Bidirectional promoters generate pervasive transcription in yeast.

PubWeight™: 9.29‹?› | Rank: Top 0.1%

🔗 View Article (PMC 2766638)

Published in Nature on January 25, 2009

Authors

Zhenyu Xu1, Wu Wei, Julien Gagneur, Fabiana Perocchi, Sandra Clauder-Münster, Jurgi Camblong, Elisa Guffanti, Françoise Stutz, Wolfgang Huber, Lars M Steinmetz

Author Affiliations

1: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Articles citing this

(truncated to the top 100)

Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86

Long noncoding RNAs: functional surprises from the RNA world. Genes Dev (2009) 9.14

Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09

Comparative functional genomics of the fission yeasts. Science (2011) 6.00

Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature (2011) 5.95

Genome-wide views of chromatin structure. Annu Rev Biochem (2009) 3.89

Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature (2012) 3.58

Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell (2010) 3.42

Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol (2010) 3.25

A comparative encyclopedia of DNA elements in the mouse genome. Nature (2014) 3.22

RNA polymerase II elongation control. Annu Rev Biochem (2012) 3.09

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol (2010) 3.09

RNA-seq: from technology to biology. Cell Mol Life Sci (2009) 3.03

A quantitative atlas of polyadenylation in five mammals. Genome Res (2012) 2.87

cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev (2011) 2.78

Transcription termination by nuclear RNA polymerases. Genes Dev (2009) 2.65

Yeast Sen1 helicase protects the genome from transcription-associated instability. Mol Cell (2011) 2.59

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol (2009) 2.58

The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol (2010) 2.53

Gene loops enhance transcriptional directionality. Science (2012) 2.50

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature (2014) 2.49

GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res (2010) 2.46

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A (2009) 2.36

Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev (2009) 2.30

Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep (2009) 2.22

Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat Struct Mol Biol (2010) 2.22

Extensive transcriptional heterogeneity revealed by isoform profiling. Nature (2013) 2.14

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat Struct Mol Biol (2013) 2.11

The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L. EMBO J (2010) 2.07

RNA degradation in Saccharomyces cerevisae. Genetics (2012) 2.06

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics (2010) 2.03

The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol (2009) 2.02

Review and application of group theory to molecular systems biology. Theor Biol Med Model (2011) 2.00

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J (2011) 1.99

Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res (2011) 1.97

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cell Mol Life Sci (2012) 1.96

Gene regulation by antisense transcription. Nat Rev Genet (2013) 1.90

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A (2011) 1.85

Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol (2011) 1.83

Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet (2015) 1.81

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev (2009) 1.77

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc Natl Acad Sci U S A (2011) 1.77

Chemical-genomic dissection of the CTD code. Nat Struct Mol Biol (2010) 1.76

Cis-acting noncoding RNAs: friends and foes. Nat Struct Mol Biol (2012) 1.73

Extensive degradation of RNA precursors by the exosome in wild-type cells. Mol Cell (2012) 1.67

Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics (2011) 1.65

Functional consequences of bidirectional promoters. Trends Genet (2011) 1.61

Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell (2012) 1.61

Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics. Cell (2012) 1.61

Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell (2015) 1.60

Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA (2010) 1.59

The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation. PLoS Genet (2010) 1.59

Decapping of long noncoding RNAs regulates inducible genes. Mol Cell (2012) 1.57

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res (2011) 1.57

A complete set of nascent transcription rates for yeast genes. PLoS One (2010) 1.56

Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome. Nat Struct Mol Biol (2009) 1.56

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Res (2011) 1.56

A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell (2013) 1.55

Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol (2010) 1.54

Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol Cell (2012) 1.53

High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat Struct Mol Biol (2014) 1.53

Molecular biology: The long and short of RNAs. Nature (2009) 1.51

Transcription. Gene expression--where to start? Science (2008) 1.50

Post-licensing Specification of Eukaryotic Replication Origins by Facilitated Mcm2-7 Sliding along DNA. Mol Cell (2015) 1.50

The Landscape of long noncoding RNA classification. Trends Genet (2015) 1.47

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Res (2013) 1.47

Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PLoS Genet (2011) 1.47

Transcriptome-wide analysis of exosome targets. Mol Cell (2012) 1.46

How eukaryotic genes are transcribed. Crit Rev Biochem Mol Biol (2009) 1.46

Stable and dynamic nucleosome states during a meiotic developmental process. Genome Res (2011) 1.44

Protein-RNA networks revealed through covalent RNA marks. Nat Methods (2015) 1.44

Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol (2012) 1.44

Regulation of transcription by long noncoding RNAs. Annu Rev Genet (2014) 1.43

The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs. Cold Spring Harb Perspect Biol (2011) 1.43

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. Proc Natl Acad Sci U S A (2010) 1.39

Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res (2011) 1.37

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci U S A (2010) 1.37

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res (2012) 1.36

The Ess1 prolyl isomerase is required for transcription termination of small noncoding RNAs via the Nrd1 pathway. Mol Cell (2009) 1.35

Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription. Mol Cell Biol (2010) 1.35

Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement. Cell (2013) 1.35

Bimodal expression of PHO84 is modulated by early termination of antisense transcription. Nat Struct Mol Biol (2013) 1.34

Distinct roles of non-canonical poly(A) polymerases in RNA metabolism. PLoS Genet (2009) 1.33

The many roles of the conserved eukaryotic Paf1 complex in regulating transcription, histone modifications, and disease states. Biochim Biophys Acta (2012) 1.32

GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. Database (Oxford) (2010) 1.31

An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res (2013) 1.30

Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing. Nucleic Acids Res (2010) 1.30

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. Genome Biol (2014) 1.30

RNA polymerase II collision interrupts convergent transcription. Mol Cell (2012) 1.28

RNA polymerase II transcription elongation control. Chem Rev (2013) 1.27

Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination. Mol Cell (2012) 1.26

Exo- and endoribonucleolytic activities of yeast cytoplasmic and nuclear RNA exosomes are dependent on the noncatalytic core and central channel. Mol Cell (2012) 1.24

Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast. Biochim Biophys Acta (2012) 1.24

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res (2013) 1.24

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res (2011) 1.23

Threading the barrel of the RNA exosome. Trends Biochem Sci (2013) 1.22

Histone variants: dynamic punctuation in transcription. Genes Dev (2014) 1.22

Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae. PLoS One (2010) 1.21

Two distinct repressive mechanisms for histone 3 lysine 4 methylation through promoting 3'-end antisense transcription. PLoS Genet (2012) 1.21

Articles cited by this

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99

The transcriptional landscape of the mammalian genome. Science (2005) 37.63

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84

Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85

Genome-scale identification of nucleosome positions in S. cerevisiae. Science (2005) 15.04

A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21

A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81

Genome-wide transcription and the implications for genomic organization. Nat Rev Genet (2007) 9.45

Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature (2007) 8.68

Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell (2005) 8.55

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res (2008) 7.89

Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature (2004) 6.83

Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol (2007) 6.53

Chromatin remodelling at promoters suppresses antisense transcription. Nature (2007) 6.11

Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol (2008) 5.88

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res (2007) 5.54

A gene expression map for the euchromatic genome of Drosophila melanogaster. Science (2004) 5.38

Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell (2007) 5.13

Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet (2008) 4.03

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A (2007) 3.52

Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2006) 3.49

Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell (2006) 3.49

Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics (2006) 2.94

A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev (2008) 2.44

Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet (2005) 2.39

A role for noncoding transcription in activation of the yeast PHO5 gene. Proc Natl Acad Sci U S A (2007) 2.33

Repression of ADH1 and ADH3 during zinc deficiency by Zap1-induced intergenic RNA transcripts. EMBO J (2006) 1.56

Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome. Nucleic Acids Res (2007) 1.36

Chance and necessity in chromosomal gene distributions. Trends Genet (2008) 1.13

Articles by these authors

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

Differential expression analysis for sequence count data. Genome Biol (2010) 64.56

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48

Enterotypes of the human gut microbiome. Nature (2011) 24.36

A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature (2010) 9.95

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (2005) 9.84

Variation in transcription factor binding among humans. Science (2010) 9.33

Software for computing and annotating genomic ranges. PLoS Comput Biol (2013) 8.20

Role of duplicate genes in genetic robustness against null mutations. Nature (2003) 7.81

Evolutionary rate in the protein interaction network. Science (2002) 7.75

A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol (2004) 7.23

Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter. Nature (2011) 6.48

Detecting differential usage of exons from RNA-seq data. Genome Res (2012) 6.34

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell (2012) 6.22

Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res (2008) 6.15

High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature (2008) 6.10

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. Bioinformatics (2008) 5.95

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res (2007) 5.54

A global map of human gene expression. Nat Biotechnol (2010) 5.32

Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci U S A (2010) 5.21

Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell (2007) 5.13

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature (2009) 4.96

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc (2013) 4.00

Analysis of cell-based RNAi screens. Genome Biol (2006) 3.99

Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature (2009) 3.85

The genomic and transcriptomic landscape of a HeLa cell line. G3 (Bethesda) (2013) 3.82

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc (2009) 3.77

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A (2007) 3.52

Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol Cell Biol (2002) 3.18

Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics (2010) 3.10

Nutrient-sensitized screening for drugs that shift energy metabolism from mitochondrial respiration to glycolysis. Nat Biotechnol (2010) 3.08

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res (2013) 2.97

Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies susceptibility loci at PLCE1 and C20orf54. Nat Genet (2010) 2.95

Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics (2006) 2.94

Extensive variation in chromatin states across humans. Science (2013) 2.83

Genetic analysis of variation in transcription factor binding in yeast. Nature (2010) 2.69

Yeast Sen1 helicase protects the genome from transcription-associated instability. Mol Cell (2011) 2.59

THO/Sub2p functions to coordinate 3'-end processing with gene-nuclear pore association. Cell (2008) 2.58

Gene loops enhance transcriptional directionality. Science (2012) 2.50

Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics (2007) 2.50

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat Methods (2011) 2.47

GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res (2010) 2.46

EBImage--an R package for image processing with applications to cellular phenotypes. Bioinformatics (2010) 2.42

Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila. Dev Cell (2008) 2.41

4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res (2007) 2.38

Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol (2004) 2.31

Importing ArrayExpress datasets into R/Bioconductor. Bioinformatics (2009) 2.17

MICU1 controls both the threshold and cooperative activation of the mitochondrial Ca²⁺ uniporter. Cell Metab (2013) 2.15

Extensive transcriptional heterogeneity revealed by isoform profiling. Nature (2013) 2.14

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat Struct Mol Biol (2013) 2.11

Directional tissue migration through a self-generated chemokine gradient. Nature (2013) 2.06

Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Nat Biotechnol (2012) 2.06

Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol Syst Biol (2010) 2.03

arrayMagic: two-colour cDNA microarray quality control and preprocessing. Bioinformatics (2004) 2.02

Complex genetic interactions in a quantitative trait locus. PLoS Genet (2006) 1.95

Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. Curr Biol (2011) 1.94

mRNA export: an assembly line from genes to nuclear pores. Curr Opin Cell Biol (2004) 1.92

Gene regulation by antisense transcription. Nat Rev Genet (2013) 1.90

Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Rep (2012) 1.84

Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol (2011) 1.83

Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2005) 1.83

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev (2009) 1.77

Cotranscriptional recruitment to the mRNA export receptor Mex67p contributes to nuclear pore anchoring of activated genes. Mol Cell Biol (2006) 1.75

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Nat Methods (2013) 1.72

Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII protein, Sec23. Nat Cell Biol (2003) 1.70

Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics (2008) 1.68

Extensive degradation of RNA precursors by the exosome in wild-type cells. Mol Cell (2012) 1.67

Perinuclear Mlp proteins downregulate gene expression in response to a defect in mRNA export. EMBO J (2005) 1.65

Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae. Science (2009) 1.63

Argatroban therapy for heparin-induced thrombocytopenia in ICU patients with multiple organ dysfunction syndrome: a retrospective study. Crit Care (2010) 1.63

Functional consequences of bidirectional promoters. Trends Genet (2011) 1.61

Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics. Cell (2012) 1.61

An Optogenetic Method to Modulate Cell Contractility during Tissue Morphogenesis. Dev Cell (2015) 1.59

Nuclear export of RNA. Biol Cell (2004) 1.56

easyRNASeq: a bioconductor package for processing RNA-Seq data. Bioinformatics (2012) 1.55

Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription. Proc Natl Acad Sci U S A (2006) 1.54

Auditory evoked potentials compared with bispectral index for monitoring of midazolam and propofol sedation during colonoscopy. Am J Gastroenterol (2009) 1.53

Incidence of acute pancreatitis does not increase during Oktoberfest, but is higher than previously described in Germany. Clin Gastroenterol Hepatol (2011) 1.52

High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol (2010) 1.51

Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3. BMC Genomics (2010) 1.50

A compendium to ensure computational reproducibility in high-dimensional classification tasks. Stat Appl Genet Mol Biol (2004) 1.48