Transcript quantitation in total yeast cellular RNA using kinetic PCR.

Abstract:

:Kinetically monitored, reverse transcriptase-initiated PCR (kinetic RT-PCR, kRT-PCR) is a novel application of kinetic PCR for high throughput transcript quantitation in total cellular RNA. The assay offers the simplicity and flexibility of an enzyme assay with distinct advantages over DNA microarray hybridization and SAGE technologies for certain applications. The reproducibility, sensitivity and accuracy of the kRT-PCR were assessed for yeast transcripts previously quantitated by a variety of methods including SAGE analysis. Changes in transcript levels between different genetic or physiological cell states were reproducibly quantitated with an accuracy of +/-20%. The assay was sufficiently sensitive to quantitate yeast transcripts over a range of more than five orders of magnitude, including low abundance transcripts encoding cell cycle and transcriptional regulators.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Kang JJ,Watson RM,Fisher ME,Higuchi R,Gelfand DH,Holland MJ

doi

10.1093/nar/28.2.e2

keywords:

subject

Has Abstract

pub_date

2000-01-15 00:00:00

pages

e2

issue

2

eissn

0305-1048

issn

1362-4962

pii

gnd002

journal_volume

28

pub_type

杂志文章
  • Differences in unwinding of supercoiled DNA induced by the two enantiomers of anti-benzo[a]pyrene diol epoxide.

    abstract::The unwinding of supercoiled phi X174 RFI DNA induced by the tumorigenic (+) and non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) has been investigated by agarose slab-gel and ethidium titration tube gel electrophoresis. The differences in adduct conformat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.23.6167

    authors: Xu R,Birke S,Carberry SE,Geacintov NE,Swenberg CE,Harvey RG

    更新日期:1992-12-11 00:00:00

  • Graphic methods to determine the function of nucleic acid sequences.

    abstract::We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.1part2.521

    authors: Staden R

    更新日期:1984-01-11 00:00:00

  • Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity.

    abstract::Despite the large number of noncoding RNAs in human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained on...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz1192

    authors: Zhang Z,Xiong P,Zhang T,Wang J,Zhan J,Zhou Y

    更新日期:2020-02-20 00:00:00

  • CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

    abstract::Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals in normal and pathological states (Cyclonet database). It integrates...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl912

    authors: Kolpakov F,Poroikov V,Sharipov R,Kondrakhin Y,Zakharov A,Lagunin A,Milanesi L,Kel A

    更新日期:2007-01-01 00:00:00

  • Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase.

    abstract::Aspartic acid residues comprising the -D-(aa) n -Y-L-D-D- DNA polymerase active site triad of reverse transcriptase from the Saccharomyces cerevisiae long terminal repeat-retrotransposon Ty3 (Asp151, Asp213 and Asp214) were evaluated via site-directed mutagenesis. An Asp151-->Glu substitution showed a dramatic decreas...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki150

    authors: Bibillo A,Lener D,Klarmann GJ,Le Grice SF

    更新日期:2005-01-12 00:00:00

  • Molecular mechanism of introduction of the hidden break into the 28S rRNA of insects: implication based on structural studies.

    abstract::We determined the structure around the gap region between 28S alpha and 28S beta rRNA of Bombyx mori, a lepidopteran insect, to know the introduction mechanism of the hidden break, an interruption of the phosphodiester bond specific to the 28S rRNA of protostomes. Sequence analysis and S1 nuclease mapping suggested th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.16.6393

    authors: Fujiwara H,Ishikawa H

    更新日期:1986-08-26 00:00:00

  • A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing.

    abstract::Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq667

    authors: Cantacessi C,Jex AR,Hall RS,Young ND,Campbell BE,Joachim A,Nolan MJ,Abubucker S,Sternberg PW,Ranganathan S,Mitreva M,Gasser RB

    更新日期:2010-09-01 00:00:00

  • Gene-regulatory interactions in embryonic stem cells represent cell-type specific gene regulatory programs.

    abstract::Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx752

    authors: Ha M,Hong S

    更新日期:2017-10-13 00:00:00

  • FGF: a web tool for Fishing Gene Family in a whole genome database.

    abstract::Gene duplication is an important process in evolution. The availability of genome sequences of a number of organisms has made it possible to conduct comprehensive searches for duplicated genes enabling informative studies of their evolution. We have established the FGF (Fishing Gene Family) program to efficiently sear...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm426

    authors: Zheng H,Shi J,Fang X,Li Y,Vang S,Fan W,Wang J,Zhang Z,Wang W,Kristiansen K,Wang J

    更新日期:2007-07-01 00:00:00

  • A promotor directing alpha-amanitin-sensitive transcription of GARP, the major surface antigen of insect stage Trypanosoma congolense.

    abstract::The major surface antigen of procyclic and epimastigote forms of Trypanosoma congolense in the tsetse fly is GARP (glutamic acid/alanine-rich protein), which is thought to be the analogue of procyclin/PARP in Trypanosoma brucei. We have studied two T.congolense GARP loci (the 4.3 and 4.4 loci) whose transcription is a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.2.272

    authors: Graham SV,Jefferies D,Barry JD

    更新日期:1996-01-15 00:00:00

  • PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

    abstract::Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1286

    authors: Elati M,Nicolle R,Junier I,Fernández D,Fekih R,Font J,Képès F

    更新日期:2013-02-01 00:00:00

  • Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences.

    abstract::MicroRNAs (miRNA) are short single-stranded RNA molecules derived from hairpin-forming precursors that play a crucial role as post-transcriptional regulators in eukaryotes and viruses. In the past years, many microRNA target genes (MTGs) have been identified experimentally. However, because of the high costs of experi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1085

    authors: Leclercq M,Diallo AB,Blanchette M

    更新日期:2017-01-25 00:00:00

  • Nucleotide sequence and corresponding amino acid sequence of the gene for the major antigen of foot and mouth disease virus.

    abstract::A segment of 1160 nucleotides of the FMDV genome has been sequenced using three overlapping fragments of cloned cDNA from FMDV strain O1K. This sequence contains the coding sequence for the viral capsid protein VP1 as shown by its homology to known and newly determined amino acid sequences from this man antigenic poly...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.8.1919

    authors: Kurz C,Forss S,Küpper H,Strohmaier K,Schaller H

    更新日期:1981-04-24 00:00:00

  • Ribosome A and P sites revealed by length analysis of ribosome profiling data.

    abstract::The high-throughput sequencing of nuclease-protected mRNA fragments bound to ribosomes, a technique known as ribosome profiling, quantifies the relative frequencies with which different regions of transcripts are translated. This technique has revealed novel translation initiation sites with unprecedented scope and ha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv200

    authors: Martens AT,Taylor J,Hilser VJ

    更新日期:2015-04-20 00:00:00

  • Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation.

    abstract::The Escherichia coli AlkB protein catalyzes the direct reversal of alkylation damage to DNA; primarily 1-methyladenine (1mA) and 3-methylcytosine (3mC) lesions created by endogenous or environmental alkylating agents. AlkB is a member of the non-heme iron (II) alpha-ketoglutarate-dependent dioxygenase superfamily, whi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm1031

    authors: Roy TW,Bhagwat AS

    更新日期:2007-01-01 00:00:00

  • Human immunodeficiency virus reverse transcriptase and protease sequence database.

    abstract::The HIV RT and Protease Sequence Database is an online relational database that catalogs evolutionary and drug-related human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease sequence variation (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protea...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.1.346

    authors: Shafer RW,Jung DR,Betts BJ,Xi Y,Gonzales MJ

    更新日期:2000-01-01 00:00:00

  • Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions.

    abstract::The wobble uridine of certain bacterial and mitochondrial tRNAs is modified, at position 5, through an unknown reaction pathway that utilizes the evolutionarily conserved MnmE and GidA proteins. The resulting modification (a methyluridine derivative) plays a critical role in decoding NNG/A codons and reading frame mai...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp762

    authors: Moukadiri I,Prado S,Piera J,Velázquez-Campoy A,Björk GR,Armengod ME

    更新日期:2009-11-01 00:00:00

  • The mouse proline-rich protein MP6 promoter binds isoprenaline-inducible parotid nuclear proteins via a highly conserved NFkB/rel-like site.

    abstract::Proline-rich protein (PRP) gene MP6 was isolated from a mouse BALB/c genomic DNA library in lambda EMBL3, characterised by hybridisation and restriction mapping and the promoter region, from -162 to +72 around the PRP consensus cap-site, was sequenced. In gel shift assays this region formed complexes C1 and C2 with pa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.19.5205

    authors: Roberts SG,Layfield R,McDonald CJ

    更新日期:1991-10-11 00:00:00

  • High level heterologous expression in E. coli using the anaerobically-activated nirB promoter.

    abstract::The anaerobically-regulated nirB promoter was used to express heterologous genes in Escherichia coli. Under anaerobic conditions the promoter was able to express tetanus toxin fragment C at approximately 20% total cell protein (tcp) and the Bordetella pertussis antigen pertactin at greater than 30% tcp. These levels a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.11.2889

    authors: Oxer MD,Bentley CM,Doyle JG,Peakman TC,Charles IG,Makoff AJ

    更新日期:1991-06-11 00:00:00

  • Replication-induced stimulation of the major late promoter of adenovirus is correlated to the binding of a factor to sequences in the first intron.

    abstract::The sequence requirements for transcriptional stimulation of the adenovirus major late promoter (MLP) by the products of the early transcription unit Ela and by the replication of viral DNA were analyzed by in vitro transcription. Sequences upstream of +33 are involved in the moderate Ela-responsiveness of the MLP, wh...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.9.3771

    authors: Jansen-Durr P,Boeuf H,Kédinger C

    更新日期:1988-05-11 00:00:00

  • COVID19 Drug Repository: text-mining the literature in search of putative COVID19 therapeutics.

    abstract::The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa969

    authors: Tworowski D,Gorohovski A,Mukherjee S,Carmi G,Levy E,Detroja R,Mukherjee SB,Frenkel-Morgenstern M

    更新日期:2021-01-08 00:00:00

  • Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection.

    abstract::Short interfering RNAs (siRNAs) are valuable reagents for sequence-specific inhibition of gene expression via the RNA interference (RNAi) pathway. Although it has been proposed that the relative thermodynamic stability at the 5'-ends of siRNAs plays a crucial role in siRNA strand selection, we demonstrate here that a ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn584

    authors: Sano M,Sierant M,Miyagishi M,Nakanishi M,Takagi Y,Sutou S

    更新日期:2008-10-01 00:00:00

  • Some bacterial tRNA genes are transcribed by eukaryotic RNA polymerase III.

    abstract::E. coli genes for tRNAasp and tRNAtrp are transcribed by eukaryotic RNA polymerase III upon injection into nuclei of Xenopus oocytes. This indicates that some bacterial tRNA genes contain RNA polymerase III promoter sequences. We discuss evolutionary aspects of this finding. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.22.7153

    authors: Folk WR,Hofstetter H,Birnstiel ML

    更新日期:1982-11-25 00:00:00

  • Ribosomal protein eL24, involved in two intersubunit bridges, stimulates translation initiation and elongation.

    abstract::Interactions between subunits in the Saccharomyces cerevisiae ribosome are mediated by universal and eukaryote-specific intersubunit bridges. Universal bridges are positioned close to the ribosomal functional centers, while eukaryote-specific bridges are mainly located on the periphery of the ribosome. Two bridges, eB...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky1083

    authors: Kisly I,Remme J,Tamm T

    更新日期:2019-01-10 00:00:00

  • Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.

    abstract::Multi-modal interactions are frequently observed in intrinsically disordered regions (IDRs) of proteins upon binding to their partners. In many cases, post-translational modifications in IDRs are accompanied by coupled folding and binding. From both molecular simulations and biochemical experiments with mutational stu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx1297

    authors: Kasahara K,Shiina M,Higo J,Ogata K,Nakamura H

    更新日期:2018-03-16 00:00:00

  • Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target.

    abstract::This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/gkr729

    authors: Krzyzosiak WJ,Sobczak K,Wojciechowska M,Fiszer A,Mykowska A,Kozlowski P

    更新日期:2012-01-01 00:00:00

  • The cellular mismatch repair system is able to repair mismatches within MLV retroviral double-stranded DNA at a low frequency.

    abstract::Eukaryotic cells possess several distinct mismatch repair pathways. A mismatch can be introduced in retroviral double-stranded DNA by a pre-existing mutation within the primer binding site (PBS) of the viral RNA genome. In order to evaluate mismatch repair of retroviral double-stranded DNA, Moloney leukemia virus (MLV...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.12.2302

    authors: Tang LY,Zhang J

    更新日期:2000-06-15 00:00:00

  • Regulation of adenovirus alternative RNA splicing at the level of commitment complex formation.

    abstract::The adenovirus late region 1 (L1) represents an example of an alternatively spliced gene where one 5' splice site is spliced to two alternative 3' splice sites, to produce two mRNAs; the 52,55K and IIIa mRNAs, respectively. Accumulation of the L1 mRNAs is temporally regulated during the infectious cycle. Thus, the pro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.3.332

    authors: Kreivi JP,Akusjärvi G

    更新日期:1994-02-11 00:00:00

  • Investigating the role of the Est3 protein in yeast telomere replication.

    abstract::The Est3 subunit of yeast telomerase, which adopts a predicted OB-fold, is essential for telomere replication. To assess the possible contributions that Est3 might make to enzyme catalysis, we compared telomerase activity from wild type and est3-Delta strains of Saccharomyces castellii, which revealed that loss of the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1173

    authors: Lee J,Mandell EK,Rao T,Wuttke DS,Lundblad V

    更新日期:2010-04-01 00:00:00

  • New observations concerning the chloroacetaldehyde reaction with some tRNA constituents. Stable intermediates, kinetics and selectivity of the reaction.

    abstract::The stable intermediates formed in the reaction of cytosine, cytidine and adenosine with chloracetaldehyde were isolated. The -CH2CH/OH/- bridge between the exo and endo nitrogen atoms of the parent base was found in these compounds by means of PMR spectroscopy. Their acid-induced dehydration resulted in formation of ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/5.3.789

    authors: Biernat J,Ciesiołka J,Górnicki P,Adamiak RW,Kryzosiak WJ,Wiewiórowski M

    更新日期:1978-03-01 00:00:00