003-08-01       Impact factor: 5.469

5.  Role of the M-loop and reactive center loop domains in the folding and bridging of nucleosome arrays by MENT.

Authors:  Evelyn M Springhetti; Natalia E Istomina; James C Whisstock; Tatiana Nikitina; Chris L Woodcock; Sergei A Grigoryev
Journal:  J Biol Chem       Date:  2003-08-19       Impact factor: 5.157

6.  Rapid spontaneous accessibility of nucleosomal DNA.

Authors:  Gu Li; Marcia Levitus; Carlos Bustamante; Jonathan Widom
Journal:  Nat Struct Mol Biol       Date:  2004-12-05       Impact factor: 15.369

7.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

8.  Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3' boundary sequence spanning 46 kilobases.

Authors:  Zhe Liu; William T Garrard
Journal:  Mol Cell Biol       Date:  2005-04       Impact factor: 4.272

9.  Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome.

Authors:  Shin-ichi Horike; Shutao Cai; Masaru Miyano; Jan-Fang Cheng; Terumi Kohwi-Shigematsu
Journal:  Nat Genet       Date:  2004-12-19       Impact factor: 38.330

10.  The core histone N-terminal tail domains function independently and additively during salt-dependent oligomerization of nucleosomal arrays.

Authors:  Faye Gordon; Karolin Luger; Jeffrey C Hansen
Journal:  J Biol Chem       Date:  2005-07-19       Impact factor: 5.157

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  18 in total

1.  Activator-dependent p300 acetylation of chromatin in vitro: enhancement of transcription by disruption of repressive nucleosome-nucleosome interactions.

Authors:  Heather J Szerlong; Jessica E Prenni; Jennifer K Nyborg; Jeffrey C Hansen
Journal:  J Biol Chem       Date:  2010-08-18       Impact factor: 5.157

2.  Cell-type specific proximity of centromeric domains of one homologue each of chromosomes 2 and 11 in nuclei of cerebellar Purkinje neurons.

Authors:  Kunjumon I Vadakkan; Baoxiang Li; Umberto De Boni
Journal:  Chromosoma       Date:  2006-06-02       Impact factor: 4.316

3.  HP1 proteins are essential for a dynamic nuclear response that rescues the function of perturbed heterochromatin in primary human cells.

Authors:  Rugang Zhang; Song-tao Liu; Wei Chen; Michael Bonner; John Pehrson; Timothy J Yen; Peter D Adams
Journal:  Mol Cell Biol       Date:  2006-11-13       Impact factor: 4.272

4.  Gold-nanoparticle-assisted laser perturbation of chromatin assembly reveals unusual aspects of nuclear architecture within living cells.

Authors:  Aprotim Mazumder; G V Shivashankar
Journal:  Biophys J       Date:  2007-05-11       Impact factor: 4.033

5.  Dense chromatin plates in metaphase chromosomes.

Authors:  Isaac Gállego; Pablo Castro-Hartmann; Juan Manuel Caravaca; Silvia Caño; Joan-Ramon Daban
Journal:  Eur Biophys J       Date:  2009-02-03       Impact factor: 1.733

Review 6.  Nuclear envelope-limited chromatin sheets (ELCS) and heterochromatin higher order structure.

Authors:  Donald E Olins; Ada L Olins
Journal:  Chromosoma       Date:  2009-06-12       Impact factor: 4.316

Review 7.  Role of chromatin states in transcriptional memory.

Authors:  Sharmistha Kundu; Craig L Peterson
Journal:  Biochim Biophys Acta       Date:  2009-02-21

8.  Features of endogenous cardiomyocyte chromatin revealed by super-resolution STED microscopy.

Authors:  Scherise Mitchell-Jordan; Haodong Chen; Sarah Franklin; Enrico Stefani; Laurent A Bentolila; Thomas M Vondriska
Journal:  J Mol Cell Cardiol       Date:  2012-07-28       Impact factor: 5.000

9.  In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications.

Authors:  Caroline Kizilyaprak; Danièle Spehner; Didier Devys; Patrick Schultz
Journal:  PLoS One       Date:  2010-06-09       Impact factor: 3.240

10.  Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.

Authors:  Thomas M Asbury; Matt Mitman; Jijun Tang; W Jim Zheng
Journal:  BMC Bioinformatics       Date:  2010-09-02       Impact factor: 3.169

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