Literature DB >> 20668006

Organization of transcription.

Lyubomira Chakalova1, Peter Fraser.   

Abstract

Investigations into the organization of transcription have their origins in cell biology. Early studies characterized nascent transcription in relation to discernable nuclear structures and components. Advances in light microscopy, immunofluorescence, and in situ hybridization helped to begin the difficult task of naming the countless individual players and components of transcription and placing them in context. With the completion of mammalian genome sequences, the seemingly boundless task of understanding transcription of the genome became finite and began a new period of rapid advance. Here we focus on the organization of transcription in mammals drawing upon information from lower organisms where necessary. The emerging picture is one of a highly organized nucleus with specific conformations of the genome adapted for tissue-specific programs of transcription and gene expression.

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Year:  2010        PMID: 20668006      PMCID: PMC2926752          DOI: 10.1101/cshperspect.a000729

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  99 in total

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Journal:  Cell       Date:  2003-03-21       Impact factor: 41.582

2.  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

3.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.

Authors:  Zhihu Zhao; Gholamreza Tavoosidana; Mikael Sjölinder; Anita Göndör; Piero Mariano; Sha Wang; Chandrasekhar Kanduri; Magda Lezcano; Kuljeet Singh Sandhu; Umashankar Singh; Vinod Pant; Vijay Tiwari; Sreenivasulu Kurukuti; Rolf Ohlsson
Journal:  Nat Genet       Date:  2006-10-08       Impact factor: 38.330

4.  Nanomechanotransduction and interphase nuclear organization influence on genomic control.

Authors:  Matthew J Dalby; Nikolaj Gadegaard; Pawel Herzyk; Duncan Sutherland; Hossein Agheli; Chris D W Wilkinson; Adam S G Curtis
Journal:  J Cell Biochem       Date:  2007-12-01       Impact factor: 4.429

Review 5.  Genome-wide transcription and the implications for genomic organization.

Authors:  Philipp Kapranov; Aarron T Willingham; Thomas R Gingeras
Journal:  Nat Rev Genet       Date:  2007-05-08       Impact factor: 53.242

6.  Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression.

Authors:  Effie Apostolou; Dimitris Thanos
Journal:  Cell       Date:  2008-07-11       Impact factor: 41.582

7.  Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei.

Authors:  D A Jackson; F J Iborra; E M Manders; P R Cook
Journal:  Mol Biol Cell       Date:  1998-06       Impact factor: 4.138

Review 8.  Long-range control of gene expression: emerging mechanisms and disruption in disease.

Authors:  Dirk A Kleinjan; Veronica van Heyningen
Journal:  Am J Hum Genet       Date:  2004-11-17       Impact factor: 11.025

Review 9.  Replication and transcription: shaping the landscape of the genome.

Authors:  Lyubomira Chakalova; Emmanuel Debrand; Jennifer A Mitchell; Cameron S Osborne; Peter Fraser
Journal:  Nat Rev Genet       Date:  2005-09       Impact factor: 53.242

10.  Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription.

Authors:  Robert-Jan Palstra; Marieke Simonis; Petra Klous; Emilie Brasset; Bart Eijkelkamp; Wouter de Laat
Journal:  PLoS One       Date:  2008-02-20       Impact factor: 3.240

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  37 in total

1.  The genome in space and time: does form always follow function? How does the spatial and temporal organization of a eukaryotic genome reflect and influence its functions?

Authors:  Zhijun Duan; Carl Anthony Blau
Journal:  Bioessays       Date:  2012-07-06       Impact factor: 4.345

2.  Dynamic Behavior of the RNA Polymerase II and the Ubiquitin Proteasome System During the Neuronal DNA Damage Response to Ionizing Radiation.

Authors:  Iñigo Casafont; Ana Palanca; Vanesa Lafarga; Jorge Mata-Garrido; Maria T Berciano; Miguel Lafarga
Journal:  Mol Neurobiol       Date:  2015-12-11       Impact factor: 5.590

3.  DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes.

Authors:  Ofir Hakim; Wolfgang Resch; Arito Yamane; Isaac Klein; Kyong-Rim Kieffer-Kwon; Mila Jankovic; Thiago Oliveira; Anne Bothmer; Ty C Voss; Camilo Ansarah-Sobrinho; Ewy Mathe; Genqing Liang; Jesse Cobell; Hirotaka Nakahashi; Davide F Robbiani; Andre Nussenzweig; Gordon L Hager; Michel C Nussenzweig; Rafael Casellas
Journal:  Nature       Date:  2012-02-07       Impact factor: 49.962

4.  Dynamic reconfiguration of long human genes during one transcription cycle.

Authors:  Joshua D Larkin; Peter R Cook; Argyris Papantonis
Journal:  Mol Cell Biol       Date:  2012-05-14       Impact factor: 4.272

5.  Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy.

Authors:  Ziqing W Zhao; Rahul Roy; J Christof M Gebhardt; David M Suter; Alec R Chapman; X Sunney Xie
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-30       Impact factor: 11.205

Review 6.  Biological implications and regulatory mechanisms of long-range chromosomal interactions.

Authors:  Zong Wei; David Huang; Fan Gao; Wen-Hsuan Chang; Woojin An; Gerhard A Coetzee; Kai Wang; Wange Lu
Journal:  J Biol Chem       Date:  2013-06-18       Impact factor: 5.157

Review 7.  RNA polymerase II C-terminal domain: Tethering transcription to transcript and template.

Authors:  Jeffry L Corden
Journal:  Chem Rev       Date:  2013-09-16       Impact factor: 60.622

8.  Isolation of the protein and RNA content of active sites of transcription from mammalian cells.

Authors:  Svitlana Melnik; Maïwen Caudron-Herger; Lilija Brant; Ian M Carr; Karsten Rippe; Peter R Cook; Argyris Papantonis
Journal:  Nat Protoc       Date:  2016-02-25       Impact factor: 13.491

9.  The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

Authors:  Erik Splinter; Elzo de Wit; Elphège P Nora; Petra Klous; Harmen J G van de Werken; Yun Zhu; Lucas J T Kaaij; Wilfred van Ijcken; Joost Gribnau; Edith Heard; Wouter de Laat
Journal:  Genes Dev       Date:  2011-06-20       Impact factor: 11.361

Review 10.  Nuclear organization and genome function.

Authors:  Kevin Van Bortle; Victor G Corces
Journal:  Annu Rev Cell Dev Biol       Date:  2012-08-17       Impact factor: 13.827

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