Discovery and characterization of Alu repeat sequences via precise local read assembly.


:Alu insertions have contributed to >11% of the human genome and ∼30-35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means to reconstruct the full sequence of insertion events from Illumina paired end reads. Comparison with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at the cost of reduced sensitivity due to the colocation of reference and non-reference repeats. We generate a highly accurate call set of 1614 completely assembled Alu variants from 53 samples from the Human Genome Diversity Project (HGDP) panel. We utilize the reconstructed alternative insertion haplotypes to genotype 1010 fully assembled insertions, obtaining >99% agreement with genotypes obtained by PCR. In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5' truncation in 16% of AluYa5 and AluYb8 insertions. The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5' truncations. Additionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotransposition mechanisms.


Nucleic Acids Res


Nucleic acids research


Wildschutte JH,Baron A,Diroff NM,Kidd JM




Has Abstract


2015-12-02 00:00:00














  • The interaction of DNA-targeted platinum phenanthridinium complexes with DNA.

    abstract::Cisplatin analogues were synthesised that consisted of platinum(II) diamine complexes tethered via a polymethylene chain ( n = 3, 5, 8 and 10) to a phenanthridinium cation. Both chloro and iodo leaving groups were examined. DNA adduct formation was quantitatively analysed using a linear amplification system with the p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Whittaker J,McFadyen WD,Wickham G,Wakelin LP,Murray V

    更新日期:1998-09-01 00:00:00

  • Promoter and enhancer activities of long terminal repeats associated with cellular retrovirus-like (VL30) elements.

    abstract::LTR units associated with cellular retrovirus-like elements are abundantly present in chromosomal DNA of animal cells. We have analyzed the promoter and enhancer activities of diverse LTR units associated with different members of the murine retrovirus-like family known as VL30. We report here that the structurally he...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rotman G,Itin A,Keshet E

    更新日期:1986-01-24 00:00:00

  • miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.

    abstract::Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we deve...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hackenberg M,Sturm M,Langenberger D,Falcón-Pérez JM,Aransay AM

    更新日期:2009-07-01 00:00:00

  • A nascent micronuclear pseudogene in the ciliate Euplotes crassus.

    abstract::The macronuclear genome of Euplotes crassus contains two different genes, EFA1 and EFA2, encoding EF-1alpha proteins. They are derived from micronuclear precursors in the course of a sexual process termed conjugation. We have found that two apparent micronuclear precursors exist for EFA1. They differ in their potentia...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Florian V,Klein A

    更新日期:1996-08-15 00:00:00

  • Induction of an abortive and futile DNA repair process in E. coli by the antitumor DNA bifunctional intercalator, ditercalinium: role in polA in death induction.

    abstract::Ditercalinium, an antitumor bifunctional intercalator which forms a high affinity reversible complex with DNA, was found to be specifically cytotoxic for polA and lig7 E. coli strains. In the polA strain, the cytotoxic effect of ditercalinium was suppressed by the uvrA mutation. DNA single strand breaks accumulated in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lambert B,Roques BP,Le Pecq JB

    更新日期:1988-02-11 00:00:00

  • CRISPR/Cas9-mediated modulation of splicing efficiency reveals short splicing isoform of Xist RNA is sufficient to induce X-chromosome inactivation.

    abstract::Alternative splicing of mRNA precursors results in multiple protein variants from a single gene and is critical for diverse cellular processes and development. Xist encodes a long noncoding RNA which is a central player to induce X-chromosome inactivation in female mammals and has two major splicing variants: long and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yue M,Ogawa Y

    更新日期:2018-03-16 00:00:00

  • Genome maintenance in Saccharomyces cerevisiae: the role of SUMO and SUMO-targeted ubiquitin ligases.

    abstract::The genome of the cell is often exposed to DNA damaging agents and therefore requires an intricate well-regulated DNA damage response (DDR) to overcome its deleterious effects. The DDR needs proper regulation for its timely activation, repression, as well as appropriate choice of repair pathway. Studies in Saccharomyc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Jalal D,Chalissery J,Hassan AH

    更新日期:2017-03-17 00:00:00

  • T7 promoter contacts essential for promoter activity in vivo.

    abstract::T7 RNA polymerase promoters consist of a highly conserved 23 base-pair sequence that spans the site of the initiation of transcription (+1) and extends from -17 to +6. To determine the bases within the T7 consensus promoter that are essential for promoter function a library of mutant T7 promoters was constructed, and ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ikeda RA,Ligman CM,Warshamana S

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  • ssDNA diffuses along replication protein A via a reptation mechanism.

    abstract::Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA alon...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mishra G,Bigman LS,Levy Y

    更新日期:2020-02-28 00:00:00

  • Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach.

    abstract::Generally, the presence of a consensus sequence in the promoter of a gene is taken as indication for regulation by the transcription factor that binds to this sequence. In light of the recent developments in genome research, we were interested to what extent this supposition is valid. We examined the relationship betw...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hamoen LW,Smits WK,de Jong A,Holsappel S,Kuipers OP

    更新日期:2002-12-15 00:00:00

  • Tolerance of 5-fluorodeoxyuridine resistant human thymidylate synthases to alterations in active site residues.

    abstract::Fluoropyrimidines, such as 5-fluorouracil (5-FU), are used extensively in cancer therapy. In the cell, 5-FU is metabolized to 5-fluorodeoxyuridylate (5-FdUMP), a tight binding covalent inhibitor of thymidylate synthase (TS). In order to create 5-FdUMP resistant enzymes to protect chemosensitive normal cells and furthe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Landis DM,Gerlach JL,Adman ET,Loeb LA

    更新日期:1999-09-15 00:00:00

  • Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL.

    abstract::The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Venditti V,Niccolai N,Butcher SE

    更新日期:2008-03-01 00:00:00

  • CNCDatabase: a database of non-coding cancer drivers.

    abstract::Most mutations in cancer genomes occur in the non-coding regions with unknown impact on tumor development. Although the increase in the number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies making it difficult to underst...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liu EM,Martinez-Fundichely A,Bollapragada R,Spiewack M,Khurana E

    更新日期:2021-01-08 00:00:00

  • Summary: the modified nucleosides of RNA.

    abstract::A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sourc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Limbach PA,Crain PF,McCloskey JA

    更新日期:1994-06-25 00:00:00

  • RAD18 promotes DNA double-strand break repair during G1 phase through chromatin retention of 53BP1.

    abstract::Recruitment of RAD18 to stalled replication forks facilitates monoubiquitination of PCNA during S-phase, promoting translesion synthesis at sites of UV irradiation-induced DNA damage. In this study, we show that RAD18 is also recruited to ionizing radiation (IR)-induced sites of DNA double-strand breaks (DSBs) forming...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Watanabe K,Iwabuchi K,Sun J,Tsuji Y,Tani T,Tokunaga K,Date T,Hashimoto M,Yamaizumi M,Tateishi S

    更新日期:2009-04-01 00:00:00

  • A new telomerase RNA element that is critical for telomere elongation.

    abstract::The stability of chromosome ends, the telomeres, is dependent on the ribonucleoprotein telomerase. In vitro, telomerase requires at least one RNA molecule and a reverse transcriptase-like protein. However, for telomere homeostasis in vivo, additional proteins are required. Telomerase RNAs of different species vary in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Laterreur N,Eschbach SH,Lafontaine DA,Wellinger RJ

    更新日期:2013-09-01 00:00:00

  • Identification, cloning and characterization of a new DNA-binding protein from the hyperthermophilic methanogen Methanopyrus kandleri.

    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


    authors: Pavlov NA,Cherny DI,Nazimov IV,Slesarev AI,Subramaniam V

    更新日期:2002-02-01 00:00:00

  • Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G.

    abstract::APOBEC3G (A3G), a host protein that inhibits HIV-1 reverse transcription and replication in the absence of Vif, displays cytidine deaminase and single-stranded (ss) nucleic acid binding activities. HIV-1 nucleocapsid protein (NC) also binds nucleic acids and has a unique property, nucleic acid chaperone activity, whic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Iwatani Y,Chan DS,Wang F,Stewart-Maynard K,Sugiura W,Gronenborn AM,Rouzina I,Williams MC,Musier-Forsyth K,Levin JG

    更新日期:2007-01-01 00:00:00

  • Nucleotide sequence of cucumber pale fruit viroid: homology to hop stunt viroid.

    abstract::Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sano T,Uyeda I,Shikata E,Ohno T,Okada Y

    更新日期:1984-04-25 00:00:00

  • The versatile thymine DNA-glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs.

    abstract::Human thymine-DNA glycosylase (TDG) is well known to excise thymine and uracil from G.T and G.U mismatches, respectively, and was therefore proposed to play a central role in the cellular defense against genetic mutation through spontaneous deamination of 5-methylcytosine and cytosine. In this study, we characterized ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hardeland U,Bentele M,Jiricny J,Schär P

    更新日期:2003-05-01 00:00:00

  • Plasmid replication in Xenopus eggs and egg extracts: a 2D gel electrophoretic analysis.

    abstract::We have examined the replication patterns of ribosomal DNA plasmids in vivo and in vitro using Xenopus eggs. Plasmids carrying different parts of the Xenopus ribosomal DNA sequence were allowed to replicate either in vitro in an egg extract or in vivo after microinjection into unfertilized eggs. The replication interm...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hyrien O,Méchali M

    更新日期:1992-04-11 00:00:00

  • An efficient string matching algorithm with k differences for nucleotide and amino acid sequences.

    abstract::There are a few algorithms designed to solve the problem of the optimal alignment of one sequence, the pattern, of length m, with another, longer sequence the text, of length n. These algorithms allow mismatches, deletions and insertions. Algorithms to date run in O(mn) time. Let us define an integer, k, which is the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Landau GM,Vishkin U,Nussinov R

    更新日期:1986-01-10 00:00:00

  • The integrase family of tyrosine recombinases: evolution of a conserved active site domain.

    abstract::The integrases are a diverse family of tyrosine recombinases which rearrange DNA duplexes by means of conservative site-specific recombination reactions. Members of this family, of which the well-studied lambda Int protein is the prototype, were previously found to share four strongly conserved residues, including an ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Esposito D,Scocca JJ

    更新日期:1997-09-15 00:00:00

  • DEAD-box RNA helicase domains exhibit a continuum between complete functional independence and high thermodynamic coupling in nucleotide and RNA duplex recognition.

    abstract::DEAD-box helicases catalyze the non-processive unwinding of double-stranded RNA (dsRNA) at the expense of adenosine triphosphate (ATP) hydrolysis. Nucleotide and RNA binding and unwinding are mediated by the RecA domains of the helicase core, but their cooperation in these processes remains poorly understood. We there...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Samatanga B,Klostermeier D

    更新日期:2014-01-01 00:00:00

  • The nucleotide sequence at the 3'-end of Neurospora crassa 25S-rRNA and the location of a 5.8S-rRNA binding site.

    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


    authors: Kelly JM,Cox RA

    更新日期:1981-03-11 00:00:00

  • NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.

    abstract::NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI. The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding. The predictions are bas...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lundegaard C,Lamberth K,Harndahl M,Buus S,Lund O,Nielsen M

    更新日期:2008-07-01 00:00:00

  • Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding.

    abstract::Rad2/XPG belongs to the flap nuclease family and is responsible for a key step of the eukaryotic nucleotide excision DNA repair (NER) pathway. To elucidate the mechanism of DNA binding by Rad2/XPG, we solved crystal structures of the catalytic core of Rad2 in complex with a substrate. Rad2 utilizes three structural mo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Miętus M,Nowak E,Jaciuk M,Kustosz P,Studnicka J,Nowotny M

    更新日期:2014-01-01 00:00:00

  • Role of nucleotide identity in effective CRISPR target escape mutations.

    abstract::Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly infl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Künne T,Zhu Y,da Silva F,Konstantinides N,McKenzie RE,Jackson RN,Brouns SJ

    更新日期:2018-11-02 00:00:00

  • Mouse genome database 2016.

    abstract::The Mouse Genome Database (MGD; is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bult CJ,Eppig JT,Blake JA,Kadin JA,Richardson JE,Mouse Genome Database Group.

    更新日期:2016-01-04 00:00:00

  • Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes.

    abstract::G-quadruplex (G4) DNA structures are linked to key biological processes and human diseases. Small molecules that target specific G4 DNA structures and signal their presence would therefore be of great value as chemical research tools with potential to further advance towards diagnostic and therapeutic developments. Ho...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kumar R,Chand K,Bhowmik S,Das RN,Bhattacharjee S,Hedenström M,Chorell E

    更新日期:2020-02-20 00:00:00