Published in PLoS Genet on September 08, 2011
RNA degradation in Saccharomyces cerevisae. Genetics (2012) 2.06
Ccr4-Not complex: the control freak of eukaryotic cells. Crit Rev Biochem Mol Biol (2012) 1.43
A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability. RNA (2012) 1.32
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
The fate of the messenger is pre-determined: a new model for regulation of gene expression. Biochim Biophys Acta (2013) 1.08
The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts. PLoS Genet (2012) 1.00
Sequestration of highly expressed mRNAs in cytoplasmic granules, P-bodies, and stress granules enhances cell viability. PLoS Genet (2012) 1.00
Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics. Sci Adv (2016) 0.93
Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects. PLoS Comput Biol (2013) 0.90
The AMP-activated protein kinase Snf1 regulates transcription factor binding, RNA polymerase II activity, and mRNA stability of glucose-repressed genes in Saccharomyces cerevisiae. J Biol Chem (2012) 0.89
Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome. Nucleic Acids Res (2012) 0.89
XRN1 stalling in the 5' UTR of Hepatitis C virus and Bovine Viral Diarrhea virus is associated with dysregulated host mRNA stability. PLoS Pathog (2015) 0.88
Uncoupling of mRNA synthesis and degradation impairs adaptation to host temperature in Cryptococcus neoformans. Mol Microbiol (2013) 0.87
The control of elongation by the yeast Ccr4-not complex. Biochim Biophys Acta (2012) 0.87
Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res (2012) 0.85
Widespread promoter-mediated coordination of transcription and mRNA degradation. Genome Biol (2012) 0.84
The Rpb4/7 module of RNA polymerase II is required for carbon catabolite repressor protein 4-negative on TATA (Ccr4-not) complex to promote elongation. J Biol Chem (2014) 0.84
hCAF1/CNOT7 regulates interferon signalling by targeting STAT1. EMBO J (2013) 0.83
The 5'-3' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs. RNA Biol (2013) 0.82
Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress. RNA Biol (2014) 0.81
Systematic dissection of the sequence determinants of gene 3' end mediated expression control. PLoS Genet (2015) 0.80
Transcriptional priming of cytoplasmic post-transcriptional regulation. Transcription (2011) 0.78
The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons. Nucleic Acids Res (2015) 0.78
A novel cis-acting element from the 3'UTR of DNA damage-binding protein 2 mRNA links transcriptional and post-transcriptional regulation of gene expression. Nucleic Acids Res (2013) 0.78
The importance of controlling mRNA turnover during cell proliferation. Curr Genet (2016) 0.77
RNA biology and the adaptation of Cryptococcus neoformans to host temperature and stress. Wiley Interdiscip Rev RNA (2014) 0.76
One third of dynamic protein expression profiles can be predicted by a simple rate equation. Mol Biosyst (2014) 0.76
Multidimensional adaptive evolution of a feed-forward network and the illusion of compensation. Evolution (2012) 0.76
The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts. PLoS One (2017) 0.75
The interplay between transcription and mRNA degradation in Saccharomyces cerevisiae. Microb Cell (2017) 0.75
Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A (2002) 8.20
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A (2002) 6.93
Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol (2007) 4.31
Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science (2010) 3.87
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
Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell (2004) 2.99
Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc Natl Acad Sci U S A (2003) 2.92
RNA polymerase II subunits link transcription and mRNA decay to translation. Cell (2010) 2.67
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci U S A (2005) 2.57
Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell (2007) 2.51
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol (2011) 2.37
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol (2008) 2.27
EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Sci Signal (2010) 2.16
Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell (2010) 2.12
Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae. RNA (2009) 1.66
Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol (2009) 1.64
The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes Dev (2005) 1.60
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
RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit. Nat Struct Mol Biol (2005) 1.48
Major role for mRNA stability in shaping the kinetics of gene induction. BMC Genomics (2010) 1.46
Coupled evolution of transcription and mRNA degradation. PLoS Biol (2011) 1.40
Global coordination of transcriptional control and mRNA decay during cellular differentiation. Mol Syst Biol (2010) 1.34
Rpb7 can interact with RNA polymerase II and support transcription during some stresses independently of Rpb4. Mol Cell Biol (1999) 1.31
The Rpb4 subunit of RNA polymerase II contributes to cotranscriptional recruitment of 3' processing factors. Mol Cell Biol (2008) 1.29
The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol (2007) 1.26
Comprehensive transcriptional analysis of the oxidative response in yeast. J Biol Chem (2008) 1.25
mRNA stability changes precede changes in steady-state mRNA amounts during hyperosmotic stress. RNA (2009) 1.25
Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud. Genes Dev (2010) 1.24
Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes. Genes Dev (2008) 1.18
Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. J Biol Chem (2008) 1.08
Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress. Mol Biol Cell (2003) 1.08
Whole genome expression profiles of yeast RNA polymerase II core subunit, Rpb4, in stress and nonstress conditions. J Biol Chem (2002) 1.05
Nucleocytoplasmic shuttling of the Rpb4p and Rpb7p subunits of Saccharomyces cerevisiae RNA polymerase II by two pathways. Eukaryot Cell (2006) 1.03
Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Mol Cell Biol (2003) 1.03
mRNA imprinting: Additional level in the regulation of gene expression. Cell Logist (2011) 0.91
Noise in protein expression scales with natural protein abundance. Nat Genet (2006) 8.03
An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell (2010) 4.45
Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol (2007) 4.31
Transcription control reprogramming in genetic backup circuits. Nat Genet (2005) 3.36
Adaptive prediction of environmental changes by microorganisms. Nature (2009) 3.19
Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep (2006) 2.96
Differentially regulated micro-RNAs and actively translated messenger RNA transcripts by tumor suppressor p53 in colon cancer. Clin Cancer Res (2006) 2.72
RNA polymerase II subunits link transcription and mRNA decay to translation. Cell (2010) 2.67
Promoter elements regulate cytoplasmic mRNA decay. Cell (2011) 2.50
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol (2008) 2.27
Determinants of translation efficiency and accuracy. Mol Syst Biol (2011) 2.24
EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Sci Signal (2010) 2.16
Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res (2002) 2.04
p53-Repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation. Mol Syst Biol (2008) 2.04
Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nat Genet (2007) 1.92
Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell (2013) 1.81
Axonal transcription factors signal retrogradely in lesioned peripheral nerve. EMBO J (2012) 1.77
Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J Mol Biol (2002) 1.73
Chromosomal duplication is a transient evolutionary solution to stress. Proc Natl Acad Sci U S A (2012) 1.61
The regulatory utilization of genetic redundancy through responsive backup circuits. Proc Natl Acad Sci U S A (2006) 1.61
The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes Dev (2005) 1.60
The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol Syst Biol (2005) 1.60
Signaling to transcription networks in the neuronal retrograde injury response. Sci Signal (2010) 1.57
A deleterious mutation in SAMD9 causes normophosphatemic familial tumoral calcinosis. Am J Hum Genet (2006) 1.57
Genetic redundancy: new tricks for old genes. Cell (2009) 1.48
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. Genome Biol (2005) 1.31
Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data. Nucleic Acids Res (2005) 1.27
Regulatory mechanisms and networks couple the different phases of gene expression. Trends Genet (2011) 1.27
Alopecia, neurological defects, and endocrinopathy syndrome caused by decreased expression of RBM28, a nucleolar protein associated with ribosome biogenesis. Am J Hum Genet (2008) 1.27
The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol (2007) 1.26
The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1. J Mol Biol (2003) 1.23
Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks. Mol Biol Cell (2002) 1.20
Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes. Genes Dev (2008) 1.18
SERKAL syndrome: an autosomal-recessive disorder caused by a loss-of-function mutation in WNT4. Am J Hum Genet (2008) 1.16
PERK-dependent compartmentalization of ERAD and unfolded protein response machineries during ER stress. Exp Cell Res (2007) 1.14
Preferential protection of protein interaction network hubs in yeast: evolved functionality of genetic redundancy. Proc Natl Acad Sci U S A (2008) 1.13
The fate of the messenger is pre-determined: a new model for regulation of gene expression. Biochim Biophys Acta (2013) 1.08
Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress. Mol Biol Cell (2003) 1.08
Coupling transcriptional and post-transcriptional miRNA regulation in the control of cell fate. Aging (Albany NY) (2009) 1.07
Bypass of glycan-dependent glycoprotein delivery to ERAD by up-regulated EDEM1. Mol Biol Cell (2011) 1.05
Subcellular transcriptomics-dissection of the mRNA composition in the axonal compartment of sensory neurons. Dev Neurobiol (2013) 1.05
Can molecular motors drive distance measurements in injured neurons? PLoS Comput Biol (2009) 1.04
Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression. J Mol Biol (2013) 1.04
Nucleocytoplasmic shuttling of the Rpb4p and Rpb7p subunits of Saccharomyces cerevisiae RNA polymerase II by two pathways. Eukaryot Cell (2006) 1.03
3D model of the Escherichia coli multidrug transporter MdfA reveals an essential membrane-embedded positive charge. Biochemistry (2005) 1.00
The eukaryotic transcriptional machinery regulates mRNA translation and decay in the cytoplasm. Biochim Biophys Acta (2012) 0.99
A mathematical model for adaptive prediction of environmental changes by microorganisms. Proc Natl Acad Sci U S A (2011) 0.99
Functional characterization of variations on regulatory motifs. PLoS Genet (2008) 0.99
The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery. Bioinformatics (2013) 0.96
tRNA genes rapidly change in evolution to meet novel translational demands. Elife (2013) 0.96
Repression of transposable-elements - a microRNA anti-cancer defense mechanism? Trends Genet (2010) 0.91
Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode. Genome Biol (2010) 0.90
Conceptual modeling in systems biology fosters empirical findings: the mRNA lifecycle. PLoS One (2007) 0.90
Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. Nucleic Acids Res (2003) 0.90
A shared endoplasmic reticulum-associated degradation pathway involving the EDEM1 protein for glycosylated and nonglycosylated proteins. J Biol Chem (2012) 0.90
Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects. PLoS Comput Biol (2013) 0.90
Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome. Nucleic Acids Res (2012) 0.89
Nucleotide variation of regulatory motifs may lead to distinct expression patterns. Bioinformatics (2007) 0.89
Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies. Nucleic Acids Res (2011) 0.88
Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression. PLoS Comput Biol (2012) 0.85
Widespread promoter-mediated coordination of transcription and mRNA degradation. Genome Biol (2012) 0.84
The role of codon selection in regulation of translation efficiency deduced from synthetic libraries. Genome Biol (2011) 0.82
Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.80
Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle. PLoS One (2012) 0.78
CpG Islands as a putative source for animal miRNAs: evolutionary and functional implications. Mol Biol Evol (2010) 0.76
Correction: Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates. PLoS Biol (2017) 0.75
Promoting human promoters. Mol Syst Biol (2006) 0.75