Abstract:
:The role of the enzyme poly(adenosine diphosphate-ribose) polymerase (PADPRP) in DNA repair at the level of the gene was investigated with human HeLa cells in which PADPRP antisense transcripts are inducible with dexamethasone. After such induction, the cellular content of PADPRP is reduced by 90%. DNA damage and its repair was studied in the essential dihydrofolate reductase (DHFR) gene after exposure of the cells to either ultraviolet (UV) irradiation or the alkylating agent nitrogen mustard. The expression of the antisense construct had no effect on gene-specific repair of UV-induced pyrimidine dimers. In contrast, induced antisense cells were deficient in the gene-specific repair of nitrogen mustard-induced lesions. Dexamethasone itself did not inhibit gene-specific repair in control cells. Thus, PADPRP appears to participate in the gene-specific repair of alkylation damage, but not in the repair of UV-induced pyrimidine dimers. Clonal survival assays revealed that cells depleted of PADPRP showed an increased susceptibility to nitrogen mustard, supporting the notion that repair of essential genes is critical for cellular survival.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Stevnsner T,Ding R,Smulson M,Bohr VAdoi
10.1093/nar/22.22.4620subject
Has Abstractpub_date
1994-11-11 00:00:00pages
4620-4issue
22eissn
0305-1048issn
1362-4962journal_volume
22pub_type
杂志文章abstract::The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh123
更新日期:2004-01-01 00:00:00
abstract::Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome v...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1525
更新日期:2016-05-05 00:00:00
abstract::The DNA photosensitisers m-iodo Hoechst and m-iodo, p-methoxy Hoechst have been co-crystallised with the oligonucleotide d(CGCGAATTCGCG)(2)and their crystal structures determined. The crystals were then subjected to slow dehydration, which reduced their solvent contents from 40 (normal) to 30 (partially dehydrated) an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.5.1252
更新日期:2000-03-01 00:00:00
abstract::Recent studies have shown that homologous recombination (HR) requires chromatin repression as well as relaxation at DNA double strand breaks (DSBs). HP1 and SUV39H1/2 are repressive factors essential for HR. Here, we identify SETDB1 as an additional compacting factor promoting HR. Depletion of HP1, SUV39, SETDB1 or BR...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv722
更新日期:2015-09-18 00:00:00
abstract::The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.55
更新日期:1999-01-01 00:00:00
abstract::The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx315
更新日期:2017-07-27 00:00:00
abstract::Bacteriophage Mu has one of the best studied, most efficient and largest transposition machineries of the prokaryotic world. To harness this attractive integration machinery for use in mammalian cells, we cloned the coding sequences of the phage factors MuA and MuB in a eukaryotic expression cassette and fused them to...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.23.e104
更新日期:2000-12-01 00:00:00
abstract::Neuroserpin is an axonally secreted serine protease inhibitor expressed in the nervous system that protects neurons from ischemia-induced apoptosis. Mutant neuroserpin forms have been found polymerized in inclusion bodies in a familial autosomal encephalopathy causing dementia, or associated with epilepsy. Regulation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.10.2202
更新日期:2002-05-15 00:00:00
abstract::This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkr729
更新日期:2012-01-01 00:00:00
abstract::Base compositions were examined at every position in codons of more than 50 genes from taxonomically different bacteria and of the corresponding antisense sequences on the bacterial genes. We propose that the nonstop frame on antisense strand [NSF(a)] of GC-rich bacterial genes is the most promising sequence for newly...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.21.4249
更新日期:1996-11-01 00:00:00
abstract::Highly conserved sequences present at an identical position near the 3' ends of eukaryotic and prokaryotic 5S rRNAs are complementary to the 5' strand of the m2(6)A hairpin structure near the 3' ends of 18S rRNA and 16S rRNA, respectively. The extent of base-pairing and the calculated stabilities of the hybrids that c...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/7.7.1913
更新日期:1979-12-11 00:00:00
abstract::Small inverted repeats (small palindromes) on plasmids have been shown to mediate a recombinational rearrangement event in Escherichia coli leading to the formation of inverted dimers (giant palindromes). This recombinational rearrangement event is efficient and independent of RecA and RecBCD. In this report, we propo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.15.3009
更新日期:1997-08-01 00:00:00
abstract::Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A searc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl732
更新日期:2006-01-01 00:00:00
abstract::NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1216
更新日期:2010-05-01 00:00:00
abstract::We have compiled the DNA sequence data for E. coli K12 available from the GENBANK and EMBO databases and over a period of several years independently from the literature. We have introduced all available genetic map data and have arranged the sequences accordingly. As far as possible the overlaps are deleted and a tot...
journal_title:Nucleic acids research
pub_type:
doi:10.1093/nar/17.suppl.r283
更新日期:1989-01-01 00:00:00
abstract::YY1 is ubiquitously expressed zinc finger DNA binding protein. It can act as a transcriptional repressor or activator and, when binding at the initiator element, as a component of the basal transcription complex. Binding sites for YY1 have been reported in a wide variety of promoters and they exhibit substantial diver...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.21.4457
更新日期:1995-11-11 00:00:00
abstract::Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh803
更新日期:2004-09-08 00:00:00
abstract::The entire nucleotide sequence of the Ad. 2 EcoRI D fragment has been determined using the Maxam and Gilbert method. This sequence of 2678 bp contains informations relative to late mRNAs ending at position 78 and for which an AATAAA sequence corresponding to their 3' ends is found at residue number 833. Position of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.10.2173
更新日期:1980-05-24 00:00:00
abstract::Guanine rich nucleic acid sequences can form G-quadruplex (G4) structures that interfere with DNA replication, repair and RNA transcription. The human FANCJ helicase contributes to maintaining genomic integrity by promoting DNA replication through G4-forming DNA regions. Here, we combined single-molecule and ensemble ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw574
更新日期:2016-10-14 00:00:00
abstract::DNA polymerase (Pol) beta null mouse embryonic fibroblasts provide a useful cell system to investigate the effects of alterations in base excision repair (BER) on genome stability. These cells are characterized by hypersensitivity to the cytotoxic effects of methyl methanesulfonate (MMS) and by decreased repair of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki168
更新日期:2005-01-12 00:00:00
abstract::Replication of the promiscuous plasmid pMV158 requires expression of the initiator repB gene, which is controlled by the repressor CopG. Genes repB and copG are co-transcribed from promoter P(cr). We have studied the interactions between RNA polymerase, CopG and the promoter to elucidate the mechanism of repression by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp503
更新日期:2009-08-01 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::The sequence of 110 nucleotides adjacent to the 3'-end of Neurospora crassa 25S-rRNA has been derived by chemical sequencing methods. Sequences present between 40 and 85 nucleotides of the 3'-end were found to complement sequences at the 3'- and 5'-ends of 5.8S-rRNA. Interaction was shown to occur between 5.8S-rRNA an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.5.1111
更新日期:1981-03-11 00:00:00
abstract::RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp542
更新日期:2009-09-01 00:00:00
abstract::Three novel DNA-binding proteins with apparent molecular masses of 7, 10 and 30 kDa have been isolated from the hyperthermophilic methanogen Methanopyrus kandleri. The proteins were identified using a blot overlay assay that was modified to emulate the high ionic strength intracellular environment of M.kandleri protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.3.685
更新日期:2002-02-01 00:00:00
abstract::The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introd...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky467
更新日期:2018-07-02 00:00:00
abstract::The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1159
更新日期:2008-02-01 00:00:00
abstract::We have recently developed a novel method for the affinity purification of the complete suite of translating mRNA from genetically labeled cell populations. This method permits comprehensive quantitative comparisons of the genes employed by each specific cell type. We provide a detailed description of tools for analys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq130
更新日期:2010-07-01 00:00:00
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 regula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq032
更新日期:2010-06-01 00:00:00
abstract::Novel techniques for high-throughput steady-state metabolomic profiling yield information about changes of nearly thousands of metabolites. Such metabolomic profiles, when analyzed together with transcriptional profiles, can reveal novel insights about underlying biological processes. While a number of conceptual appr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw266
更新日期:2016-07-08 00:00:00