Literature DB >> 21292462

Gene positioning and expression.

Defne Egecioglu1, Jason H Brickner.   

Abstract

Within the nucleus, the genome is spatially organized. Individual chromosomes are non-randomly positioned with respect to each other and with respect to nuclear landmarks [1,2]. Furthermore, the position of individual genes can reflect their expression. Here we discuss two well-characterized examples of gene relocalization associated with transcriptional activation: 1) developmentally regulated genes that move from the nuclear periphery to transcription factories in the nucleoplasm upon induction and 2) genes that are targeted from the nucleoplasm to the nuclear periphery, through interactions with the nuclear pore complex (NPC), upon activation. Finally, we speculate as to the mechanistic and functional commonalities of these phenomena.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21292462      PMCID: PMC3097288          DOI: 10.1016/j.ceb.2011.01.001

Source DB:  PubMed          Journal:  Curr Opin Cell Biol        ISSN: 0955-0674            Impact factor:   8.382


  76 in total

1.  The topological organization of chromosomes 9 and 22 in cell nuclei has a determinative role in the induction of t(9,22) translocations and in the pathogenesis of t(9,22) leukemias.

Authors:  S Kozubek; E Lukásová; A Marecková; M Skalníková; M Kozubek; E Bártová; V Kroha; E Krahulcová; J Slotová
Journal:  Chromosoma       Date:  1999-12       Impact factor: 4.316

2.  The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion.

Authors:  Angela Taddei; Griet Van Houwe; Shigeki Nagai; Ionas Erb; Erik van Nimwegen; Susan M Gasser
Journal:  Genome Res       Date:  2009-01-29       Impact factor: 9.043

3.  The nuclear periphery of embryonic stem cells is a transcriptionally permissive and repressive compartment.

Authors:  Li Luo; Katherine L Gassman; Lydia M Petell; Christian L Wilson; Joerg Bewersdorf; Lindsay S Shopland
Journal:  J Cell Sci       Date:  2009-09-22       Impact factor: 5.285

4.  Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex.

Authors:  Sue Mei Tan-Wong; Hashanthi D Wijayatilake; Nick J Proudfoot
Journal:  Genes Dev       Date:  2009-11-15       Impact factor: 11.361

5.  A physiological role for gene loops in yeast.

Authors:  Jean-Philippe Lainé; Badri Nath Singh; Shankarling Krishnamurthy; Michael Hampsey
Journal:  Genes Dev       Date:  2009-11-15       Impact factor: 11.361

6.  Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm.

Authors:  Bernike Kalverda; Helen Pickersgill; Victor V Shloma; Maarten Fornerod
Journal:  Cell       Date:  2010-02-05       Impact factor: 41.582

7.  Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes.

Authors:  Maya Capelson; Yun Liang; Roberta Schulte; William Mair; Ulrich Wagner; Martin W Hetzer
Journal:  Cell       Date:  2010-02-05       Impact factor: 41.582

8.  Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells.

Authors:  Stefan Schoenfelder; Tom Sexton; Lyubomira Chakalova; Nathan F Cope; Alice Horton; Simon Andrews; Sreenivasulu Kurukuti; Jennifer A Mitchell; David Umlauf; Daniela S Dimitrova; Christopher H Eskiw; Yanquan Luo; Chia-Lin Wei; Yijun Ruan; James J Bieker; Peter Fraser
Journal:  Nat Genet       Date:  2009-12-13       Impact factor: 38.330

9.  Functional characterization of an inositol-sensitive upstream activation sequence in yeast. A cis-regulatory element responsible for inositol-choline mediated regulation of phospholipid biosynthesis.

Authors:  N Bachhawat; Q Ouyang; S A Henry
Journal:  J Biol Chem       Date:  1995-10-20       Impact factor: 5.157

10.  DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery.

Authors:  Sara Ahmed; Donna G Brickner; William H Light; Ivelisse Cajigas; Michele McDonough; Alexander B Froyshteter; Tom Volpe; Jason H Brickner
Journal:  Nat Cell Biol       Date:  2010-01-24       Impact factor: 28.824

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  46 in total

Review 1.  Long-Range Chromatin Interactions.

Authors:  Job Dekker; Tom Misteli
Journal:  Cold Spring Harb Perspect Biol       Date:  2015-10-01       Impact factor: 10.005

2.  Position effect modifying gene expression in a patient with ring chromosome 14.

Authors:  Roberta Santos Guilherme; Mariana Moysés-Oliveira; Anelisa Gollo Dantas; Vera Ayres Meloni; Mileny Esbravatti Colovati; Leslie Domenici Kulikowski; Maria Isabel Melaragno
Journal:  J Appl Genet       Date:  2015-08-28       Impact factor: 3.240

3.  Light-regulated gene repositioning in Arabidopsis.

Authors:  Chun-Miao Feng; Yongjian Qiu; Elise K Van Buskirk; Emily J Yang; Meng Chen
Journal:  Nat Commun       Date:  2014       Impact factor: 14.919

4.  Approaches to studying subnuclear organization and gene-nuclear pore interactions.

Authors:  Defne Emel Egecioglu; Agustina D'Urso; Donna Garvey Brickner; William H Light; Jason H Brickner
Journal:  Methods Cell Biol       Date:  2014       Impact factor: 1.441

5.  Vps factors are required for efficient transcription elongation in budding yeast.

Authors:  Naseem A Gaur; Jiri Hasek; Donna Garvey Brickner; Hongfang Qiu; Fan Zhang; Chi-Ming Wong; Ivana Malcova; Pavla Vasicova; Jason H Brickner; Alan G Hinnebusch
Journal:  Genetics       Date:  2013-01-18       Impact factor: 4.562

6.  Visualization of the spatial positioning of the SNRPN, UBE3A, and GABRB3 genes in the normal human nucleus by three-color 3D fluorescence in situ hybridization.

Authors:  Rie Kawamura; Hideyuki Tanabe; Takahito Wada; Shinji Saitoh; Yoshimitsu Fukushima; Keiko Wakui
Journal:  Chromosome Res       Date:  2012-07-17       Impact factor: 5.239

7.  Chromatin organization as an indicator of glucocorticoid induced natural killer cell dysfunction.

Authors:  Michael S Misale; Linda Witek Janusek; Dina Tell; Herbert L Mathews
Journal:  Brain Behav Immun       Date:  2017-09-12       Impact factor: 7.217

8.  Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination.

Authors:  Frank R Neumann; Vincent Dion; Lutz R Gehlen; Monika Tsai-Pflugfelder; Roger Schmid; Angela Taddei; Susan M Gasser
Journal:  Genes Dev       Date:  2012-02-15       Impact factor: 11.361

9.  Shaping the p53 response with nucleoporins.

Authors:  Melanie L Yarbrough; Michael A White; Beatriz M A Fontoura
Journal:  Mol Cell       Date:  2012-12-14       Impact factor: 17.970

Review 10.  Structure and function in the budding yeast nucleus.

Authors:  Angela Taddei; Susan M Gasser
Journal:  Genetics       Date:  2012-09       Impact factor: 4.562

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