Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization.
Jason M. Casolari,Christopher R. Brown,Suzanne Komili,Jason A. West,Haley Hieronymus,Pamela A. Silver +5 more
TLDR
It is shown that transcriptional activation of the GAL genes results in their association with nuclear pore proteins, relocation to the nuclear periphery, and loss of RanGEF association, which indicates that the organization of the genome is coupled via transcriptional state to thenuclear transport machinery.About:
This article is published in Cell.The article was published on 2004-05-14 and is currently open access. It has received 586 citations till now. The article focuses on the topics: Nucleoporin & Nuclear pore.read more
Citations
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Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling
TL;DR: Using singular value decomposition in transforming genome-wide expression data from genes x arrays space to reduced diagonalized "eigengenes" x "eigenarrays" space gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype.
Journal Article
The Genomic Code for Nucleosome Positioning
TL;DR: In this article, a nucleosome-DNA interaction model was proposed to predict the genome-wide organization of nucleosomes, and it was shown that genomes encode an intrinsic nucleosomal organization and that this intrinsic organization can explain ∼50% of the in-vivo positions.
Journal ArticleDOI
A genomic code for nucleosome positioning
Eran Segal,Yvonne N. Fondufe-Mittendorf,Lingyi Chen,Annchristine Thåström,Yair Field,Irene K. Moore,Ji Ping Wang,Jonathan Widom +7 more
TL;DR: This work isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosom–DNA interaction model, and to predict the genome-wide organization of nucleosomes.
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Beyond the sequence : Cellular organization of genome function
TL;DR: The functional relevance of spatial and temporal genome organization at three hierarchical levels: the organization of nuclear processes, the higher-order organization of the chromatin fiber, and the spatial arrangement of genomes within the cell nucleus are discussed.
Journal ArticleDOI
Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions
TL;DR: This work has shown that the dynamic nature of the positioning of genetic material in the nuclear space and the higher-order architecture of the nucleus are integrated is essential to the overall understanding of gene regulation.
References
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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Systematic determination of genetic network architecture
TL;DR: A systematic set of statistical algorithms are applied, based on whole-genome mRNA data, partitional clustering and motif discovery, to identify transcriptional regulatory sub-networks in yeast—without any a priori knowledge of their structure or any assumptions about their dynamics.
PatentDOI
Dissecting the regulatory circuitry of a eukaryotic genome
TL;DR: The results reveal an unanticipated level of regulation which is superimposed on that due to gene-specific transcription factors, a novel mechanism for coordinate regulation of specific sets of genes when cells encounter limiting nutrients, and evidence that the ultimate targets of signal transduction pathways can be identified within the initiation apparatus.
PatentDOI
Genome-wide location and function of dna binding proteins
TL;DR: In this paper, a method for identifying a set of genes where cell cycle regulator binding correlates with gene expression and identifying genomic targets of cell cycle transcription activators in living cells is also encompassed.
Journal ArticleDOI
Singular value decomposition for genome-wide expression data processing and modeling
TL;DR: In this article, singular value decomposition is used to transform genome-wide expression data from genes 3 arrays space to reduced diagonalized eigengenes 3 eigenarrays space.
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