Post-transcriptional control of gene expression: a genome-wide perspective.

Gene expression is regulated at multiple levels, and cells need to integrate and coordinate different layers of control to implement the information in the genome. Post-transcriptional levels of regulation such as transcript turnover and translational control are an integral part of gene expression and might rival the sophistication and importance of transcriptional control. Microarray-based methods are increasingly used to study not only transcription but also global patterns of transcript decay and translation rates in addition to comprehensively identify targets of RNA-binding proteins. Such large-scale analyses have recently provided supplementary and unique insights into gene expression programs. Integration of several different datasets will ultimately lead to a system-wide understanding of the varied and complex mechanisms for gene expression control.

[1]  J. Heierhorst,et al.  Ccr4-Not Complex mRNA Deadenylase Activity Contributes to DNA Damage Responses in Saccharomyces cerevisiae , 2005, Genetics.

[2]  T. E. Dever,et al.  Gene-Specific Regulation by General Translation Factors , 2002, Cell.

[3]  R. Aebersold,et al.  Gene Expression Analyzed by High-resolution State Array Analysis and Quantitative Proteomics , 2004, Molecular & Cellular Proteomics.

[4]  J. Lieb,et al.  Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. , 2004, Current opinion in genetics & development.

[5]  H. Beug,et al.  Translation control: bridging the gap between genomics and proteomics? , 2001, Trends in biochemical sciences.

[6]  N. Socci,et al.  Oncogenic Ras and Akt signaling contribute to glioblastoma formation by differential recruitment of existing mRNAs to polysomes. , 2003, Molecular cell.

[7]  P. Brown,et al.  Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast , 2004, PLoS biology.

[8]  Roger E Bumgarner,et al.  The Transcriptome and Its Translation during Recovery from Cell Cycle Arrest in Saccharomyces cerevisiae* , 2003, Molecular & Cellular Proteomics.

[9]  S. Hanash,et al.  Global and Specific Translational Control by Rapamycin in T Cells Uncovered by Microarrays and Proteomics* , 2002, The Journal of Biological Chemistry.

[10]  C. Guthrie,et al.  Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Daniel Herschlag,et al.  Dissecting eukaryotic translation and its control by ribosome density mapping , 2005, Nucleic acids research.

[12]  Andreas Beyer,et al.  Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale*S , 2004, Molecular & Cellular Proteomics.

[13]  C. Norbury,et al.  Translation initiation and its deregulation during tumorigenesis , 2002, British Journal of Cancer.

[14]  S. Tenenbaum,et al.  Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Wilusz,et al.  Bringing the role of mRNA decay in the control of gene expression into focus. , 2004, Trends in genetics : TIG.

[16]  Arkady B. Khodursky,et al.  Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Steven E Brenner,et al.  Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. , 2004, Molecular cell.

[18]  E. Winzeler,et al.  Genomics, gene expression and DNA arrays , 2000, Nature.

[19]  Haiwei Song,et al.  The enzymes and control of eukaryotic mRNA turnover , 2004, Nature Structural &Molecular Biology.

[20]  G. Church,et al.  Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. , 2003, Genome research.

[21]  M. Schummer,et al.  Messenger RNA translation state: the second dimension of high-throughput expression screening. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[22]  A. Khodursky,et al.  Life after transcription--revisiting the fate of messenger RNA. , 2003, Trends in genetics : TIG.

[23]  T. Preiss,et al.  Translational profiling: the genome-wide measure of the nascent proteome. , 2004, Briefings in functional genomics & proteomics.

[24]  M. Gorospe,et al.  Global analysis of stress-regulated mRNA turnover by using cDNA arrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Francisco Martinez-Murillo,et al.  Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise , 2004, Nature Genetics.

[26]  S. Peltz,et al.  The cap-to-tail guide to mRNA turnover , 2001, Nature Reviews Molecular Cell Biology.

[27]  P. Pandolfi,et al.  Does the ribosome translate cancer? , 2003, Nature Reviews Cancer.

[28]  M. Collart.  Global control of gene expression in yeast by the Ccr4-Not complex. , 2003, Gene.

[29]  D. Thiele,et al.  Coordinated Remodeling of Cellular Metabolism during Iron Deficiency through Targeted mRNA Degradation , 2005, Cell.

[30]  S. Kuersten,et al.  The power of the 3′ UTR: translational control and development , 2003, Nature Reviews Genetics.

[31]  J. Boothroyd,et al.  Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay , 2005, Nature Biotechnology.

[32]  Patrick O. Brown,et al.  Global and Specific Translational Regulation in the Genomic Response of Saccharomyces cerevisiae to a Rapid Transfer from a Fermentable to a Nonfermentable Carbon Source , 2001, Molecular and Cellular Biology.

[33]  J. Pérez-Ortín,et al.  Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. , 2004, Molecular cell.

[34]  S. Tenenbaum,et al.  Eukaryotic mRNPs may represent posttranscriptional operons. , 2002, Molecular cell.

[35]  P. Brown,et al.  Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Cornelia I Bargmann,et al.  Comparing genomic expression patterns across species identifies shared transcriptional profile in aging , 2004, Nature Genetics.

[37]  Shuyun Dong,et al.  Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. , 2003, Molecular cell.

[38]  G. Orphanides,et al.  A Unified Theory of Gene Expression , 2002, Cell.

[39]  John D. Storey,et al.  Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[40]  S G Oliver,et al.  Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway. , 2003, Physiological genomics.

[41]  M. Hentze,et al.  Molecular mechanisms of translational control , 2004, Nature Reviews Molecular Cell Biology.

[42]  E. Holland,et al.  Postgenomic global analysis of translational control induced by oncogenic signaling , 2004, Oncogene.

[43]  N. Sonenberg,et al.  Translational control in stress and apoptosis , 2005, Nature Reviews Molecular Cell Biology.

[44]  Jack D. Keene,et al.  Post-transcriptional operons and regulons co-ordinating gene expression , 2005, Chromosome Research.

[45]  Pier Paolo Pandolfi,et al.  Aberrant mRNA translation in cancer pathogenesis: an old concept revisited comes finally of age , 2004, Oncogene.

[46]  P. Brown,et al.  Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Thomas Preiss,et al.  Starting the protein synthesis machine: eukaryotic translation initiation. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[48]  C. Guthrie,et al.  Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles. , 2005, RNA.

[49]  M. Magnasco,et al.  Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. , 2003, Genome research.

[50]  H. Beug,et al.  Isolation of translationally controlled mRNAs by differential screening , 2000, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[51]  J. Darnell,et al.  Microarray Identification of FMRP-Associated Brain mRNAs and Altered mRNA Translational Profiles in Fragile X Syndrome , 2001, Cell.

[52]  Ruedi Aebersold,et al.  Gene expression in yeast responding to mating pheromone: Analysis by high-resolution translation state analysis and quantitative proteomics , 2004 .

[53]  J. Cherry,et al.  Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[54]  H. Hieronymus,et al.  Genome-wide analysis of RNA–protein interactions illustrates specificity of the mRNA export machinery , 2003, Nature Genetics.

[55]  Michael N. Hall,et al.  TOR signalling in bugs, brain and brawn , 2003, Nature Reviews Molecular Cell Biology.

[56]  A. Furger,et al.  Integrating mRNA Processing with Transcription , 2002, Cell.

[57]  Thomas Preiss,et al.  Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock , 2003, Nature Structural Biology.

[58]  C. Reilly,et al.  Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. , 2002, Nucleic acids research.

[59]  T. Hughes,et al.  Genome-Wide Analysis of mRNA Stability Using Transcription Inhibitors and Microarrays Reveals Posttranscriptional Control of Ribosome Biogenesis Factors , 2004, Molecular and Cellular Biology.

[60]  Gwenael Badis,et al.  Targeted mRNA degradation by deadenylation-independent decapping. , 2004, Molecular cell.

[61]  M. Gorospe,et al.  Global mRNA Stabilization Preferentially Linked to Translational Repression during the Endoplasmic Reticulum Stress Response , 2004, Molecular and Cellular Biology.

[62]  H. Hieronymus,et al.  A systems view of mRNP biology. , 2004, Genes & development.

[63]  John D. Storey,et al.  Precision and functional specificity in mRNA decay , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Marvin Wickens,et al.  A PUF family portrait: 3'UTR regulation as a way of life. , 2002, Trends in genetics : TIG.

[65]  J. Keene.  Posttranscriptional generation of macromolecular complexes. , 2003, Molecules and Cells.

[66]  Mike Tyers,et al.  How Cells Coordinate Growth and Division , 2004, Current Biology.

[67]  James T Kadonaga,et al.  Regulation of RNA Polymerase II Transcription by Sequence-Specific DNA Binding Factors , 2004, Cell.

[68]  A. E. Hirsh,et al.  Noise Minimization in Eukaryotic Gene Expression , 2004, PLoS biology.

[69]  A. Corbett,et al.  Process or perish: quality control in mRNA biogenesis , 2005, Nature Structural &Molecular Biology.

[70]  J. Derisi,et al.  Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. , 2000, Science.

[71]  Phillip D Zamore,et al.  Perspective: machines for RNAi. , 2005, Genes & development.