Abstract：
:Autosomal dominant and/or recessive progressive external ophthalmoplegia (ad/arPEO) is associated with mtDNA mutagenesis. It can be caused by mutations in three nuclear genes, encoding the adenine nucleotide translocator 1, the mitochondrial helicase Twinkle or DNA polymerase gamma (POLG). How mutations in these genes result in progressive accumulation of multiple mtDNA deletions in post- mitotic tissues is still unclear. A recent hypothesis suggested that mtDNA replication infidelity could promote slipped mispairing, thereby stimulating deletion formation. This hypothesis predicts that mtDNA of ad/arPEO patients will contain frequent mutations throughout; in fact, our analysis of muscle from ad/arPEO patients revealed an age-dependent, enhanced accumulation of point mutations in addition to deletions, but specifically in the mtDNA control region. Both deleted and non-deleted mtDNA molecules showed increased point mutation levels, as did mtDNAs of patients with a single mtDNA deletion, suggesting that point mutations do not cause multiple deletions. Deletion breakpoint analysis showed frequent breakpoints around homopolymeric runs, which could be a signature of replication stalling. Therefore, we propose replication stalling as the principal cause of deletion formation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wanrooij S,Luoma P,van Goethem G,van Broeckhoven C,Suomalainen A,Spelbrink JNdoi
10.1093/nar/gkh634keywords:
subject
Has Abstractpub_date
2004-06-04 00:00:00pages
3053-64issue
10eissn
0305-1048issn
1362-4962pii
32/10/3053journal_volume
32pub_type
杂志文章abstract：:The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The objective of ENA is to support and promote the use of nucleotide sequencing as an experimen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq967
更新日期：2011-01-01 00:00:00
abstract：:Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Exi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1130
更新日期：2012-01-01 00:00:00
abstract：:The compilation of 5S rRNA and 5S rRNA gene nucleotide sequences as of 30 September 1996, contains a total of 1661 primary structures of 5S rRNAs or their genes, which is an increase of 928 new sequence entries over the last compilation. It covers sequences from 54 archaea, 449 eubacteria, 34 plastids, nine mitochondr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.1.96
更新日期：1997-01-01 00:00:00
abstract：:The Human Disease Ontology (DO) (http://www.disease-ontology.org), database has undergone significant expansion in the past three years. The DO disease classification includes specific formal semantic rules to express meaningful disease models and has expanded from a single asserted classification to include multiple-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1032
更新日期：2019-01-08 00:00:00
abstract：:Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their circularity as well as biochemically enrich these transcripts, it has become standard in the field to use the 3'-5' exonuclease RNase R. Here, we demonst...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz576
更新日期：2019-09-19 00:00:00
abstract：:High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng015
更新日期：2003-02-15 00:00:00
abstract：:An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been ide...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.16.3424
更新日期：2001-08-15 00:00:00
abstract：:The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughpu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn292
更新日期：2008-07-01 00:00:00
abstract：:The DEAH-box NTPase Prp43 disassembles spliceosomes in co-operation with the cofactors Ntr1/Spp382 and Ntr2, forming the NTR complex. How Prp43 is regulated by its cofactors to discard selectively only intron-lariat spliceosomes (ILS) and defective spliceosomes and to prevent disassembly of earlier and properly assemb...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1225
更新日期：2017-04-20 00:00:00
abstract：:The structure of a ribonuclease III processing signal from bacteriophage T7 was examined by NMR spectroscopy, optical melting, and chemical and enzymatic modification. A 41 nucleotide variant of the T7 R1.1 processing signal has two Watson-Crick base-paired helices separated by an internal loop, consistent with its pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.4.604
更新日期：1994-02-25 00:00:00
abstract：:Phosphorylation of the easily accessible 3',5'-diesters 1a-d with diphenyl phosphorochloridate, followed by selective 5'-deacylation, affords the phosphotriester derivatives 2a-d in good yields. Alkaline treatment of 2a-d results in the formation of the 2',3'-cyclic phosphates (3a-d). The usefulness of the phosphotrie...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.10.2731
更新日期：1976-10-01 00:00:00
abstract：:DNA swivel (nicking-rejoining) enzyme activity has been studied in various cell fractions of a human lymphoid cell line. Swivel activity is found only in chromatin and in a nuclear membrane fraction containing DNA and possessing endogenous DNA synthesizing activity. Twenty percent of the total swivel activity and less...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.1.223
更新日期：1977-01-01 00:00:00
abstract：:This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.9.2951
更新日期：1982-05-11 00:00:00
abstract：:The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nasce...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx318
更新日期：2017-07-27 00:00:00
abstract：:Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary meta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq340
更新日期：2010-07-01 00:00:00
abstract：:In the virion core of retroviruses, the genomic RNA is tightly associated with nucleocapsid (NC) protein molecules, forming the nucleocapsid structure. NC protein, a highly basic protein with two zinc fingers, is indispensable for RNA dimerization, encapsidation and the initiation of reverse transcription in avian, mu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.4.831
更新日期：1993-02-25 00:00:00
abstract：:A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emissi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx942
更新日期：2017-12-01 00:00:00
abstract：:Redefinition of UAG, UAA and UGA to specify a standard amino acid occurs in response to recoding signals present in a minority of mRNAs. This 'read-through' is in competition with termination and is utilized for gene expression. One of the recoding signals known to stimulate read-through is a hexanucleotide sequence o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.9.2011
更新日期：2002-05-01 00:00:00
abstract：:A RNA interference (RNAi) like mechanism is involved in elimination of thousands of DNA segments from the developing somatic macronucleus of Tetrahymena, yet how specific internal eliminated sequences (IESs) are recognized remains to be fully elucidated. To define requirements for DNA rearrangement, we performed mutag...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl699
更新日期：2006-01-01 00:00:00
abstract：:We have developed a PCR-based short interfering RNA (siRNA) quantification method based on competition between siRNA and a homologous DNA primer for annealing to template DNA, avoiding the requirement for prior conversion of RNA to cDNA. Primers and probe were designed to amplify regions of the human papillomavirus E6...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn903
更新日期：2009-01-01 00:00:00
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：:Aspects of the metabolism of RNA have been studied in enzymatically isolated protoplasts from cotyledon and first leaf mesophyll tissue of two cultivars of cucumber. The first leaf mesophyll protoplasts incorporated (3H)-uridine into ribosomal RNA at a constant rate for up to 25 hr in a simple salts medium and for up ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.7.1111
更新日期：1975-07-01 00:00:00
abstract：:Intrinsic energetic and solvation factors contributing to the unusual structural and biochemical properties of N3'-phosphoramidate DNA analogs have been re-examined using a combination of quantum mechanical and molecular dynamics methods. Evaluation of the impact of the N3'-H substitution was performed via comparison ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.15.3219
更新日期：2001-08-01 00:00:00
abstract：:Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of (C leads to) CO+2 ion with res...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.1.101
更新日期：1976-01-01 00:00:00
abstract：:Based on parameters governing promoter activity and using regulatory elements of the lac, ara and tet operon transcription control sequences were composed which permit the regulation in Escherichia coli of several gene activities independently and quantitatively. The novel promoter PLtetO-1 allows the regulation of ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.6.1203
更新日期：1997-03-15 00:00:00
abstract：:In Escherichia coli transcription of individual genes generally requires concomitant translation, and thus the decay of mRNAs cannot be studied without the complication of translation. Here we have used T7 RNA polymerase to transcribe in vivo lacZ genes carrying ribosome binding sites of variable efficiency. We show t...
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
abstract：:The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa980
更新日期：2021-01-08 00:00:00
abstract：:eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 euka...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1085
更新日期：2019-01-08 00:00:00
abstract：:The essential splicing factor Prp24 contains four RNA Recognition Motif (RRM) domains, and functions to anneal U6 and U4 RNAs during spliceosome assembly. Here, we report the structure and characterization of the C-terminal RRM4. This domain adopts a novel non-canonical RRM fold with two additional flanking α-helices ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr455
更新日期：2011-09-01 00:00:00
abstract：:Infrared Spectroscopy was used to determine the numbers of base pairs for yeast 5S RNA and 5.8S RNA. The spectra were recorded at 20 degrees C and 50 degrees C, where tertiary interactions are assumed to be of less importance. It may be concluded that the structure of both RNAs is highly ordered and that there are lar...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3851
更新日期：1981-08-11 00:00:00
