Published in RNA on April 15, 2009
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol (2011) 2.37
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Coupled evolution of transcription and mRNA degradation. PLoS Biol (2011) 1.40
The HOG pathway dictates the short-term translational response after hyperosmotic shock. Mol Biol Cell (2010) 1.21
Kaposi's sarcoma-associated herpesvirus ORF57 protein binds and protects a nuclear noncoding RNA from cellular RNA decay pathways. PLoS Pathog (2010) 1.18
Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II. PLoS Genet (2011) 1.16
Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res (2012) 1.14
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Yeast mRNA cap-binding protein Cbc1/Sto1 is necessary for the rapid reprogramming of translation after hyperosmotic shock. Mol Biol Cell (2011) 0.91
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Distinct redox regulation in sub-cellular compartments in response to various stress conditions in Saccharomyces cerevisiae. PLoS One (2013) 0.90
The Hog1 stress-activated protein kinase targets nucleoporins to control mRNA export upon stress. J Biol Chem (2013) 0.88
Stress granule-defective mutants deregulate stress responsive transcripts. PLoS Genet (2014) 0.88
Integrity and function of the Saccharomyces cerevisiae spindle pole body depends on connections between the membrane proteins Ndc1, Rtn1, and Yop1. Genetics (2012) 0.86
Mediator phosphorylation prevents stress response transcription during non-stress conditions. J Biol Chem (2012) 0.85
What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast. PLoS Comput Biol (2016) 0.84
Diverse functions of mRNA metabolism factors in stress defense and aging of Caenorhabditis elegans. PLoS One (2014) 0.83
Systematic analysis of the role of RNA-binding proteins in the regulation of RNA stability. PLoS Genet (2014) 0.81
Stress-induced nuclear RNA degradation pathways regulate yeast bromodomain factor 2 to promote cell survival. PLoS Genet (2014) 0.81
Comparing transcription rate and mRNA abundance as parameters for biochemical pathway and network analysis. PLoS One (2010) 0.81
Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress. RNA Biol (2014) 0.81
Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress. PLoS One (2013) 0.81
An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Mol Microbiol (2014) 0.80
Hog1 targets Whi5 and Msa1 transcription factors to downregulate cyclin expression upon stress. Mol Cell Biol (2015) 0.80
Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes. PLoS Genet (2015) 0.80
Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals. PLoS Genet (2015) 0.80
TimeXNet: identifying active gene sub-networks using time-course gene expression profiles. BMC Syst Biol (2014) 0.80
RNA-dependent regulation of the cell wall stress response. Nucleic Acids Res (2012) 0.79
Osmostress-induced gene expression--a model to understand how stress-activated protein kinases (SAPKs) regulate transcription. FEBS J (2015) 0.79
Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex. RNA (2016) 0.78
cDREM: inferring dynamic combinatorial gene regulation. J Comput Biol (2015) 0.78
A stress-activated, p38 mitogen-activated protein kinase-ATF/CREB pathway regulates posttranscriptional, sequence-dependent decay of target RNAs. Mol Cell Biol (2013) 0.78
A novel role for lncRNAs in cell cycle control during stress adaptation. Curr Genet (2014) 0.78
Cth2 Protein Mediates Early Adaptation of Yeast Cells to Oxidative Stress Conditions. PLoS One (2016) 0.77
The importance of controlling mRNA turnover during cell proliferation. Curr Genet (2016) 0.77
Analysis of osmoadaptation system in budding yeast suggests that regulated degradation of glycerol synthesis enzyme is key to near-perfect adaptation. Syst Synth Biol (2013) 0.77
Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae. BMC Genomics (2014) 0.77
The bidirectional cytomegalovirus immediate/early promoter is regulated by Hog1 and the stress transcription factors Sko1 and Hot1 in yeast. Mol Genet Genomics (2010) 0.77
Genomic insights into the different layers of gene regulation in yeast. Genet Res Int (2011) 0.76
The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast. Transcription (2012) 0.75
A prior-based integrative framework for functional transcriptional regulatory network inference. Nucleic Acids Res (2016) 0.75
Regulation of mRNA decay in plant responses to salt and osmotic stress. Cell Mol Life Sci (2016) 0.75
Growth rate controls mRNA turnover in steady and non-steady states. RNA Biol (2016) 0.75
Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response. Mol Cell Proteomics (2016) 0.75
An mRNA decapping mutant deficient in P body assembly limits mRNA stabilization in response to osmotic stress. Sci Rep (2017) 0.75
The interplay between transcription and mRNA degradation in Saccharomyces cerevisiae. Microb Cell (2017) 0.75
Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis. Plant Cell (2017) 0.75
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Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science (2003) 12.90
Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell (2006) 12.73
P bodies and the control of mRNA translation and degradation. Mol Cell (2007) 9.98
The highways and byways of mRNA decay. Nat Rev Mol Cell Biol (2007) 8.42
Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A (2002) 8.20
Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA (2005) 6.54
Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Science (2005) 6.26
Mammalian stress granules and processing bodies. Methods Enzymol (2007) 4.76
The transcriptional response of Saccharomyces cerevisiae to osmotic shock. Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J Biol Chem (2000) 4.51
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Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol (2004) 3.72
Global analysis of stress-regulated mRNA turnover by using cDNA arrays. Proc Natl Acad Sci U S A (2002) 3.71
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An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. Nucleic Acids Res (1998) 2.92
The transcriptional response of yeast to saline stress. J Biol Chem (2000) 2.91
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Stress-induced map kinase Hog1 is part of transcription activation complexes. Mol Cell (2001) 2.23
Yeast osmoregulation. Methods Enzymol (2007) 2.18
MAP kinase-mediated stress relief that precedes and regulates the timing of transcriptional induction. Cell (2004) 2.09
Hog1 mediates cell-cycle arrest in G1 phase by the dual targeting of Sic1. Nat Cell Biol (2004) 2.07
Dealing with osmostress through MAP kinase activation. EMBO Rep (2002) 2.04
Osmostress-induced transcription by Hot1 depends on a Hog1-mediated recruitment of the RNA Pol II. EMBO J (2003) 1.90
The stress-activated Hog1 kinase is a selective transcriptional elongation factor for genes responding to osmotic stress. Mol Cell (2006) 1.85
Control of mRNA decay by phosphorylation of tristetraprolin. Biochem Soc Trans (2008) 1.85
Transient inhibition of translation initiation by osmotic stress. J Biol Chem (2002) 1.78
Regulated ARE-mediated mRNA decay in Saccharomyces cerevisiae. Mol Cell (2001) 1.75
A third osmosensing branch in Saccharomyces cerevisiae requires the Msb2 protein and functions in parallel with the Sho1 branch. Mol Cell Biol (2002) 1.58
Genomics and gene transcription kinetics in yeast. Trends Genet (2007) 1.50
Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol Cell Biol (2005) 1.50
Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA (2008) 1.45
Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae. RNA (2006) 1.40
Global mRNA stabilization preferentially linked to translational repression during the endoplasmic reticulum stress response. Mol Cell Biol (2004) 1.38
RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress. EMBO J (2003) 1.35
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. Genome Biol (2005) 1.31
Comprehensive transcriptional analysis of the oxidative response in yeast. J Biol Chem (2008) 1.25
Stressed out! Effects of environmental stress on mRNA metabolism. FEMS Yeast Res (2006) 1.14
Genome-wide location analysis of the stress-activated MAP kinase Hog1 in yeast. Methods (2006) 1.13
Inhibition of mRNA deadenylation and degradation by different types of cell stress. Biol Chem (2006) 1.07
Expression of the HXT13, HXT15 and HXT17 genes in Saccharomyces cerevisiae and stabilization of the HXT1 gene transcript by sugar-induced osmotic stress. Curr Genet (2006) 0.99
Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell (2004) 2.99
Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell (2013) 1.81
A complete set of nascent transcription rates for yeast genes. PLoS One (2010) 1.56
Genomics and gene transcription kinetics in yeast. Trends Genet (2007) 1.50
The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression. J Cell Biol (2008) 1.40
The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes. Genome Biol (2007) 1.31
Comprehensive transcriptional analysis of the oxidative response in yeast. J Biol Chem (2008) 1.25
Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Yeast (2002) 1.19
SRC1: an intron-containing yeast gene involved in sister chromatid segregation. Yeast (2002) 1.17
A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding. Nucleic Acids Res (2010) 1.17
The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast. Yeast (2008) 1.14
Saccharomyces cerevisiae glutaredoxin 5-deficient cells subjected to continuous oxidizing conditions are affected in the expression of specific sets of genes. J Biol Chem (2004) 1.13
The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors. Nucleic Acids Res (2010) 1.12
Regulon-specific control of transcription elongation across the yeast genome. PLoS Genet (2009) 1.10
A new set of DNA macrochips for the yeast Saccharomyces cerevisiae: features and uses. Int Microbiol (2004) 1.10
Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities. PLoS One (2011) 1.07
Regulation of copper transport in Arabidopsis thaliana: a biochemical oscillator? J Biol Inorg Chem (2009) 1.04
Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression. J Mol Biol (2013) 1.04
Common gene expression strategies revealed by genome-wide analysis in yeast. Genome Biol (2007) 1.04
Chimeric genomes of natural hybrids of Saccharomyces cerevisiae and Saccharomyces kudriavzevii. Appl Environ Microbiol (2009) 0.98
There is a steady-state transcriptome in exponentially growing yeast cells. Yeast (2010) 0.92
Yeast mRNA cap-binding protein Cbc1/Sto1 is necessary for the rapid reprogramming of translation after hyperosmotic shock. Mol Biol Cell (2011) 0.91
Study of the first hours of microvinification by the use of osmotic stress-response genes as probes. Syst Appl Microbiol (2002) 0.89
A genomic study of the inter-ORF distances in Saccharomyces cerevisiae. Yeast (2006) 0.87
Preoperative inspiratory muscular training to prevent postoperative hypoxemia in morbidly obese patients undergoing laparoscopic bariatric surgery. A randomized clinical trial. Obes Surg (2015) 0.86
Cysteines 449 and 459 modulate the reduction-oxidation conformational changes of ribulose 1.5-bisphosphate carboxylase/oxygenase and the translocation of the enzyme to membranes during stress. Plant Cell Environ (2006) 0.86
Modification of the proteolytic fragmentation pattern upon oxidation of cysteines from ribulose 1,5-bisphosphate carboxylase/oxygenase. Biochemistry (2003) 0.83
What do you mean by transcription rate?: the conceptual difference between nascent transcription rate and mRNA synthesis rate is essential for the proper understanding of transcriptomic analyses. Bioessays (2013) 0.82
Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress. PLoS One (2013) 0.81
Arginase activity is a useful marker of nitrogen limitation during alcoholic fermentations. Syst Appl Microbiol (2003) 0.80
Structural characterization of chromosome I size variants from a natural yeast strain. Yeast (2003) 0.80
Dissection of the elements of osmotic stress response transcription factor Hot1 involved in the interaction with MAPK Hog1 and in the activation of transcription. Biochim Biophys Acta (2013) 0.79
The conserved foot domain of RNA pol II associates with proteins involved in transcriptional initiation and/or early elongation. Genetics (2011) 0.79
Substitution of tyrosine residues at the aromatic cluster around the betaA-betaB loop of rubisco small subunit affects the structural stability of the enzyme and the in vivo degradation under stress conditions. Biochemistry (2006) 0.79
External conditions inversely change the RNA polymerase II elongation rate and density in yeast. Biochim Biophys Acta (2013) 0.78
Tracking organic matter and microbiota dynamics during the stages of lignocellulosic waste composting. Bioresour Technol (2013) 0.77
Topoisomerase II regulates yeast genes with singular chromatin architectures. Nucleic Acids Res (2013) 0.77
The bidirectional cytomegalovirus immediate/early promoter is regulated by Hog1 and the stress transcription factors Sko1 and Hot1 in yeast. Mol Genet Genomics (2010) 0.77
Yeast HAT1 and HAT2 deletions have different life-span and transcriptome phenotypes. FEBS Lett (2005) 0.77
Reversible inhibition of CO2 fixation by ribulose 1,5-bisphosphate carboxylase/oxygenase through the synergic effect of arsenite and a monothiol. Plant Cell Environ (2013) 0.76
Genomic-wide methods to evaluate transcription rates in yeast. Methods Mol Biol (2011) 0.76
Compost as a source of microbial isolates for the bioremediation of heavy metals: in vitro selection. Sci Total Environ (2012) 0.76
mRNAStab--a web application for mRNA stability analysis. Bioinformatics (2013) 0.75
The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast. Transcription (2012) 0.75
Ecotoxicity and fungal deterioration of recycled polypropylene/wood composites: effect of wood content and coupling. Chemosphere (2013) 0.75
Global estimation of mRNA stability in yeast. Methods Mol Biol (2011) 0.75