Diverse transcriptional initiation revealed by fine, large‐scale mapping of mRNA start sites

No abstract is available for this paper.

• Publication year

  2001

• Venue

  EMBO Reports

• Publication date

  2001-05-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/embo-reports/kve085PMID 11375929PMCID PMC1083880
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Identification and characterization of the potential promoter regions of 1031 kinds of human genes.

  2001cited by this paper
• The Eukaryotic Promoter Database (EPD)

  2000cited by this paper
• Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries.

  2000cited by this paper
• Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms

  1999cited by this paper
• Yeast RNA polymerase II at 5 A resolution.

  1999cited by this paper
• Estimating transcription factor bindability on DNA

  1999cited by this paper
• The Eukaryotic Promoter Database EPD

  1998cited by this paper
• Regulation of gene expression by TBP-associated proteins.

  1998cited by this paper
• Analysis of exon/intron structure and 400 kb of genomic sequence surrounding the 5'-promoter and 3'-terminal ends of the human glypican 3 (GPC3) gene.

  1997cited by this paper
• Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library.

  1997cited by this paper
• Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes.

  1997influential reference
• The general transcription factors of RNA polymerase II.

  1996cited by this paper
• The role of general initiation factors in transcription by RNA polymerase II.

  1996cited by this paper
• Censor - a Program for Identification and Elimination of Repetitive Elements From DNA Sequences

  1996cited by this paper
• Core promoters and transcriptional control.

  1996cited by this paper
• Revolutions in rapid amplification of cDNA ends: new strategies for polymerase chain reaction cloning of full-length cDNA ends.

  1995cited by this paper
• Crystal structure of a TFIIB–TBP–TATA-element ternary complex

  1995cited by this paper
• Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides.

  1994cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins.

  1989cited by this paper
• Alternative processing of RNA transcribed from NMYC

  1987cited by this paper
• The human albumin gene. Characterization of the 5' and 3' flanking regions and the polymorphic gene transcripts.

  1986cited by this paper
• Transcriptional control signals of a eukaryotic protein-coding gene.

  1982cited by this paper
• Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids.

  1977cited by this paper
• Yeast RNA Polymerases

  1976cited by this paper

• Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels

  2024cites this paper
• Saccharomyces 1 cerevisiae reveals control by DNA sequence , RNA Polymerase II activity , and NTP 2 levels 3 4

  2023cites this paper
• Prediction of transcript structure and concentration using RNA-Seq data

  2023cites this paper
• Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics

  2022cites this paper
• Implications of differential transcription start site selection on chronic myeloid leukemia and prostate cancer cell protein expression

  2022cites this paper
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  2022cites this paper
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  2021cites this paper
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  2021cites this paper
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  2019cites this paper
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  2018influential citation
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  2018cites this paper
• Promoter shape varies across populations and affects promoter evolution and expression noise

  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2016cites this paper
• Association of U2AF35, U2AF65 and U2 snRNP with constitutively and alternatively spliced pre-mRNA

  2016cites this paper
• Identification and characterization of a novel promoter for the human ANO1 gene regulated by the transcription factor signal transducer and activator of transcription 6 (STAT6)

  2015cites this paper
• TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis

  2015cites this paper
• The genome-wide identification of promoter regions in Toxoplasma gondii.

  2015cites this paper
• CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

  2015cites this paper
• Identification and refinement of two strong constitutive promoters for gene expression system of Schizosaccharomyces pombe

  2014cites this paper
• Bioinformatic methods for eukaryotic RNA-Seq-based promoter identification

  2014cites this paper
• DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data

  2014cites this paper
• Analysis of changes in transcription start site distribution by a classification approach.

  2014cites this paper
• 5′-Cap selection methods and their application in full-length cDNA library construction and transcription start site profiling

  2014cites this paper
• Explaining the correlations among properties of mammalian promoters

  2014cites this paper
• The transcription start site landscape of C. elegans

  2013cites this paper
• Mechanism of action of GGA, a targeted oligonucleotide enhancer of splicing developed for the treatment of spinal muscular atrophy

  2013cites this paper
• Identification of a novel Pfkfb1 mRNA variant in rat fetal liver.

  2013cites this paper
• In silico investigation of glossina morsitans promoters

  2013cites this paper
• Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters

  2013cites this paper
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  2013cites this paper
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  2012cites this paper
• Transcription start sites and usage of the first exon of mouse Foxp3 gene

  2012cites this paper
• Species-specific 5'-genomic structure and multiple transcription start sites in the chicken Pax5 gene.

  2011cites this paper
• DBTSS: DataBase of Transcriptional Start Sites progress report in 2012

  2011cites this paper
• A new algorithm of promoter prediction and identification

  2011cites this paper
• Emergence of the Diversified Short ORFeome by Mass Spectrometry-Based Proteomics

  2011influential citation
• Predicting promoter activities of primary human DNA sequences

  2011cites this paper
• Global identification of transcription start sites in the genome of Apis mellifera using 5'LongSAGE.

  2011cites this paper
• Genomic and chromatin signals underlying transcription start-site selection.

  2011cites this paper
• Systematic Clustering of Transcription Start Site Landscapes

  2011cites this paper
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  2010cites this paper
• Systems biology of mammalian circadian clocks.

  2010cites this paper
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  2010cites this paper
• Comprehensive gene expression analysis of 5'-end of mRNA identified novel intronic transcripts associated with hepatocellular carcinoma.

  2010cites this paper
• Alternative translation start sites are conserved in eukaryotic genomes

  2010cites this paper
• Regulation of gene expression via the core promoter and the basal transcriptional machinery.

  2010cites this paper
• High-throughput functional analysis of human gene promoters using transfected cell arrays

  2010cites this paper
• Regulatory feedback loop between NF‐κB and MCP‐1‐induced protein 1 RNase

  2009cites this paper
• An ensemble model of competitive multi-factor binding of the genome.

  2009cites this paper
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  2009cites this paper
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  2009cites this paper
• Lessons Learned from Genomic CAGE

  2009cites this paper
• Generating EST libraries: trans-spliced cDNAs.

  2009cites this paper
• P2Y2 Receptor Transcription Is Increased by NF-κB and Stimulates Cyclooxygenase-2 Expression and PGE2 Released by Intestinal Epithelial Cells1

  2009cites this paper
• Expressed Sequence Tags (ESTs) Generation and Analysis

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• IRF9 is a Key Factor for Eliciting the Antiproliferative Activity of IFN-α

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• genome An ensemble model of competitive multi-factor binding of the Material

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• Transcriptional control of human organic anion transporting polypeptide 2B1 gene.

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• Transcriptional regulation of the human ST6GAL2 gene in cerebral cortex and neuronal cells

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• Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions

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• Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics

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• Regulation of the ETn/MusD family of active mouse long terminal repeat retrotransposons

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• DNA sequence and structural properties as predictors of human and mouse promoters

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• Alternative splicing: current perspectives

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• Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms

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• Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method

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• Transcription of the human plasma prekallikrein gene: demonstration of alternative promoters, multiple initiation sites, and alternative splicing and identification of cis-acting DNA elements.

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• The RNA continent.

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• Hormonal regulation of cardiac KCNE2 gene expression.

  2008cites this paper
• Opisthorchis viverrini: Gene expression profiling of carcinogenic adult liver fluke worms using 5' SAGE.

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