Abstract：
:Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that are coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and viral RNA (vRNA) is depicted as a uniform pattern of 'beads on a string'. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP), we identified the vRNA binding profiles of NP for two H1N1 IAV strains in virions. Contrary to the prevailing model for vRNA packaging, NP does not bind vRNA uniformly in the A/WSN/1933 and A/California/07/2009 strains, but instead each vRNA segment exhibits a unique binding profile, containing sites that are enriched or poor in NP association. Intriguingly, both H1N1 strains have similar yet distinct NP binding profiles despite extensive sequence conservation. Peaks identified by HITS-CLIP were verified as true NP binding sites based on insensitivity to DNA antisense oligonucleotide-mediated RNase H digestion. Moreover, nucleotide content analysis of NP peaks revealed that these sites are relatively G-rich and U-poor compared to the genome-wide nucleotide content, indicating an as-yet unidentified sequence bias for NP association in vivo. Taken together, our genome-wide study of NP-vRNA interaction has implications for the understanding of influenza vRNA architecture and genome packaging.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lee N,Le Sage V,Nanni AV,Snyder DJ,Cooper VS,Lakdawala SSdoi
10.1093/nar/gkx584subject
Has Abstractpub_date
2017-09-06 00:00:00pages
8968-8977issue
15eissn
0305-1048issn
1362-4962pii
3933580journal_volume
45pub_type
杂志文章abstract：:The somatic V(D)J recombination for the assembly of the Ig and TCR genes is mediated by the recombination signal sequences (Rss) and the V(D)J recombinase. A cDNA clone was isolated from a lambda gt11 expression library made from mouse thymocyte poly(A)+ RNA, using the Rss as a ligand. The deduced amino acid sequence ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.22.5067
更新日期：1993-11-11 00:00:00
abstract：:Preparation of the two nonanucleotides, d(pG-G-A-G-G-A-G-A-A) and d(pT-T-C-T-G-T-T-G-A), and the octanucleotide, d(pT-G-G-C-C-C-A-T) is described by a rapid solid-phase method on a polyamide support. The syntheses were carried out using a modified solid-phase peptide synthesiser and required one day for each nucleotid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.12.4391
更新日期：1977-12-01 00:00:00
abstract：:The effect of UV-irradiation on the conversion of the single-stranded DNA of the parvovirus Minute-Virus-of-Mice (MVM) to duplex Replicative Forms (RF) was studied after infection of mouse A9 fibroblasts. UV-irradiation of the virus prior to infection of unirradiated cells resulted in a dose-dependent, single-hit, inh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.8.2577
更新日期：1982-04-24 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp452
更新日期：2009-08-01 00:00:00
abstract：:Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the uniq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1237
更新日期：2014-02-01 00:00:00
abstract：:MHCPEP is a curated database comprising over 6000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains peptide sequence, MHC specificity and when available, experimental method, observed activity, binding...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.1.242
更新日期：1996-01-01 00:00:00
abstract：:The photostability and narrow emission spectra of non-organic quantum dot fluorophores (QDs) make them desirable candidates for fluorescent in situ hybridization (FISH) to study the expression of specific mRNA transcripts. We developed a novel method for direct QD labeling of modified oligonucleotide probes through st...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni162
更新日期：2005-10-13 00:00:00
abstract：:The nucleotide sequence of the Klebsiella pneumoniae ntrA gene has been determined. NtrA encodes a 53,926 Dalton acidic polypeptide; a calculated molecular weight which is significantly lower than that determined by SDS polyacrylamide gel analysis. NtrA is followed by another open-reading frame (orf) of at least 75 am...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.21.7607
更新日期：1985-11-11 00:00:00
abstract：:A database (http://perso.curie.fr/tsoussi ) is described, in which over 1000 mutations in the human APC gene of tumors (colon cancer predominantly) are compiled from the literature. It includes both molecular information about the mutations and clinical data about the patients. Software has been designed to analyse al...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.269
更新日期：1998-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.10.3255
更新日期：1983-05-25 00:00:00
abstract：:Fluoropyrimidines, such as 5-fluorouracil (5-FU), are used extensively in cancer therapy. In the cell, 5-FU is metabolized to 5-fluorodeoxyuridylate (5-FdUMP), a tight binding covalent inhibitor of thymidylate synthase (TS). In order to create 5-FdUMP resistant enzymes to protect chemosensitive normal cells and furthe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.18.3702
更新日期：1999-09-15 00:00:00
abstract：:The p53 transcription factor confers its potent tumor suppressor functions primarily through the regulation of a large network of target genes. The recent explosion of next generation sequencing protocols has enabled the study of the p53 gene regulatory network (GRN) and underlying mechanisms at an unprecedented depth...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa666
更新日期：2020-09-18 00:00:00
abstract：:Restriction-free cloning (RF-cloning) is a PCR-based technology that expands on the QuikChange™ mutagenesis process originally popularized by Stratagene in the mid-1990s, and allows the insertion of essentially any sequence into any plasmid at any location. While RF-cloning is a powerful tool for the design of custom ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks396
更新日期：2012-07-01 00:00:00
abstract：:7,8-Dihydro-8-oxo-deoxyguanosine (8oxodG) is a highly premutagenic DNA lesion due to its ability to mispair with adenine. Schizosaccharomyces pombe lacks homologs for relevant enzymes that repair 8oxodG, which suggests that this lesion could be persistent and must be tolerated. Here we show that SpPol4, the unique Pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku711
更新日期：2014-09-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.8.1394
更新日期：1994-04-25 00:00:00
abstract：:The log kobs vs. pH profiles were determined in the intermediate acidity region for the glycosyl hydrolysis of guanosine and its 8-amino, 8-monomethylamino, 8-dimethylamino and 8-bromo derivatives. The decreased rate of the 8-amino and enhanced rate of the 8-bromo compound compared to guanosine support an A type mecha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.3.697
更新日期：1977-03-01 00:00:00
abstract：:The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and format...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1096
更新日期：2008-02-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.19.5787
更新日期：1990-10-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw198
更新日期：2016-06-20 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1999-05-01 00:00:00
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更新日期：2018-05-18 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki900
更新日期：2005-10-26 00:00:00
abstract：:Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresisdagger; (I...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.3.331
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp115
更新日期：2009-05-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.2.279
更新日期：1991-01-25 00:00:00
abstract：:Arabidopsis thaliana is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from A. thaliana, which has facilitated data-driven approaches to unravel the genetic organization o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1053
更新日期：2015-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks229
更新日期：2012-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni005
更新日期：2005-01-07 00:00:00
abstract：:Rad18 is a ubiquitin E3 ligase that monoubiquitinates PCNA on stalled replications forks. This allows recruitment of damage-tolerant polymerases for damage bypass and DNA repair. In this activity, the Rad18 protein has to interact with Rad6, the E2 ubiquitin-conjugating enzyme, ubiquitin, PCNA and DNA. Here we analyze...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm615
更新日期：2007-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.16.6607
更新日期：1987-08-25 00:00:00
