Abstract：
:A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called identification of specific cleavage position (ISCP), which enables the identification of direct endoribonuclease targets in vivo by comparing the 5΄ and 3΄ ends of processed transcripts between wild type and RNase deficient strains. To demonstrate the ISCP method, we used as a model the double-stranded specific RNase III in the human pathogen Streptococcus pyogenes. We mapped 92 specific cleavage positions (SCPs) among which, 48 were previously described and 44 are new, with the characteristic 2 nucleotides 3΄ overhang of RNase III. Most SCPs were located in untranslated regions of RNAs. We screened for RNase III targets using transcriptomic differential expression analysis (DEA) and compared those with the RNase III targets identified using the ISCP method. Our study shows that in S. pyogenes, under standard growth conditions, RNase III has a limited impact both on antisense transcripts and on global gene expression with the expression of most of the affected genes being downregulated in an RNase III deletion mutant.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Le Rhun A,Lécrivain AL,Reimegård J,Proux-Wéra E,Broglia L,Della Beffa C,Charpentier Edoi
10.1093/nar/gkw1316subject
Has Abstractpub_date
2017-03-17 00:00:00pages
2329-2340issue
5eissn
0305-1048issn
1362-4962pii
gkw1316journal_volume
45pub_type
杂志文章abstract：:Interleukin 2 (IL2) mRNA has a short half-life in the cytoplasm of T lymphocytes, relative to most mRNA. We have discovered a candidate ribonuclease to account for the rapid turnover of IL2 mRNA in the cytosol of the human T lymphocyte cell line Jurkat. In partially purified form, this RNase is about 7 times as active...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.1.155
更新日期：1993-01-11 00:00:00
abstract：:In many viruses and transposons, expression of some genes requires alternative reading of the genetic code, also called recoding. Such events depend on specific mRNA sequences and can lead to read through of an in-frame stop codon or to +1 or -1 frameshifting. Here, we addressed the issue of conservation of recoding r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.9.1557
更新日期：1995-05-11 00:00:00
abstract：:The gene encoding myelin basic protein (MBP) contains multiple activator sequences spanning upstream of its transcriptional initiation site which differentially promote transcription in glial cells. The proximal activator sequence, designated MB1, activates transcription in a glial cell type specific manner. This sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.545
更新日期：1992-02-11 00:00:00
abstract：:Muscle creatine kinase (MCK) is a major enzyme of cellular energy metabolism that is expressed upon differentiation of myoblasts into myotubes. Previously we cloned and sequenced the entire rabbit enzyme cDNA which was used as a probe in these studies to obtain a genomic clone from a rabbit library. The transcription ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.11.3027
更新日期：1991-06-11 00:00:00
abstract：:The glycoprotein C (gC) gene of herpes simplex virus type 1 is a true late gene, in that its expression occurs late in infection with a strict requirement for viral DNA replication. Recently, we reported on gC expression during infection with mutant viruses carrying deletions in the gC gene promoter. Analysis of RNA e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.7.3097
更新日期：1987-04-10 00:00:00
abstract：:Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.3.831
更新日期：1999-02-01 00:00:00
abstract：:JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister's Millennium Project. The aim of this undertaking is to identify and collate up to 150 000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.158
更新日期：2002-01-01 00:00:00
abstract：:A filter binding assay was developed that allows measurement of specific binding of trp repressor to operator DNA. The most important feature of this procedure is the concentration and type of salt present in the binding buffer. Using this assay the dissociation constant of the repressor-operator complex was determine...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.13.5339
更新日期：1987-07-10 00:00:00
abstract：:Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz553
更新日期：2019-09-05 00:00:00
abstract：:Antisense oligodeoxynucleotides targeted to Ha-ras mRNA have been designed to discriminate between the codon 12-mutated oncogene and the normal proto-oncogene. An in vitro assay using two different sources of RNase H (rabbit reticulocyte lysates and nuclear extract from HeLa cells) was used to characterize oligonucleo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.17.3411
更新日期：1995-09-11 00:00:00
abstract：:The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.22.9163
更新日期：1987-11-25 00:00:00
abstract：:Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.18.3631
更新日期：1999-09-15 00:00:00
abstract：:The human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA contains two RNase III domains, RIIIDa and RIIIDb, which simultaneously cleave the 3p- and 5p-strands of pri-miRNAs, respect...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa018
更新日期：2020-03-18 00:00:00
abstract：:Although the thermophilic bacterium Thermus aquaticus grows optimally at 70 degrees C and cannot grow at moderate temperatures, its DNA polymerase I has significant activity at 20-37 degrees C. This activity is a bane to some PCRs, since it catalyzes non-specific priming. We report mutations of Klentaq (an N-terminal ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg813
更新日期：2003-11-01 00:00:00
abstract：:A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw786
更新日期：2017-01-25 00:00:00
abstract：:Augmented biological activity in vitro has been demonstrated in oligonucleotides (oligos) modified to provide nuclease resistance, to enhance cellular uptake or to increase target affinity. How chemical modification affects the duration of effect of an oligo with potent activity has not been investigated directly. We ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.6.977
更新日期：1994-03-25 00:00:00
abstract：:Short DNA sequence motifs have been identified in viral and cellular enhancers which represent the binding sites for a variety of trans- acting factors. One such HeLa cell factor, EBP1, has been purified and shown to bind to sequences in the SV40 enhancer. The PRDII element in the human beta-interferon gene regulatory...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.2.499
更新日期：1989-01-25 00:00:00
abstract：:Messenger RNA in eukaryotes is comprised of several abundance classes. Also, the decay of these unstable molecules shows at least two very different lifetimes. Two independent techniques are used here to examine the relation between message abundance and lifetime in cell lines from very different organisms. The method...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.8.3057
更新日期：1978-08-01 00:00:00
abstract：:We report the complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1, as 6633 base pairs of composition 79.5% G+C. This contains immediate early gene 3, encoding the IE175 protein, an important transcriptional activator of later virus genes. The IE175 coding region was identified...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.4.1727
更新日期：1986-02-25 00:00:00
abstract：:A positive cis-acting DNA element in the near 5'-upstream region of the CYP2B1/B2 genes in rat liver was found to play an important role in the transcription of these genes. An oligonucleotide covering -69 to -98 nt mimicked the gel mobility shift pattern given by the fragment -179 to +29 nt, which was earlier found a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.557
更新日期：1992-02-11 00:00:00
abstract：:We have used computer assisted dot matrix and oligonucleotide frequency analyses to identify highly recurring sequence elements of 7-11 base pairs in eukaryotic genes and viral DNAs. Such elements are found much more frequently than expected, often with an average spacing of a few hundred base pairs. Furthermore, the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.4.1835
更新日期：1987-02-25 00:00:00
abstract：:Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz571
更新日期：2019-09-05 00:00:00
abstract：:DNA synthesis is a fundamental requirement for cell proliferation and DNA repair, but no single method can identify the location, direction and speed of replication forks with high resolution. Mammalian cells have the ability to incorporate thymidine analogs along with the natural A, T, G and C bases during DNA synthe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa517
更新日期：2020-09-04 00:00:00
abstract：:The irradiation of native or unmodified yeast tRNA(Phe) by short wavelength UV light (260 nM) results in an intramolecular crosslink that has been mapped to occur between C48 in the variable loop and U59 in the T loop. Photo-reversibility of the crosslink and the absence of fluorescent photo adducts suggest that the c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.15.4055
更新日期：1992-08-11 00:00:00
abstract：:Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (N...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.10.2457
更新日期：1998-05-15 00:00:00
abstract：:A stable conformer of Escherichia coli tRNA(Glu), obtained in the absence of Mg(2+), is inactive in the aminoacylation reaction. Probing it with diethylpyrocarbonate, dimethyl sulfate and ribonuclease V1 revealed that it has a hairpin structure with two internal loops; the helical segments at both extremities have the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.17.3583
更新日期：1999-09-01 00:00:00
abstract：:Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1003
更新日期：2013-01-07 00:00:00
abstract：:Abasic (AP) sites, the most common DNA lesions are frequently associated with double strand breaks (DSBs) and can pose a block to the final ligation. In many prokaryotes, nonhomologous end joining (NHEJ) repair of DSBs relies on a two-component machinery constituted by the ring-shaped DNA-binding Ku that recruits the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz265
更新日期：2019-06-04 00:00:00
abstract：:Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting so...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx389
更新日期：2017-07-03 00:00:00
abstract：:Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori. We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1343
更新日期：2017-05-05 00:00:00
