Abstract:
:We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28,199 'UniTraps', i.e. distinct collections of unambiguous insertions at the same subgenic region of annotated genes. The UniTrap resource contains data relative to 9583 trapped genes, which represent 42.3% of the mouse gene content. Among the trapped genes, 7,728 have a counterpart in humans, and 677 are known to be involved in the pathogenesis of human diseases. The aim of this analysis is to provide the wet lab researchers with a comprehensive database and curated tools for (i) identifying and comparing the clones carrying a trap into the genes of interest, (ii) evaluating the severity of the mutation to the protein function in each independent trapping event and (iii) supplying complete information to perform PCR, RT-PCR and restriction experiments to verify the clone and identify the exact point of vector insertion. To share this unique resource with the scientific community, we have designed and implemented a web interface that is freely accessible at http://unitrap.cbm.fvg.it/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Roma G,Sardiello M,Cobellis G,Cruz P,Lago G,Sanges R,Stupka Edoi
10.1093/nar/gkm825subject
Has Abstractpub_date
2008-01-01 00:00:00pages
D741-6issue
Database issueeissn
0305-1048issn
1362-4962pii
gkm825journal_volume
36pub_type
杂志文章abstract::Deamination of cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) occurs spontaneously in mammalian DNA with several hundred deaminations occurring in each cell every day. The resulting potentially mutagenic mispairs of uracil (U), thymine (T) or 5-hydroxymethyluracil (hmU) with guanine (G) are subs...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks259
更新日期:2012-07-01 00:00:00
abstract::The discovery of hydroxymethyl-, formyl- and carboxylcytosine, generated through oxidation of methylcytosine by TET dioxygenases, raised the question how these modifications contribute to epigenetic regulation. As they are subjected to complex regulation in vivo, we dissected links to gene expression with in vitro mod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku552
更新日期:2014-07-01 00:00:00
abstract::Message-specific translational regulation mechanisms shape the biogenesis of multimeric oxidative phosphorylation (OXPHOS) enzyme in mitochondria from the yeast Saccharomyces cerevisiae. These mechanisms, driven mainly by the action of mRNA-specific translational activators, help to coordinate synthesis of OXPHOS cata...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz266
更新日期:2019-06-20 00:00:00
abstract::Cdc48/p97 is an evolutionary conserved ubiquitin-dependent chaperone involved in a broad array of cellular functions due to its ability to associate with multiple cofactors. Aside from its role in removing RNA polymerase II from chromatin after DNA damage, little is known about how this AAA-ATPase is involved in the t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku786
更新日期:2014-01-01 00:00:00
abstract::The temperature-sensitive Neurospora nuclear mutant cyt18-1 is deficient in splicing many Group I mitochondrial introns when grown at its non-permissive temperature; however, splicing of intron 1 in the coI gene of the Adiopodoume (formerly called North Africa) strain is unaffected (R.A. Collins and A.M. Lambowitz, J....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.22.9087
更新日期:1989-11-25 00:00:00
abstract::The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.18.7007
更新日期:1984-09-25 00:00:00
abstract::Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt961
更新日期:2014-01-01 00:00:00
abstract::Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytopl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx496
更新日期:2017-07-07 00:00:00
abstract::Emerging evidence suggests that recombinant adeno-associated viral (rAAV) vectors can be used for specific gene targeting in human somatic cells. We have developed an rAAV vector construction procedure employing fusion PCR and a single cloning step that considerably simplifies the knockout process. We demonstrate its ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh009
更新日期:2004-01-02 00:00:00
abstract::Linear motifs are short, evolutionarily plastic components of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1064
更新日期:2012-01-01 00:00:00
abstract::A long-range physical map of the centromeric region of human chromosome 7 has been constructed in order to define the region containing sequences with potential involvement in centromere function. The map is centered around alpha satellite DNA, a family of tandemly repeated DNA forming arrays of hundreds to thousands ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.9.2295
更新日期:1991-05-11 00:00:00
abstract::Sexual differentiation in Drosophila is regulated through alternative splicing of doublesex. Female-specific splicing is activated through the activity of splicing enhancer complexes assembled on multiple repeat elements. Each of these repeats serves as a binding platform for the cooperative assembly of a heterotrimer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl984
更新日期:2006-01-01 00:00:00
abstract::We have examined the ability of a cationic planar chromophore, ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.7.1521
更新日期:1991-04-11 00:00:00
abstract::Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an addi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr054
更新日期:2011-06-01 00:00:00
abstract::Here we report proof-of-principle for a microsphere-based genotyping assay that detects single nucleotide polymorphisms (SNPs) directly from human genomic DNA samples. This assay is based on a structure-specific cleavage reaction that achieves single base discrimination with a 5'-nuclease which recognizes a tripartite...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng066
更新日期:2003-06-01 00:00:00
abstract::5' mediated cytoplasmic RNA decay is a conserved cellular process in eukaryotes. While the functions of the structured core domains in this pathway are well-studied, the role of abundant intrinsically disordered regions (IDRs) is lacking. Here we reconstitute the Dcp1:Dcp2 complex containing a portion of the disordere...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky233
更新日期:2018-07-06 00:00:00
abstract::Ribotoxins are potent inhibitors of protein biosynthesis and inactivate ribosomes from a variety of organisms. The ribotoxin alpha-sarcin cleaves the large 23S ribosomal RNA (rRNA) at the universally conserved sarcin-ricin loop (SRL) leading to complete inactivation of the ribosome and cellular death. The SRL interact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq151
更新日期:2010-07-01 00:00:00
abstract::Cultured mammalian cells transduced with the Escherichia coli gene, Ecogpt, synthesize the bacterial enzyme xanthine-guanine phosphoribosyl transferase (XGPT) (1). This paper describes a method for measuring XGPT activity in crude cell extracts by following the conversion of 14C-xanthine (X) to 14C-xanthine monophosph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.8.2921
更新日期:1985-04-25 00:00:00
abstract::Human U6 small nuclear RNA (U6 snRNA), an abundant snRNA required for splicing of pre-mRNAs, contains several post-transcriptional modifications including a single m6A (N-6-methyladenosine) at position 43. This A-43 residue is critical for the function of U6 snRNA in splicing of pre-mRNAs. Yeast and plant U6 snRNAs al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.13.2421
更新日期:1995-07-11 00:00:00
abstract::Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea that grow over an unusually broad temperature range. Transfer RNAs from Methanococcus vannielii, Methanococcus maripalu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.22.4699
更新日期:2001-11-15 00:00:00
abstract::The eukaryotic genome evolves under the dual constraint of maintaining coordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx198
更新日期:2017-06-02 00:00:00
abstract::The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.7119
更新日期:1990-12-11 00:00:00
abstract::RNA molecules play different roles in coding, decoding and gene expression regulation. Such roles are often associated to the RNA secondary or tertiary structures. The folding dynamics lead to multiple secondary structures of long RNA molecules, since an RNA molecule might fold into multiple distinct native states. De...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1249
更新日期:2014-12-16 00:00:00
abstract::Bacillus stearothermophilus large ribosomal subunits were reconstituted in the presence of 5S rRNAs from different origins and tested for their biological activities. The results obtained have shown that eubacterial and archaebacterial 5S rRNAs can easily substitute for B. stearothermophilus 5S rRNA in the reconstitut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.8.3511
更新日期:1988-04-25 00:00:00
abstract::The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9861
更新日期:1987-12-10 00:00:00
abstract::The nucleobase modification 5-methylcytosine (m(5)C) is widespread both in DNA and different cellular RNAs. The functions and enzymatic mechanisms of DNA m(5)C-methylation were extensively studied during the last decades. However, the location, the mechanism of formation and the cellular function(s) of the same modifi...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkp1117
更新日期:2010-03-01 00:00:00
abstract::During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the homologous protein EF-P. While a structure of EF-P bound to the 70S ribosome exists, structural insight into eIF-5A on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1517
更新日期:2016-02-29 00:00:00
abstract::DNA sequences, that control expression of the spliced leader (SL) RNA gene in the parasitic protozoan Leishmania amazonensis, were mapped by block substitution mutagenesis. In the absence of a functional in vitro system for transcription, no promoter elements have yet been identified in this organism. We therefore dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.11.1959
更新日期:1994-06-11 00:00:00
abstract::The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.1.51
更新日期:1995-01-11 00:00:00
abstract::Differential display of mRNA is a simple, sensitive and powerful method to identify differentially expressed gene fragments. The main drawback of differential display is the lack of reproducibility and the inability to read and compare complex gels. This issue results from employing unoptimized primer combinations and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.3.854
更新日期:1998-02-01 00:00:00