Literature DB >> 20484389

Gene positioning.

Carmelo Ferrai1, Inês Jesus de Castro, Liron Lavitas, Mita Chotalia, Ana Pombo.   

Abstract

Eukaryotic gene expression is an intricate multistep process, regulated within the cell nucleus through the activation or repression of RNA synthesis, processing, cytoplasmic export, and translation into protein. The major regulators of gene expression are chromatin remodeling and transcription machineries that are locally recruited to genes. However, enzymatic activities that act on genes are not ubiquitously distributed throughout the nucleoplasm, but limited to specific and spatially defined foci that promote preferred higher-order chromatin arrangements. The positioning of genes within the nuclear landscape relative to specific functional landmarks plays an important role in gene regulation and disease.

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Year:  2010        PMID: 20484389      PMCID: PMC2869523          DOI: 10.1101/cshperspect.a000588

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


  152 in total

1.  Nuclear domains enriched in RNA 3'-processing factors associate with coiled bodies and histone genes in a cell cycle-dependent manner.

Authors:  W Schul; I van Der Kraan; A G Matera; R van Driel; L de Jong
Journal:  Mol Biol Cell       Date:  1999-11       Impact factor: 4.138

2.  Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes.

Authors:  J A Skok; K E Brown; V Azuara; M L Caparros; J Baxter; K Takacs; N Dillon; D Gray; R P Perry; M Merkenschlager; A G Fisher
Journal:  Nat Immunol       Date:  2001-09       Impact factor: 25.606

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.  Chromosome positioning in the interphase nucleus.

Authors:  Luis Parada; Tom Misteli
Journal:  Trends Cell Biol       Date:  2002-09       Impact factor: 20.808

5.  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

6.  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

7.  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

8.  RNAi components are required for nuclear clustering of Polycomb group response elements.

Authors:  Charlotte Grimaud; Frédéric Bantignies; Manika Pal-Bhadra; Pallavi Ghana; Utpal Bhadra; Giacomo Cavalli
Journal:  Cell       Date:  2006-03-10       Impact factor: 41.582

9.  Chromosome territory reorganization in a human disease with altered DNA methylation.

Authors:  Maria R Matarazzo; Shelagh Boyle; Maurizio D'Esposito; Wendy A Bickmore
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-08       Impact factor: 11.205

10.  Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription.

Authors:  Séverine Chambeyron; Wendy A Bickmore
Journal:  Genes Dev       Date:  2004-05-15       Impact factor: 11.361

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  38 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.  Metazoan promoters: emerging characteristics and insights into transcriptional regulation.

Authors:  Boris Lenhard; Albin Sandelin; Piero Carninci
Journal:  Nat Rev Genet       Date:  2012-03-06       Impact factor: 53.242

3.  Dynamical modeling of three-dimensional genome organization in interphase budding yeast.

Authors:  Naoko Tokuda; Tomoki P Terada; Masaki Sasai
Journal:  Biophys J       Date:  2012-01-18       Impact factor: 4.033

4.  Association of adipogenic genes with SC-35 domains during porcine adipogenesis.

Authors:  Izabela Szczerbal; Joanna M Bridger
Journal:  Chromosome Res       Date:  2010-12-03       Impact factor: 5.239

5.  Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping.

Authors:  Sigal Shachar; Ty C Voss; Gianluca Pegoraro; Nicholas Sciascia; Tom Misteli
Journal:  Cell       Date:  2015-08-13       Impact factor: 41.582

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.  Functional and mechanistic diversity of distal transcription enhancers.

Authors:  Michael Bulger; Mark Groudine
Journal:  Cell       Date:  2011-02-04       Impact factor: 41.582

8.  Linking dosage compensation and X chromosome nuclear organization in C. elegans.

Authors:  Rahul Sharma; Peter Meister
Journal:  Nucleus       Date:  2015-06-09       Impact factor: 4.197

9.  Expression of the DYRK1A gene correlates with its 3D positioning in the interphase nucleus of Down syndrome cells.

Authors:  Nerea Paz; Izaskun Felipe-Blanco; Félix Royo; Amaia Zabala; Isabel Guerra-Merino; África García-Orad; José L Zugaza; Luis A Parada
Journal:  Chromosome Res       Date:  2015-02-03       Impact factor: 5.239

Review 10.  The cell biology of disease: FSHD: copy number variations on the theme of muscular dystrophy.

Authors:  Daphne Selvaggia Cabianca; Davide Gabellini
Journal:  J Cell Biol       Date:  2010-12-13       Impact factor: 10.539

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