Abstract:
:Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary phase a tailored RNA-seq-based technology, which allows transcriptome-wide mapping of RNase III cleavage sites at a nucleotide resolution. Our analysis of the large-scale in vivo cleavage data substantiated the established cleavage pattern of a double cleavage in an intra-molecular stem structure, leaving 2-nt-long 3' overhangs, and refined the base-pairing preferences in the cleavage site vicinity. Intriguingly, we observed that the two stem positions between the cleavage sites are highly base-paired, usually involving at least one G-C or C-G base pair. We present a clear distinction between intra-molecular stem structures that are RNase III substrates and intra-molecular stem structures randomly selected across the transcriptome, emphasizing the in vivo specificity of RNase III. Our study provides a comprehensive map of the cleavage sites in both intra-molecular and inter-molecular duplex substrates, providing novel insights into the involvement of RNase III in post-transcriptional regulation in the bacterial cell.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Altuvia Y,Bar A,Reiss N,Karavani E,Argaman L,Margalit Hdoi
10.1093/nar/gky684subject
Has Abstractpub_date
2018-11-02 00:00:00pages
10380-10394issue
19eissn
0305-1048issn
1362-4962pii
5064785journal_volume
46pub_type
杂志文章abstract::DNA molecules with covalently sealed (hairpin) ends are probable intermediates in V(D)J recombination. According to current models hairpin ends are opened to produce short single-stranded extensions that are thought to be precursors of a particular type of extra nucleotides, termed P nucleotides, which are frequently ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.19.3872
更新日期:1995-10-11 00:00:00
abstract::We recently identified a region of preferential replication initiation, oriGNAI3, near the 3' end of the Chinese hamster GNAI3 gene. oriGNAI3 is co-amplified in mutants selected for AMPD2 amplification, a process generating chromosomal rearrangements. In this report we have taken advantage of cell lines with truncated...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.7.1600
更新日期:1999-04-01 00:00:00
abstract::In this paper, we present evidence that an efficient Rho-dependent terminator can be created by introducing a simple (AG/TC) n DNA repeat into a transcription unit. The Rho termination activity in vivo and in vitro is dependent on the length and the orientation of the insert. The transcription of at least 30 bp of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.21.4895
更新日期:1998-11-01 00:00:00
abstract::Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni142
更新日期:2005-09-30 00:00:00
abstract::Controllable gene delivery via vector-based systems remains a formidable challenge in mammalian synthetic biology and a desirable asset in gene therapy applications. Here, we introduce a methodology to control the copies and residence time of a gene product delivered in host human cells but also selectively disrupt fr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1326
更新日期:2015-01-01 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::The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku397
更新日期:2014-07-01 00:00:00
abstract::The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr981
更新日期:2012-01-01 00:00:00
abstract::The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. As...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.2.655
更新日期:1998-01-15 00:00:00
abstract::Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm322
更新日期:2007-07-01 00:00:00
abstract::The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki014
更新日期:2005-01-01 00:00:00
abstract::Programmed -1 ribosomal frameshifting is employed in the expression of a number of viral and cellular genes. In this process, the ribosome slips backwards by a single nucleotide and continues translation of an overlapping reading frame, generating a fusion protein. Frameshifting signals comprise a heptanucleotide slip...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks629
更新日期:2012-09-01 00:00:00
abstract::The base excision repair DNA glycosylase MutY homolog (MYH) is responsible for removing adenines misincorporated into DNA opposite guanine or 7,8-dihydro-8-oxo-guanine (8-oxoG), thereby preventing G:C to T:A mutations. Biallelic germline mutations in the human MYH gene predispose individuals to multiple colorectal ade...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki209
更新日期:2005-01-26 00:00:00
abstract::Generally, the presence of a consensus sequence in the promoter of a gene is taken as indication for regulation by the transcription factor that binds to this sequence. In light of the recent developments in genome research, we were interested to what extent this supposition is valid. We examined the relationship betw...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf698
更新日期:2002-12-15 00:00:00
abstract::Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa427
更新日期:2020-07-09 00:00:00
abstract::Short repetitive DNA sequences are believed to be one of the primordial genetic elements that served as a source of complex large DNA found in the genome of modern organisms. However, the mechanism of its expansion (increase in repeat number) during the course of evolution is unclear. We demonstrate that the DNA polym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.20.3999
更新日期:2000-10-15 00:00:00
abstract::A cDNA (2855 nt) encoding a putative cytotoxic ribonuclease (rapLR1) related to the antitumor protein onconase was cloned from a library derived from the liver of gravid female amphibian Rana pipiens. The cDNA was mainly comprised (83%) of 3' untranslated region (UTR). Secondary structure analysis predicted two unusua...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.12.2375
更新日期:2000-06-15 00:00:00
abstract::Mutations help us to understand the molecular origins of diseases. Researchers, therefore, both publish and seek disease-relevant mutations in public databases and in scientific literature, e.g. Medline. The retrieval tends to be time-consuming and incomplete. Automated screening of the literature is more efficient. W...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh162
更新日期:2004-01-02 00:00:00
abstract::Unlike short interfering RNAs (siRNAs), which are commonly designed to repress a single messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RNAs that have evolved to concurrently repress multiple mRNA targets through imperfect complementarity. MicroRNA target recognition i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku171
更新日期:2014-05-01 00:00:00
abstract::Herein, we describe a case study into the population dynamics of in vitro selection, using RNA-cleaving DNAzymes as a model system. We sought to understand how the composition of the population can change over time in response to different levels of selection pressure, and how well these changes are correlated with se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp222
更新日期:2009-06-01 00:00:00
abstract::A simple and effective modified ethanol precipitation-based protocol is described for the preparation of DNA from ancient human bones. This method is fast and requires neither hazardous chemicals nor special devices. After the powdering and incubating of the bone samples Dextran Blue was added as a carrier for removin...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章
doi:10.1093/nar/28.12.e67
更新日期:2000-06-15 00:00:00
abstract::Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv311
更新日期:2015-05-19 00:00:00
abstract::The cause of 50S ribosomal subunit collapse reportedly triggered by hybridization of a 14-base cDNA probe to the alpha-sarcin region of 23S rRNA was investigated by physical measurement of probe-subunit complexes in varying buffer conditions. The results reported here show that this probe was unable to hybridize to it...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.22.10817
更新日期:1988-11-25 00:00:00
abstract::Despite much information as to the structure and function of the general transcription factors, little is known about the regulation of their expression. Transcription of the Saccharomyces cerevisiae SUA7 (TFIIB) gene results in the formation of two discrete transcripts. It was originally reported that the two transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.22.4435
更新日期:2000-11-15 00:00:00
abstract::Topoisomerases (topos) maintain DNA topology and influence DNA transaction processes by catalysing relaxation, supercoiling and decatenation reactions. In the cellular milieu, division of labour between different topos ensures topological homeostasis and control of central processes. In Escherichia coli, DNA gyrase is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks843
更新日期:2012-11-01 00:00:00
abstract::We have investigated the substrate specificity of the Ogg1 protein of Saccharomyces cerevisiae (yOgg1 protein) for excision of modified DNA bases from oxidatively damaged DNA substrates using gas chromatography/isotope dilution mass spectrometry. Four DNA substrates prepared by treatment with H2O2/Fe(III)-EDTA/ascorbi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.5.1228
更新日期:1998-03-01 00:00:00
abstract::Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku923
更新日期:2014-11-10 00:00:00
abstract::The genomic distribution of 23 nuclear genes from three dicotyledons (pea, sunflower, tobacco) and five monocotyledons of the Gramineae family (barley, maize, rice, oat, wheat) was studied by localizing these genes in DNA fractions obtained by preparative centrifugation in Cs2SO4/BAMD density gradients. Each one of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.7.1859
更新日期:1990-04-11 00:00:00
abstract::MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1139
更新日期:2018-01-04 00:00:00
abstract::Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying the Qβ (+)-RNA genome. Here, we use X-ray crystallography, NMR spect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1212
更新日期:2015-12-15 00:00:00