Abstract：
:An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regulator protein Hfq as bait, because it can interact with a large number of RNAs, promoting their interaction. The enriched SELEX pool was subjected to deep sequencing, and 8865 sequences were mapped to the E. coli genome. These short sequences represent genomic Hfq-aptamers and are part of potential regulatory elements within RNA molecules. The motif 5'-AAYAAYAA-3' was enriched in the selected RNAs and confers low-nanomolar affinity to Hfq. The motif was confirmed to bind Hfq by DMS footprinting. The Hfq aptamers are 4-fold more frequent on the antisense strand of protein coding genes than on the sense strand. They were enriched opposite to translation start sites or opposite to intervening sequences between ORFs in operons. These results expand the repertoire of Hfq targets and also suggest that Hfq might regulate the expression of a large number of genes via interaction with cis-antisense RNAs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lorenz C,Gesell T,Zimmermann B,Schoeberl U,Bilusic I,Rajkowitsch L,Waldsich C,von Haeseler A,Schroeder Rdoi
10.1093/nar/gkq032subject
Has Abstractpub_date
2010-06-01 00:00:00pages
3794-808issue
11eissn
0305-1048issn
1362-4962pii
gkq032journal_volume
38pub_type
杂志文章abstract：:The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (WWW) or Sequin programs to send t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.1
更新日期：1998-01-01 00:00:00
abstract：:We have determined the complete nucleotide sequence of the regions of mouse ribosomal RNA transcription unit which separate mature rRNA genes. These internal transcribed spacers (ITS) are excised from rRNA precursor during ribosome biosynthesis. ITS 1, between 18S and 5.8S rRNA genes, is 999 nucleotides long. ITS 2, b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.10.3375
更新日期：1983-05-25 00:00:00
abstract：:Mariner transposition is a complex reaction that involves three recombination sites and six strand breaking and joining reactions. This requires precise spatial and temporal coordination between the different components to ensure a productive outcome and minimize genomic instability. We have investigated how the cleav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku172
更新日期：2014-05-01 00:00:00
abstract：:We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduced, fragmented and rear...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr501
更新日期：2011-09-01 00:00:00
abstract：:A number of cysteine-rich proteins have recently been isolated by homology screening, differential library screens, and association with other proteins. In this report, we describe the isolation of the rat cysteine-rich protein from a rat brain library during a search for clones with homology to the delta-opioid recep...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.24.5477
更新日期：1994-12-11 00:00:00
abstract：:Genomic meta-analysis to combine relevant and homogeneous studies has been widely applied, but the quality control (QC) and objective inclusion/exclusion criteria have been largely overlooked. Currently, the inclusion/exclusion criteria mostly depend on ad-hoc expert opinion or naïve threshold by sample size or platfo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1071
更新日期：2012-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw776
更新日期：2016-11-02 00:00:00
abstract：:The centromere complex is a multicomponent structure essential for faithful chromosome transmission. Here we show that the S. cerevisiae centromere protein Cpf1 bends centromere DNA element I (CDEI) with the bend angle ranging from 66 degrees to 71 degrees. CDEI DNA sequences that carry point mutations which lead to r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.20.4726
更新日期：1993-10-11 00:00:00
abstract：:We have prepared several novel phosphoramidites and have synthesised oligonucleotides incorporating them internally. The presence of these residues in an oligonucleotide template presents an impossible barrier to primed synthesis by Taq DNA polymerase. When extended as polymerase chain reaction products, these oligonu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.5.1155
更新日期：1993-03-11 00:00:00
abstract：:The nucleotide sequence of the chick beta-actin gene was determined. The gene contains 5 introns; 4 interrupt the translated region at codons 41/42, 120/122, 267, 327/328 and a large intron occurs in the 5' untranslated region. The gene has a 97 nucleotide 5'-untranslated region and a 594 nucleotide 3'-untranslated re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.23.8287
更新日期：1983-12-10 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf139
更新日期：2002-12-15 00:00:00
abstract：:We have studied the role of the C-terminal domain of the alpha subunit (alphaCTD) of Escherichia coli RNA polymerase during transcription initiation at promoters lacking an UP-element. The temperature requirement for open complex formation was used as an indication of the kinetics of this process. We have previously s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.9.2051
更新日期：1999-05-01 00:00:00
abstract：:The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.19.4467
更新日期：1993-09-25 00:00:00
abstract：:Chemically modified antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages have been extensively studied as research and therapeutic agents. PS-ASOs can enter the cell and trigger cleavage of complementary RNA by RNase H1 even in the absence of transfection reagent. A number of cell surface proteins hav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky145
更新日期：2018-04-20 00:00:00
abstract：:We have developed a new bioinformatics approach called ECMFinder (Evolutionary Conserved Motif Finder). This program searches for a given DNA motif within the entire genome of one species and uses the gene association information of a potential transcription factor-binding site (TFBS) to screen the homologous regions ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp077
更新日期：2009-04-01 00:00:00
abstract：:DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku613
更新日期：2014-01-01 00:00:00
abstract：:Guanine-quadruplexes (G4) consist of non-canonical four-stranded helical arrangements of guanine-rich nucleic acid sequences. The bulky and thermodynamically stable features of G4 structures have been shown in many respects to affect normal nucleic acid metabolism. In vivo conversion of G4 structures to single-strande...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr630
更新日期：2011-11-01 00:00:00
abstract：:Transcription of the bacteriophage Mu mom operon requires transactivation by the phage-encoded C protein. DNase I footprinting showed that in the absence of C, Escherichia coli RNA polymerase E(sigma)70 (RNAP) binds to the mom promoter (Pmom) region at a site, P2 (from -64 to -11 with respect to the transcription star...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.20.4042
更新日期：1996-10-15 00:00:00
abstract：:Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analy...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg457
更新日期：2003-07-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.16.5467
更新日期：1983-08-25 00:00:00
abstract：:We have examined the formation of alternate strand triple-helices at the target sequence A11(TC)6.(GA)6T11 using the oligonucleotides T11(AG)6 and T11(TG)6, by DNase I footprinting. These third strands were designed so as to form parallel T.AT triplets together with antiparallel G.GC and A.AT or T.AT triplets. We find...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.19.3977
更新日期：1994-09-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.23.5288
更新日期：1998-12-01 00:00:00
abstract：:The paper describes an improved method for the synthesis of oligodeoxyribonucleotides using phosphoramidite chemistry. Our procedure relies on novel phosphoramidite intermediates, the deoxyribonucleoside-3'-morpholine-methoxyphosphins. These compounds are extremely stable and can be purified readily. Condensation reac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.9.2575
更新日期：1983-05-11 00:00:00
abstract：:Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a wide...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2018-04-06 00:00:00
abstract：:Period2 (Per2) is an essential component of the mammalian clock mechanism and robust circadian expression of Per2 is essential for the maintenance of circadian rhythms. Although recent studies have shown that the circadian E2 enhancer (a non-canonical E-box) accounts for most of the circadian transcriptional drive of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl868
更新日期：2007-01-01 00:00:00
abstract：:With the abundant mammalian lncRNAs identified recently, a comprehensive annotation resource for these novel lncRNAs is an urgent need. Since its first release in November 2016, AnnoLnc has been the only online server for comprehensively annotating novel human lncRNAs on-the-fly. Here, with significant updates to mult...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa368
更新日期：2020-07-02 00:00:00
abstract：:Genomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku667
更新日期：2014-09-01 00:00:00
abstract：:Complementary DNA clones encoding the human kidney epidermal growth factor (EGF) precursor have been isolated and sequenced. They predict the sequence of a 1,207 amino acid protein which contains EGF flanked by polypeptide segments of 970 and 184 residues at its NH2- and COOH-termini, respectively. The structural orga...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.21.8427
更新日期：1986-11-11 00:00:00
abstract：:X chromosome inactivation results in the cis-limited inactivation of most, but not all, genes on one of the two X chromosomes in mammalian females. The molecular basis for inactivation is unknown. In order to examine the transcriptional activity of human X-linked genes, a series of mouse-human somatic cell hybrids und...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.14.4191
更新日期：1990-07-25 00:00:00
abstract：:Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt416
更新日期：2013-07-01 00:00:00
