Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells

Persistent Link:
http://hdl.handle.net/10150/610400
Title:
Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells
Author:
Barthelson, Roger; Lambert, Georgina; Vanier, Cheryl; Lynch, Ronald; Galbraith, David
Affiliation:
Bio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA; Department of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154, USA; Department of Physiology, University of Arizona, Tucson, Arizona 85721, USA
Issue Date:
2007
Publisher:
BioMed Central
Citation:
BMC Genomics 2007, 8:340 doi:10.1186/1471-2164-8-340
Journal:
BMC Genomics
Rights:
© 2007 Barthelson et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:In the most general sense, studies involving global analysis of gene expression aim to provide a comprehensive catalog of the components involved in the production of recognizable cellular phenotypes. These studies are often limited by the available technologies. One technology, based on microarrays, categorizes gene expression in terms of the abundance of RNA transcripts, and typically employs RNA prepared from whole cells, where cytoplasmic RNA predominates.RESULTS:Using microarrays comprising oligonucleotide probes that represent either protein-coding transcripts or microRNAs (miRNA), we have studied global transcript accumulation patterns for the HepG2 (human hepatoma) cell line. Through subdividing the total pool of RNA transcripts into samples from nuclei, the cytoplasm, and whole cells, we determined the degree of correlation of these patterns across these different subcellular locations. The transcript and miRNA abundance patterns for the three RNA fractions were largely similar, but with some exceptions: nuclear RNA samples were enriched with respect to the cytoplasm in transcripts encoding proteins associated with specific nuclear functions, such as the cell cycle, mitosis, and transcription. The cytoplasmic RNA fraction also was enriched, when compared to the nucleus, in transcripts for proteins related to specific nuclear functions, including the cell cycle, DNA replication, and DNA repair. Some transcripts related to the ubiquitin cycle, and transcripts for various membrane proteins were sorted into either the nuclear or cytoplasmic fractions.CONCLUSION:Enrichment or compartmentalization of cell cycle and ubiquitin cycle transcripts within the nucleus may be related to the regulation of their expression, by preventing their translation to proteins. In this way, these cellular functions may be tightly controlled by regulating the release of mRNA from the nucleus and thereby the expression of key rate limiting steps in these pathways. Many miRNA precursors were also enriched in the nuclear samples, with significantly fewer being enriched in the cytoplasm. Studies of mRNA localization will help to clarify the roles RNA processing and transport play in the regulation of cellular function.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-8-340
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/8/340

Full metadata record

DC FieldValue Language
dc.contributor.authorBarthelson, Rogeren
dc.contributor.authorLambert, Georginaen
dc.contributor.authorVanier, Cherylen
dc.contributor.authorLynch, Ronalden
dc.contributor.authorGalbraith, Daviden
dc.date.accessioned2016-05-20T09:05:59Z-
dc.date.available2016-05-20T09:05:59Z-
dc.date.issued2007en
dc.identifier.citationBMC Genomics 2007, 8:340 doi:10.1186/1471-2164-8-340en
dc.identifier.doi10.1186/1471-2164-8-340en
dc.identifier.urihttp://hdl.handle.net/10150/610400-
dc.description.abstractBACKGROUND:In the most general sense, studies involving global analysis of gene expression aim to provide a comprehensive catalog of the components involved in the production of recognizable cellular phenotypes. These studies are often limited by the available technologies. One technology, based on microarrays, categorizes gene expression in terms of the abundance of RNA transcripts, and typically employs RNA prepared from whole cells, where cytoplasmic RNA predominates.RESULTS:Using microarrays comprising oligonucleotide probes that represent either protein-coding transcripts or microRNAs (miRNA), we have studied global transcript accumulation patterns for the HepG2 (human hepatoma) cell line. Through subdividing the total pool of RNA transcripts into samples from nuclei, the cytoplasm, and whole cells, we determined the degree of correlation of these patterns across these different subcellular locations. The transcript and miRNA abundance patterns for the three RNA fractions were largely similar, but with some exceptions: nuclear RNA samples were enriched with respect to the cytoplasm in transcripts encoding proteins associated with specific nuclear functions, such as the cell cycle, mitosis, and transcription. The cytoplasmic RNA fraction also was enriched, when compared to the nucleus, in transcripts for proteins related to specific nuclear functions, including the cell cycle, DNA replication, and DNA repair. Some transcripts related to the ubiquitin cycle, and transcripts for various membrane proteins were sorted into either the nuclear or cytoplasmic fractions.CONCLUSION:Enrichment or compartmentalization of cell cycle and ubiquitin cycle transcripts within the nucleus may be related to the regulation of their expression, by preventing their translation to proteins. In this way, these cellular functions may be tightly controlled by regulating the release of mRNA from the nucleus and thereby the expression of key rate limiting steps in these pathways. Many miRNA precursors were also enriched in the nuclear samples, with significantly fewer being enriched in the cytoplasm. Studies of mRNA localization will help to clarify the roles RNA processing and transport play in the regulation of cellular function.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/8/340en
dc.rights© 2007 Barthelson et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleComparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cellsen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentBio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USAen
dc.contributor.departmentDepartment of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154, USAen
dc.contributor.departmentDepartment of Physiology, University of Arizona, Tucson, Arizona 85721, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
All Items in UA Campus Repository are protected by copyright, with all rights reserved, unless otherwise indicated.