Literature DB >> 16900099

Gene expression within a dynamic nuclear landscape.

Yaron Shav-Tal1, Xavier Darzacq, Robert H Singer.   

Abstract

Molecular imaging in living cells or organisms now allows us to observe macromolecular assemblies with a time resolution sufficient to address cause-and-effect relationships on specific molecules. These emerging technologies have gained much interest from the scientific community since they have been able to reveal novel concepts in cell biology, thereby changing our vision of the cell. One main paradigm is that cells stochastically vary, thus implying that population analysis may be misleading. In fact, cells should be analyzed within time-resolved single-cell experiments rather than being compared to other cells within a population. Technological imaging developments as well as the stochastic events present in gene expression have been reviewed. Here, we discuss how the structural organization of the nucleus is revealed using noninvasive single-cell approaches, which ultimately lead to the resolution required for the analysis of highly controlled molecular processes taking place within live cells. We also describe the efforts being made towards physiological approaches within the context of living organisms.

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Year:  2006        PMID: 16900099      PMCID: PMC1538565          DOI: 10.1038/sj.emboj.7601226

Source DB:  PubMed          Journal:  EMBO J        ISSN: 0261-4189            Impact factor:   11.598


  136 in total

Review 1.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells.

Authors:  T Cremer; C Cremer
Journal:  Nat Rev Genet       Date:  2001-04       Impact factor: 53.242

2.  Replication-dependent histone gene expression is related to Cajal body (CB) association but does not require sustained CB contact.

Authors:  L S Shopland; M Byron; J L Stein; J B Lian; G S Stein; J B Lawrence
Journal:  Mol Biol Cell       Date:  2001-03       Impact factor: 4.138

Review 3.  Protein dynamics: implications for nuclear architecture and gene expression.

Authors:  T Misteli
Journal:  Science       Date:  2001-02-02       Impact factor: 47.728

Review 4.  Translating the histone code.

Authors:  T Jenuwein; C D Allis
Journal:  Science       Date:  2001-08-10       Impact factor: 47.728

5.  Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs.

Authors:  Xavier Darzacq; Beáta E Jády; Céline Verheggen; Arnold M Kiss; Edouard Bertrand; Tamás Kiss
Journal:  EMBO J       Date:  2002-06-03       Impact factor: 11.598

Review 6.  Visualizing chromatin dynamics in interphase nuclei.

Authors:  Susan M Gasser
Journal:  Science       Date:  2002-05-24       Impact factor: 47.728

7.  Dynamic analyses of the expression of the HISTONE::YFP fusion protein in arabidopsis show that syncytial endosperm is divided in mitotic domains.

Authors:  C Boisnard-Lorig; A Colon-Carmona; M Bauch; S Hodge; P Doerner; E Bancharel; C Dumas; J Haseloff; F Berger
Journal:  Plant Cell       Date:  2001-03       Impact factor: 11.277

8.  Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus.

Authors:  J Vazquez; A S Belmont; J W Sedat
Journal:  Curr Biol       Date:  2001-08-21       Impact factor: 10.834

9.  Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter.

Authors:  W G Müller; D Walker; G L Hager; J G McNally
Journal:  J Cell Biol       Date:  2001-07-09       Impact factor: 10.539

10.  Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B.

Authors:  H Kimura; P R Cook
Journal:  J Cell Biol       Date:  2001-06-25       Impact factor: 10.539

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  17 in total

1.  The life of an mRNA in space and time.

Authors:  Ya'ara Ben-Ari; Yehuda Brody; Noa Kinor; Amir Mor; Toshiro Tsukamoto; David L Spector; Robert H Singer; Yaron Shav-Tal
Journal:  J Cell Sci       Date:  2010-04-27       Impact factor: 5.285

2.  Intranuclear trafficking of episomal DNA is transcription-dependent.

Authors:  Joshua Z Gasiorowski; David A Dean
Journal:  Mol Ther       Date:  2007-07-31       Impact factor: 11.454

3.  Evolution of the global internal dynamics of a living cell nucleus during interphase.

Authors:  M Suissa; C Place; E Goillot; E Freyssingeas
Journal:  Biophys J       Date:  2009-07-22       Impact factor: 4.033

4.  The dynamics of the alternatively spliced NOL7 gene products and role in nucleolar architecture.

Authors:  Noa Kinor; Yaron Shav-Tal
Journal:  Nucleus       Date:  2011 May-Jun       Impact factor: 4.197

Review 5.  Connecting the dots of RNA-directed DNA methylation in Arabidopsis thaliana.

Authors:  Pedro Costa-Nunes; Alexa Vitins; Olga Pontes
Journal:  Chromosome Res       Date:  2014-06       Impact factor: 5.239

Review 6.  How to build a paraspeckle.

Authors:  Yasnory T F Sasaki; Tetsuro Hirose
Journal:  Genome Biol       Date:  2009-07-16       Impact factor: 13.583

7.  Single-molecule dynamics of nuclear mRNA.

Authors:  Yaron Shav-Tal; Yosef Gruenbaum
Journal:  F1000 Biol Rep       Date:  2009-04-29

Review 8.  The architecture of functional neighborhoods within the mammalian cell nucleus.

Authors:  Kishore S Malyavantham; Sambit Bhattacharya; Ronald Berezney
Journal:  Adv Enzyme Regul       Date:  2009-12-03

9.  Regulation of TATA-binding protein dynamics in living yeast cells.

Authors:  Rebekka O Sprouse; Tatiana S Karpova; Florian Mueller; Arindam Dasgupta; James G McNally; David T Auble
Journal:  Proc Natl Acad Sci U S A       Date:  2008-09-02       Impact factor: 11.205

10.  A method for in silico identification of SNAIL/SLUG DNA binding potentials to the E-box sequence using molecular dynamics and evolutionary conserved amino acids.

Authors:  Jeremy W Prokop; Yuanjie Liu; Amy Milsted; Hongzhuang Peng; Frank J Rauscher
Journal:  J Mol Model       Date:  2013-05-25       Impact factor: 1.810

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