Abstract：
:Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what types of complex mutation occur, and we cannot routinely characterize arbitrarily-complex mutations in a high-throughput, genome-wide manner. Long-read DNA sequencing methods (e.g. PacBio, nanopore) are promising for this task, because one read may encompass a whole complex mutation. We describe an analysis pipeline to characterize arbitrarily-complex 'local' mutations, i.e. intrachromosomal mutations encompassed by one DNA read. We apply it to nanopore and PacBio reads from one human cell line (NA12878), and survey sequence rearrangements, both real and artifactual. Almost all the real rearrangements belong to recurring patterns or motifs: the most common is tandem multiplication (e.g. heptuplication), but there are also complex patterns such as localized shattering, which resembles DNA damage by radiation. Gene conversions are identified, including one between hemoglobin gamma genes. This study demonstrates a way to find intricate rearrangements with any number of duplications, deletions, and repositionings. It demonstrates a probability-based method to resolve ambiguous rearrangements involving highly similar sequences, as occurs in gene conversion. We present a catalog of local rearrangements in one human cell line, and show which rearrangement patterns occur.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Frith MC,Khan Sdoi
10.1093/nar/gkx1266subject
Has Abstractpub_date
2018-02-28 00:00:00pages
1661-1673issue
4eissn
0305-1048issn
1362-4962pii
4758613journal_volume
46pub_type
杂志文章abstract：:PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing Partnership (RWCP) in August 1997, it developed to the present system of PDB-REPRDB. In April 2001, the system was moved to the Computational Biology Research Center (CBRC), National Institut...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg022
更新日期：2003-01-01 00:00:00
abstract：:Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methox...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.3.921
更新日期：1987-02-11 00:00:00
abstract：:The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw667
更新日期：2016-11-16 00:00:00
abstract：:We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Q beta. The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.13.6205
更新日期：1988-07-11 00:00:00
abstract：:Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment st...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp603
更新日期：2009-11-01 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
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt776
更新日期：2014-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.17.3392
更新日期：2000-09-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.17.3603
更新日期：2001-09-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa550
更新日期：2020-09-18 00:00:00
abstract：:Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.9.3843
更新日期：1984-05-11 00:00:00
abstract：:DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw993
更新日期：2017-01-04 00:00:00
abstract：:In continuation with work regarding the evaluation of the energy of association of various RNA bases with various base pairs, the results of the computations of the electrostatic interaction energy of A-U base pair with four RNA bases viz. Adenine, Uracil, Guanine and Cytosine have been reported. Non bonded induced po...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.17.3983
更新日期：1980-09-11 00:00:00
abstract：:The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1226
更新日期：2016-01-04 00:00:00
abstract：:In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-β-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 Å and 2.80 Å reso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv732
更新日期：2015-09-18 00:00:00
abstract：:A sensitive gel retention assay has been utilized to detect proteins from uninfected Hela nuclei which interact with the adenovirus type 2 enhancer. This assay has been employed to monitor fractionation of nuclear extracts. Three enhancer binding factors were resolved by chromatography on DEAE-Sepharose and one of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.6.2719
更新日期：1987-03-25 00:00:00
abstract：:The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1050
更新日期：2019-01-08 00:00:00
abstract：:Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.12.2212
更新日期：1995-06-25 00:00:00
abstract：:LTR-IS elements are middle repetitive sequences in the mouse genome with structural features of solitary retroviral LTRs. In order to get some insight in the possible functional role of these sequences the promotor activity of two LTR-IS representatives differing by 105 bp in their U3 region was investigated. Gene fus...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.7.2631
更新日期：1985-04-11 00:00:00
abstract：:As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality fac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.9.e43
更新日期：2000-05-01 00:00:00
abstract：:In many organisms (e.g., gram-positive eubacteria) Gin-tRNA is not formed by direct glutaminylation of tRNAGln but by a specific transamidation of Glu-tRNAGln. We wondered whether a similar transamidation pathway also operates in the formation of Asn-tRNA in these organisms. Therefore we tested in S-100 preparations o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.14.2648
更新日期：1996-07-15 00:00:00
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journal_title：Nucleic acids research
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更新日期：1997-03-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg310
更新日期：2003-04-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr600
更新日期：2011-10-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa915
更新日期：2021-01-08 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.199
更新日期：2001-01-01 00:00:00
abstract：:Alternative splicing constitutes a major mechanism creating protein diversity in humans. This diversity can result from the alternative skipping of entire exons or by alternative selection of the 5' or 3' splice sites that define the exon boundaries. In this study, we analyze the sequence and evolutionary characterist...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm603
更新日期：2007-01-01 00:00:00
abstract：:The third intron from Physarum polycephalum (Pp LSU 3) is one of the closest known relatives to the well-studied Tetrahymena group I intron. Both introns are located at the same position in the 26S rRNA gene, and with the exception of an open reading frame in Pp LSU 3, are highly homologous. While Pp LSU 3 has been sh...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1994-10-11 00:00:00
abstract：:We have developed a simple method to measure RNA synthesis in real time. In this technique, transcription reactions are performed in the presence of molecular beacons that possess a 2'-O-methylribonucleotide backbone. These probes become fluorescent as they hybridize to nascent RNA during the course of synthesis. We f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh068
更新日期：2004-05-20 00:00:00
abstract：:We have used in vitro site-directed mutagenesis with synthetic DNA oligonucleotides to introduce single nucleotide mutations in yeast mtDNA. In addition to the expected DNA alterations we also recovered with high frequency mutants with large deletions and insertions which arose through interaction with the synthetic D...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.24.8595
更新日期：1983-12-20 00:00:00
