Published in Mol Cell on April 15, 2005
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet (2007) 9.56
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell (2009) 6.54
Genome-wide views of chromatin structure. Annu Rev Biochem (2009) 3.89
Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol (2010) 3.25
Glucose signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev (2006) 3.16
A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res (2009) 2.89
Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Biochim Biophys Acta (2010) 2.86
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res (2008) 2.62
Isolation of quiescent and nonquiescent cells from yeast stationary-phase cultures. J Cell Biol (2006) 2.60
beta-Catenin primes organizer gene expression by recruiting a histone H3 arginine 8 methyltransferase, Prmt2. Dev Cell (2010) 2.44
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol (2006) 2.43
Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. Proc Natl Acad Sci U S A (2009) 2.39
Global regulation of promoter melting in naive lymphocytes. Cell (2013) 2.05
Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA (2007) 1.99
A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nat Genet (2006) 1.86
The transition from transcriptional initiation to elongation. Curr Opin Genet Dev (2008) 1.78
Cellular strategies of protein quality control. Cold Spring Harb Perspect Biol (2011) 1.74
Interaction of a DNA zip code with the nuclear pore complex promotes H2A.Z incorporation and INO1 transcriptional memory. Mol Cell (2010) 1.71
Transcription factor distribution in Escherichia coli: studies with FNR protein. Nucleic Acids Res (2006) 1.70
Promoter proximal pausing on genes in metazoans. Chromosoma (2008) 1.64
A global view of transcriptional regulation by nuclear receptors: gene expression, factor localization, and DNA sequence analysis. Nucl Recept Signal (2008) 1.62
Postrecruitment regulation of RNA polymerase II directs rapid signaling responses at the promoters of estrogen target genes. Mol Cell Biol (2008) 1.60
Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response. Mol Cell Biol (2008) 1.54
Actin bodies in yeast quiescent cells: an immediately available actin reserve? Mol Biol Cell (2006) 1.49
How eukaryotic genes are transcribed. Crit Rev Biochem Mol Biol (2009) 1.46
DNA replication stress is a determinant of chronological lifespan in budding yeast. PLoS One (2007) 1.46
Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res (2008) 1.45
Transcription through chromatin by RNA polymerase II: histone displacement and exchange. Mutat Res (2007) 1.38
Transcriptional regulation in yeast during diauxic shift and stationary phase. OMICS (2010) 1.38
The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders. Genome Biol (2006) 1.36
Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation. J Bacteriol (2011) 1.31
To grow or not to grow: nutritional control of development during Caenorhabditis elegans L1 arrest. Genetics (2013) 1.30
Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol (2009) 1.29
A conserved role for human Nup98 in altering chromatin structure and promoting epigenetic transcriptional memory. PLoS Biol (2013) 1.27
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
Metabolic status rather than cell cycle signals control quiescence entry and exit. J Cell Biol (2011) 1.25
Two distinct repressive mechanisms for histone 3 lysine 4 methylation through promoting 3'-end antisense transcription. PLoS Genet (2012) 1.21
Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun (2012) 1.19
Differentiation-dependent functional and epigenetic landscapes for cytokine genes in virus-specific CD8+ T cells. Proc Natl Acad Sci U S A (2011) 1.18
RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast. Genome Biol (2010) 1.17
Defining the chromatin signature of inducible genes in T cells. Genome Biol (2009) 1.15
Spn1 regulates the recruitment of Spt6 and the Swi/Snf complex during transcriptional activation by RNA polymerase II. Mol Cell Biol (2007) 1.14
A rapid genome-wide response to Drosophila melanogaster social interactions. BMC Genomics (2007) 1.14
The Spt4-Spt5 complex: a multi-faceted regulator of transcription elongation. Biochim Biophys Acta (2012) 1.11
Protein kinase A, TOR, and glucose transport control the response to nutrient repletion in Saccharomyces cerevisiae. Eukaryot Cell (2007) 1.11
Regulon-specific control of transcription elongation across the yeast genome. PLoS Genet (2009) 1.10
Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. J Biol Chem (2008) 1.08
Global distribution of negative cofactor 2 subunit-alpha on human promoters. Proc Natl Acad Sci U S A (2007) 1.08
Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks. Genome Biol (2007) 1.07
Dominant mutants of the Saccharomyces cerevisiae ASF1 histone chaperone bypass the need for CAF-1 in transcriptional silencing by altering histone and Sir protein recruitment. Genetics (2006) 1.07
Chromatin architecture and transcription factor binding regulate expression of erythrocyte membrane protein genes. Mol Cell Biol (2009) 1.06
Global Promoter Targeting of a Conserved Lysine Deacetylase for Transcriptional Shutoff during Quiescence Entry. Mol Cell (2015) 1.04
Mouse cofactor of BRCA1 (Cobra1) is required for early embryogenesis. PLoS One (2009) 1.01
Genome reprogramming during sporulation. Int J Dev Biol (2009) 0.99
Genome-wide location analysis reveals a role for Sub1 in RNA polymerase III transcription. Proc Natl Acad Sci U S A (2009) 0.99
Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress. Genome Biol (2006) 0.98
Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Mol Syst Biol (2013) 0.97
Nuclear pore interactions with the genome. Curr Opin Genet Dev (2014) 0.94
Pol II docking and pausing at growth and stress genes in C. elegans. Cell Rep (2014) 0.91
A Screen for Germination Mutants in Saccharomyces cerevisiae. G3 (Bethesda) (2011) 0.91
Transcription reactivation steps stimulated by oocyte maturation in C. elegans. Dev Biol (2006) 0.90
A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover. PLoS Genet (2011) 0.89
Proliferation/Quiescence: When to start? Where to stop? What to stock? Cell Div (2011) 0.89
Stb3 plays a role in the glucose-induced transition from quiescence to growth in Saccharomyces cerevisiae. Genetics (2010) 0.89
Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome. BMC Evol Biol (2006) 0.87
Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase. BMC Syst Biol (2009) 0.86
Exploiting Issatchenkia orientalis SD108 for succinic acid production. Microb Cell Fact (2014) 0.85
Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae. G3 (Bethesda) (2011) 0.85
Histone methylation has dynamics distinct from those of histone acetylation in cell cycle reentry from quiescence. Mol Cell Biol (2014) 0.84
Nuclear pore proteins regulate chromatin structure and transcriptional memory by a conserved mechanism. Nucleus (2013) 0.84
RNA polymerase trafficking in Bacillus subtilis cells. J Bacteriol (2010) 0.84
Timing of transcriptional quiescence during gametogenesis is controlled by global histone H3K4 demethylation. Dev Cell (2012) 0.83
Cordycepin-hypersensitive growth links elevated polyphosphate levels to inhibition of poly(A) polymerase in Saccharomyces cerevisiae. Nucleic Acids Res (2007) 0.83
Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response. BMC Genomics (2012) 0.83
Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis. BMC Genomics (2012) 0.82
How epigenomics contributes to the understanding of gene regulation in Toxoplasma gondii. J Eukaryot Microbiol (2009) 0.82
m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence. Genome Biol (2012) 0.81
Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory. Elife (2016) 0.81
Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes. Genome Biol (2014) 0.81
Splitting hares and tortoises: a classification of neuronal immediate early gene transcription based on poised RNA polymerase II. Neuroscience (2013) 0.81
Glucose, nitrogen, and phosphate repletion in Saccharomyces cerevisiae: common transcriptional responses to different nutrient signals. G3 (Bethesda) (2012) 0.81
Proliferation/quiescence: the controversial "aller-retour". Cell Div (2011) 0.80
A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. BMC Biol (2015) 0.79
Sub1 and Maf1, two effectors of RNA polymerase III, are involved in the yeast quiescence cycle. PLoS One (2014) 0.78
The Transition of Poised RNA Polymerase II to an Actively Elongating State Is a "Complex" Affair. Genet Res Int (2011) 0.78
Global genetic response in a cancer cell: self-organized coherent expression dynamics. PLoS One (2014) 0.78
Histone hypoacetylation-activated genes are repressed by acetyl-CoA- and chromatin-mediated mechanism. Biochim Biophys Acta (2014) 0.77
RNAP-II molecules participate in the anchoring of the ORC to rDNA replication origins. PLoS One (2013) 0.77
Interferon-γ resets muscle cell fate by stimulating the sequential recruitment of JARID2 and PRC2 to promoters to repress myogenesis. Sci Signal (2013) 0.77
Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae. Biotechnol Biofuels (2014) 0.76
Microtubules move the nucleus to quiescence. Nucleus (2014) 0.76
CRP-cyclic AMP dependent inhibition of the xylene-responsive σ(54)-promoter Pu in Escherichia coli. PLoS One (2014) 0.76
Ups and Downs of Poised RNA Polymerase II in B-Cells. PLoS Comput Biol (2016) 0.75
Distinct histone methylation and transcription profiles are established during the development of cellular quiescence in yeast. BMC Genomics (2017) 0.75
Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. Microb Cell (2016) 0.75
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2003) 15.48
Mediator and cohesin connect gene expression and chromatin architecture. Nature (2010) 14.34
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics (2007) 7.93
Specific inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector. EMBO Rep (2003) 4.52
Expression Profiler: next generation--an online platform for analysis of microarray data. Nucleic Acids Res (2004) 4.21
Functional organization of the S. cerevisiae phosphorylation network. Cell (2009) 3.15
Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell (2002) 3.07
An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas. Nat Genet (2005) 3.04
My5C: web tools for chromosome conformation capture studies. Nat Methods (2009) 2.96
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol (2011) 2.79
Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Rep (2003) 2.51
Poised RNA polymerase II gives pause for thought. Cell (2008) 2.48
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J (2011) 2.38
Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell (2010) 2.29
Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol Cell (2005) 2.21
Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol Cell (2006) 2.16
A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res (2004) 2.15
The specificity and topology of chromatin interaction pathways in yeast. Mol Cell (2011) 2.04
Genome-wide RNA polymerase II: not genes only! Trends Biochem Sci (2008) 2.02
Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet (2012) 1.98
From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell (2013) 1.87
Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol (2011) 1.85
A central role for TFIID in the pluripotent transcription circuitry. Nature (2013) 1.82
Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol (2012) 1.80
ArrayExpress: a public database of gene expression data at EBI. C R Biol (2004) 1.78
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res (2012) 1.65
Gene expression profiling of early intervertebral disc degeneration reveals a down-regulation of canonical Wnt signaling and caveolin-1 expression: implications for development of regenerative strategies. Arthritis Res Ther (2013) 1.57
Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome. Nat Struct Mol Biol (2009) 1.56
In control: systematic assessment of microarray performance. EMBO Rep (2004) 1.55
Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation. EMBO J (2012) 1.55
A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. Mol Syst Biol (2009) 1.43
Redox-sensitive cysteines bridge p300/CBP-mediated acetylation and FoxO4 activity. Nat Chem Biol (2009) 1.40
Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes Dev (2008) 1.38
CCR4/NOT complex associates with the proteasome and regulates histone methylation. Proc Natl Acad Sci U S A (2007) 1.30
Multiple robust signatures for detecting lymph node metastasis in head and neck cancer. Cancer Res (2006) 1.27
E2F7 represses a network of oscillating cell cycle genes to control S-phase progression. Nucleic Acids Res (2011) 1.26
Mot1p is essential for TBP recruitment to selected promoters during in vivo gene activation. EMBO J (2002) 1.25
Twenty-two novel mutations in the lysosomal alpha-glucosidase gene (GAA) underscore the genotype-phenotype correlation in glycogen storage disease type II. Hum Mutat (2004) 1.22
Predicting gene function through systematic analysis and quality assessment of high-throughput data. Bioinformatics (2004) 1.21
Two distinct repressive mechanisms for histone 3 lysine 4 methylation through promoting 3'-end antisense transcription. PLoS Genet (2012) 1.21
Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Nucleic Acids Res (2011) 1.20
A consensus of core protein complex compositions for Saccharomyces cerevisiae. Mol Cell (2010) 1.19
Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One (2012) 1.16
The Ccr4-NOT deadenylase subunits CNOT7 and CNOT8 have overlapping roles and modulate cell proliferation. Mol Biol Cell (2009) 1.14
PDGFRB promotes liver metastasis formation of mesenchymal-like colorectal tumor cells. Neoplasia (2013) 1.11
Adaptable gene-specific dye bias correction for two-channel DNA microarrays. Mol Syst Biol (2009) 1.09
Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification. Nucleic Acids Res (2008) 1.07
Cotranslational assembly of the yeast SET1C histone methyltransferase complex. EMBO J (2009) 1.06
Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol (2010) 1.05
Distinct role of Mediator tail module in regulation of SAGA-dependent, TATA-containing genes in yeast. EMBO J (2011) 1.05
Critical roles for a genetic code alteration in the evolution of the genus Candida. EMBO J (2007) 1.04
Balancing of histone H3K4 methylation states by the Kdm5c/SMCX histone demethylase modulates promoter and enhancer function. Cell Rep (2013) 1.03
Possible role of the innate immunity in temporal lobe epilepsy. Epilepsia (2007) 1.03
Structure-system correlation identifies a gene regulatory Mediator submodule. Genes Dev (2008) 1.03
Tight control of MEK-ERK activation is essential in regulating proliferation, survival, and cytokine production of CD34+-derived neutrophil progenitors. Blood (2009) 1.00
Maintenance of head and neck tumor gene expression profiles upon lymph node metastasis. Cancer Res (2006) 0.99
Gene expression profiling and phenotype analyses of S. cerevisiae in response to changing copper reveals six genes with new roles in copper and iron metabolism. Physiol Genomics (2005) 0.98
Retinoic acid-dependent and -independent gene-regulatory pathways of Pitx3 in meso-diencephalic dopaminergic neurons. Development (2011) 0.98
H2B ubiquitylation controls the formation of export-competent mRNP. Mol Cell (2012) 0.97
Specification of dopaminergic subsets involves interplay of En1 and Pitx3. Development (2013) 0.96
CoCAS: a ChIP-on-chip analysis suite. Bioinformatics (2009) 0.95
Early host responses to avian influenza A virus are prolonged and enhanced at transcriptional level depending on maturation of the immune system. Mol Immunol (2010) 0.95
Fibronectin is a hypoxia-independent target of the tumor suppressor VHL. FEBS Lett (2004) 0.94
Initiating RNA polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity. Transcription (2011) 0.94