Abstract：
:A 5',7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed due to its participation in RNA-fate decisions via interactions with RNA productive factors as well as with adapters of the degradative RNA exosome. A novel cap-binding protein, NCBP3, was recently proposed to form an alternative CBC together with NCBP1, and to interact with the canonical CBC along with the protein SRRT. The theme of post-transcriptional RNA fate, and how it relates to co-transcriptional ribonucleoprotein assembly, is abundant with complicated, ambiguous, and likely incomplete models. In an effort to clarify the compositions of NCBP1-, 2- and 3-related macromolecular assemblies, we have applied an affinity capture-based interactome screen where the experimental design and data processing have been modified to quantitatively identify interactome differences between targets under a range of experimental conditions. This study generated a comprehensive view of NCBP-protein interactions in the ribonucleoprotein context and demonstrates the potential of our approach to benefit the interpretation of complex biological pathways.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dou Y,Kalmykova S,Pashkova M,Oghbaie M,Jiang H,Molloy KR,Chait BT,Rout MP,Fenyö D,Jensen TH,Altukhov I,LaCava Jdoi
10.1093/nar/gkaa743subject
Has Abstractpub_date
2020-10-09 00:00:00pages
10456-10469issue
18eissn
0305-1048issn
1362-4962pii
5909927journal_volume
48pub_type
杂志文章abstract：:The gene for the small subunit of human calcium-activated neutral protease was isolated and sequenced. It is 11 kb long and comprises 11 exons. No TATA or CAT box was found upstream of the possible transcription initiation sites, but there are three so-called G-C box sequences and one G-C box-like sequence, which are ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.22.8805
更新日期：1986-11-25 00:00:00
abstract：:The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1089
更新日期：2017-01-04 00:00:00
abstract：:An improved contact hybridization technique for the analysis of labelled RNA species is presented. The method combines high sensitivity of detection with the high resolution of polyacrylamide gel electrophoresis and should be especially useful for the characterization of transient RNA precursor molecules. Its applicat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.9.2963
更新日期：1979-07-11 00:00:00
abstract：:The behaviour of highly purified bacterial expressed rat O6-methylguanine-DNA methyltransferase (MGMT) towards the repair of CGCm6GAGCTCGCG and CGCe6GAGCTCGCG (km6G/ke6G = 1.45, where k is the second order repair rate constant determined, m6G and e6G are O6-methyl and O6-ethylguanine) is similar to that of E. coli 39k...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.9.1613
更新日期：1994-05-11 00:00:00
abstract：:Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx246
更新日期：2017-07-03 00:00:00
abstract：:Giant chromatin-modifying complexes regulate gene transcription in eukaryotes by acting on chromatin substrates and 'setting' the histone code. The histone deacetylase (HDAC)-associated mammalian Sin3 corepressor complex regulates a wide variety of genes involved in all aspects of cellular physiology. The recruitment ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp051
更新日期：2009-04-01 00:00:00
abstract：:Highly repetitive Hind III restriction fragments of 0.72-0.76 KBP from total Xenopus laevis genomic DNA are organized in a tandem like arrangement. Cloning of these fragments in pBR 322 with subsequent restriction site mapping and nucleotide sequence analysis of some selected clones showed two different types of seque...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.20.6997
更新日期：1983-10-25 00:00:00
abstract：:In kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g)RNAs. Currently popular mechanisms for the editing process envisage a series of consecutive 'cut-and-paste' reactions, carried out by a compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.14.2950
更新日期：2001-07-15 00:00:00
abstract：:A 30 nt RNA with a sequence designed to form an intramolecular triple helix was analyzed by one-and two-dimensional NMR spectroscopy and UV absorption measurements. NMR data show that the RNA contains seven pyrimidine-purine-pyrimidine base triples stabilized by Watson-Crick and Hoogsteen interactions. The temperature...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.14.2841
更新日期：1996-07-15 00:00:00
abstract：:The role of uracil in genomic DNA has been recently re-evaluated. It is now widely accepted to be a physiologically important DNA element in diverse systems from specific phages to antibody maturation and Drosophila development. Further relevant investigations would largely benefit from a novel reliable and fast metho...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv977
更新日期：2016-02-18 00:00:00
abstract：:Immunoglobulin (Ig) diversification by somatic hypermutation in germinal center B cells is instrumental for maturation of the humoral immune response, but also bears the risk of excessive or aberrant genetic changes. Thus, introduction of DNA damage by activation-induced cytidine deaminase as well as DNA repair by mul...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1378
更新日期：2014-04-01 00:00:00
abstract：:Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm947
更新日期：2007-01-01 00:00:00
abstract：:Lytic infection with polyoma virus leads in Go-arrested primary mouse kidney cell cultures to a mitotic host response. In the present work we focused our attention on cellular RNA synthesis shortly after onset of polyoma T-antigen synthesis. Onset of polyoma-induced stimulation of 45S pre-rRNA synthesis was determined...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.19.6611
更新日期：1983-10-11 00:00:00
abstract：:Restriction endonucleases are highly specific in recognizing the particular DNA sequence they act on. However, their activity is affected by sequence context, enzyme concentration and buffer composition. Changes in these factors may lead to either ineffective cleavage at the cognate restriction site or relaxed specifi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt257
更新日期：2013-06-01 00:00:00
abstract：:Primase synthesizes decaribonucleotides for priming of lagging and possibly leading strand synthesis at a replication fork. The sites of initiation by purified mouse primase were shown to be highly specific within the SV40 origin of replication. This study further examines the role of the 27-bp inverted repeat in the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.5.1953
更新日期：1989-03-11 00:00:00
abstract：:A novel method combining elements of suppression subtractive hybridization with high throughput differential screening permits the efficient and rapid cloning of rarely transcribed differentially expressed genes. The experimental strategy virtually excludes the possibility of isolating false positive clones. The poten...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.13.2598
更新日期：1997-07-01 00:00:00
abstract：:Measuring minimal residual disease in cancer has applications for prognosis, monitoring treatment and detection of recurrence. Simple sequence-based methods to detect nucleotide substitution variants have error rates (about 10-3) that limit sensitive detection. We developed and characterized the performance of MASQ (m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa090
更新日期：2020-04-17 00:00:00
abstract：:Uracil may occur in DNA due to either cytosine deamination or thymine replacing incorporation. Its quantitative characterization is important in assessing DNA damages in cells with perturbed thymidylate metabolism or within different DNA segments involved in immunoglobulin gene diversification. The archaeal DNA polyme...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq815
更新日期：2010-11-01 00:00:00
abstract：:During the formation of a transcriptionally active macronucleus, ciliated protozoa excise large numbers of interstitial segments of DNA (internal eliminated sequences; IESs) from their chromosomes. In this study we analyze the published sequences of 20 IESs that interrupt surface protein genes of Paramecium and identi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.11.2006
更新日期：1995-06-11 00:00:00
abstract：:A mass culture of human diploid fibroblasts, and eight clones isolated from that mass culture, were examined for methylation patterns in several regions of DNA. Plasmid-inserted cDNA sequences were used as probes for alpha-hCG, beta-globin, A gamma- and G gamma-globin, and beta- and gamma-actin gene regions. Each prob...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.14.4293
更新日期：1982-07-24 00:00:00
abstract：:Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw843
更新日期：2016-11-16 00:00:00
abstract：:The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The B...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg032
更新日期：2003-01-01 00:00:00
abstract：:Human prostatic acid phosphatase (PAcP) is a prostate epithelium-specific differentiation antigen. Cellular PAcP functions as a neutral protein tyrosine phosphatase and is involved in regulating androgen-promoted prostate cancer cell proliferation. Despite the fact that the promoter of the PAcP gene has been cloned, t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh677
更新日期：2004-07-07 00:00:00
abstract：:During the splicing process, spliceosomal snRNAs undergo numerous conformational rearrangements that appear to be catalyzed by proteins belonging to the DEAD/H-box superfamily of RNA helicases. We have cloned a new RNA helicase gene, designated DBP2 (DEAH-boxprotein), homologous to the Schizosaccaromyces pombe cdc28(+...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.9.2063
更新日期：1998-05-01 00:00:00
abstract：:We cloned and sequenced a portion of chloroplast DNA from the hornwort Anthoceros formosae. A nucleotide sequence of 7556 bp contained structures similar to those of ndhK, ndhC, trnV, trnM, atpE, atpB, rbcL, trnR and accD. The arrangement of these was the same as that of other chloroplast DNA. However, two nonsense co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.6.1008
更新日期：1996-03-15 00:00:00
abstract：:Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz296
更新日期：2019-06-20 00:00:00
abstract：:Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 ca...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm485
更新日期：2007-01-01 00:00:00
abstract：:The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt462
更新日期：2013-07-01 00:00:00
abstract：:The covalent attachment of thiol-modified DNA oligomers; to self-assembled monolayer silane films on fused silica and oxidized silicon substrates is described. A heterobifunctional crosslinking molecule bearing both thiol- and amino-reactive moieties was used to tether a DNA oligomer (modified at its terminus with a t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.15.3031
更新日期：1996-08-01 00:00:00
abstract：:The pac1+ gene of the fission yeast Schizosaccharomyces pombe is essential for viability and its overexpression induces sterility and suppresses mutations in the pat1+ and snm1+ genes. The pac1+ gene encodes a protein that is structurally similar to RNase III from Escherichia coli, but its normal function is unknown. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.12.2377
更新日期：1996-06-15 00:00:00
