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














  • Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.

    abstract::MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome som...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sales G,Coppe A,Bicciato S,Bortoluzzi S,Romualdi C

    更新日期:2010-04-01 00:00:00

  • HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.

    abstract::HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic datab...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sumbalova L,Stourac J,Martinek T,Bednar D,Damborsky J

    更新日期:2018-07-02 00:00:00

  • The telomere resolvase of the Lyme disease spirochete, Borrelia burgdorferi, promotes DNA single-strand annealing and strand exchange.

    abstract::Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpin telomeres. Hairpin telomeres present an uninterrupted DNA chain to the replication machinery overcoming ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mir T,Huang SH,Kobryn K

    更新日期:2013-12-01 00:00:00

  • RaftProt: mammalian lipid raft proteome database.

    abstract::RaftProt ( is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shah A,Chen D,Boda AR,Foster LJ,Davis MJ,Hill MM

    更新日期:2015-01-01 00:00:00

  • The kinetic properties of cruciform extrusion are determined by DNA base-sequence.

    abstract::The extrusion kinetics of two cruciforms derived from unrelated DNA sequences differ markedly. Kinetic barriers exist for both reactions, necessitating elevated temperatures before extrusion proceeds at measureable speeds, but the dependence upon temperature and ionic strength is quite different for the two sequences....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lilley DM

    更新日期:1985-03-11 00:00:00

  • The yeast RNA polymerase I promoter: ribosomal DNA sequences involved in transcription initiation and complex formation in vitro.

    abstract::Using an in vitro transcription system for Saccharomyces cerevisiae RNA polymerase I, we have analyzed Pol I promoter deletion mutants and mapped the boundaries of the promoter between positions -155 and +27. The 5'-boundary of the minimal core promoter capable of transcription initiation, however, was found to lie be...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kulkens T,Riggs DL,Heck JD,Planta RJ,Nomura M

    更新日期:1991-10-11 00:00:00

  • LOCnet and LOCtarget: sub-cellular localization for structural genomics targets.

    abstract::LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nair R,Rost B

    更新日期:2004-07-01 00:00:00

  • NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs.

    abstract::We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Morisset D,Dobnik D,Hamels S,Zel J,Gruden K

    更新日期:2008-10-01 00:00:00

  • Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica.

    abstract::Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alterna...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hon CC,Weber C,Sismeiro O,Proux C,Koutero M,Deloger M,Das S,Agrahari M,Dillies MA,Jagla B,Coppee JY,Bhattacharya A,Guillen N

    更新日期:2013-02-01 00:00:00

  • Defective chromatin recruitment and retention of NHEJ core components in human tumor cells expressing a Cyclin E fragment.

    abstract::Exposure to genotoxic agents, such as ionizing radiation (IR), produces double-strand breaks, repaired predominantly in mammalian cells by non-homologous end-joining (NHEJ). Ku70 was identified as an interacting partner of a proteolytic Cyclin E (CycE) fragment, p18CycE. p18CycE endogenous generation during IR-induced...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chatterjee P,Plesca D,Mazumder S,Boutros J,Yannone SM,Almasan A

    更新日期:2013-12-01 00:00:00

  • Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs.

    abstract::We have determined the nucleotide sequence of the major species of E. coli tRNASer and of a minor species having the same GGA anticodon. These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E. coli. The two sequences differ in only one positio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Grosjean H,Nicoghosian K,Haumont E,Söll D,Cedergren R

    更新日期:1985-08-12 00:00:00

  • Characterization of a RecA/RAD51 homologue from the hyperthermophilic archaeon Pyrococcus sp. KOD1.

    abstract::The Pk-rec gene, encoding a RecA/RAD51 homologue from the hyperthermophilic archaeon Pyrococcussp. KOD1, was expressed in Escherichia coli. The recombinant Pk-REC was purified to homogeneity and was shown to be in a dimeric form. A striking property of the purified recombinant Pk-REC was the unusual DNase activity on ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rashid N,Morikawa M,Nagahisa K,Kanaya S,Imanaka T

    更新日期:1997-02-15 00:00:00

  • A circular trans-acting hepatitis delta virus ribozyme.

    abstract::A circular trans-acting ribozyme designed to adopt the motif of the hepatitis delta virus (HDV) trans-acting ribozyme was produced. The circular form was generated in vitro by splicing a modified group I intron precursor RNA in which the relative order of the 5' and 3' splice sites, flanking the single HDV-like ribozy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Puttaraju M,Perrotta AT,Been MD

    更新日期:1993-09-11 00:00:00

  • The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).

    abstract::The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (, ontology supported search functionality and an improved curation ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: MacArthur J,Bowler E,Cerezo M,Gil L,Hall P,Hastings E,Junkins H,McMahon A,Milano A,Morales J,Pendlington ZM,Welter D,Burdett T,Hindorff L,Flicek P,Cunningham F,Parkinson H

    更新日期:2017-01-04 00:00:00

  • Exposition of a family of RNA m(5)C methyltransferases from searching genomic and proteomic sequences.

    abstract::The Escherichia coli fmu gene product has recently been determined to be the 16S rRNA m(5)C 967 methyltransferase. As such, Fmu represents the first protein identified as an S -adenosyl-L-methionine (AdoMet)- dependent RNA m(5)C methyltransferase whose amino acid sequence is known. Using the amino acid sequence of Fmu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Reid R,Greene PJ,Santi DV

    更新日期:1999-08-01 00:00:00

  • Alternative-splicing-based bicistronic vectors for ratio-controlled protein expression and application to recombinant antibody production.

    abstract::In the last decade polycistronic vectors have become essential tools for both basic science and gene therapy applications. In order to co-express heterologous polypeptides, different systems have been developed from Internal Ribosome Entry Site (IRES) based vectors to the use of the 2A peptide. Unfortunately, these me...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fallot S,Ben Naya R,Hieblot C,Mondon P,Lacazette E,Bouayadi K,Kharrat A,Touriol C,Prats H

    更新日期:2009-11-01 00:00:00

  • Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome.

    abstract::The endoribonuclease RNase E is a key enzyme in RNA metabolism for many bacterial species. In Escherichia coli, RNase E contributes to the majority of RNA turnover and processing events, and the enzyme has been extensively characterized as the central component of the RNA degradosome assembly. A similar RNA degradosom...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Voss JE,Luisi BF,Hardwick SW

    更新日期:2014-12-01 00:00:00

  • Genome engineering of isogenic human ES cells to model autism disorders.

    abstract::Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic suc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Martinez RA,Stein JL,Krostag AR,Nelson AM,Marken JS,Menon V,May RC,Yao Z,Kaykas A,Geschwind DH,Grimley JS

    更新日期:2015-05-26 00:00:00

  • A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases.

    abstract::Exome sequencing strategy is promising for finding novel mutations of human monogenic disorders. However, pinpointing the casual mutation in a small number of samples is still a big challenge. Here, we propose a three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Li MX,Gui HS,Kwan JS,Bao SY,Sham PC

    更新日期:2012-04-01 00:00:00

  • Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications.

    abstract::Quantitative real-time PCR has revolutionized many aspects of genetic research, biomedical diagnostics and pathogen detection. Nevertheless, the full potential of this technology has yet to be realized, primarily due to the limitations of the threshold-based methodologies that are currently used for quantitative analy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rutledge RG

    更新日期:2004-12-15 00:00:00

  • oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques.

    abstract::The nature of mammalian origins of DNA replication remains controversial and this is primarily because two-dimensional gel replicon mapping techniques have identified broad zones of replication initiation whereas several other techniques, such as quantitative PCR, have disclosed more discrete sites of initiation at th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Toledo F,Baron B,Fernandez MA,Lachagès AM,Mayau V,Buttin G,Debatisse M

    更新日期:1998-05-15 00:00:00

  • Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae.

    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


    authors: Tsochatzidou M,Malliarou M,Papanikolaou N,Roca J,Nikolaou C

    更新日期:2017-06-02 00:00:00

  • AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.

    abstract::We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bryson K,Loux V,Bossy R,Nicolas P,Chaillou S,van de Guchte M,Penaud S,Maguin E,Hoebeke M,Bessières P,Gibrat JF

    更新日期:2006-07-19 00:00:00

  • The complete nucleotide sequence of the I-E alpha d immune response gene.

    abstract::We have isolated and sequenced the complete murine I-E alpha immune response gene of the H-2db haplotype. The I-E alpha d gene consists of 5300 basepairs and is organized into five or possibly six exons that correspond to different domains of the alpha chain. The amino acid sequence deduced from the I-E alpha gene sho...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hyldig-Nielsen JJ,Schenning L,Hammerling U,Widmark E,Heldin E,Lind P,Servenius B,Lund T,Flavell R,Lee JS,Trowsdale J,Schreier PH,Zablitzky F,Larhammar D,Peterson PA,Rask L

    更新日期:1983-08-11 00:00:00

  • Cloning and expression of the hypoxanthine-guanine phosphoribosyltransferase gene from Trypanosoma brucei.

    abstract::The hypoxanthine-guanine phosphoribosyltransferase (HGPRT) enzyme of Trypanosoma brucei and related parasites provides a rational target for the treatment of African sleeping sickness and several other parasitic diseases. To characterize the T. brucei HGPRT enzyme in detail, the T. brucei hgprt was isolated within a 4...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Allen TE,Ullman B

    更新日期:1993-11-25 00:00:00

  • Premature termination of RNA polymerase II mediated transcription of a seed protein gene in Schizosaccharomyces pombe.

    abstract::The poly(A) signal and downstream elements with transcriptional pausing activity play an important role in termination of RNA polymerase II transcription. We show that an intronic sequence derived from the plant seed protein gene (AmA1) specifically acts as a transcriptional terminator in the fission yeast, Schizosacc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chakraborty S,Sarmah B,Chakraborty N,Datta A

    更新日期:2002-07-01 00:00:00

  • MRPrimerV: a database of PCR primers for RNA virus detection.

    abstract::Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and speci...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kim H,Kang N,An K,Kim D,Koo J,Kim MS

    更新日期:2017-01-04 00:00:00

  • Nicking is asynchronous and stimulated by synapsis in 12/23 rule-regulated V(D)J cleavage.

    abstract::The first step in DNA cleavage at V(D)J recombination signals by RAG1 and RAG2 is creation of a nick at the heptamer/coding flank border. Under proper conditions in vitro the second step, hairpin formation, requires two signals with spacers of 12 and 23 bp, a restriction referred to as the 12/23 rule. Under these cond...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Eastman QM,Schatz DG

    更新日期:1997-11-01 00:00:00

  • Coding and spacer sequences in the 5.8S-2S region of Sciara coprophila ribosomal DNA.

    abstract::The sequence of 436 nucleotides around the region coding for 5.8S RNA in the Sciara coprophila rDNA transcription unit (1) has been determined. Regions coding for 5.8S and 2S RNAs have been identified; they are 80 - 90% homologous to the corresponding Drosophila sequences and are separated by a 22 nucleotide long spac...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jordan BR,Latil-Damotte M,Jourdan R

    更新日期:1980-08-25 00:00:00

  • Molecular dissection of the domain architecture and catalytic activities of human PrimPol.

    abstract::PrimPol is a primase-polymerase involved in nuclear and mitochondrial DNA replication in eukaryotic cells. Although PrimPol is predicted to possess an archaeo-eukaryotic primase and a UL52-like zinc finger domain, the role of these domains has not been established. Here, we report that the proposed zinc finger domain ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Keen BA,Jozwiakowski SK,Bailey LJ,Bianchi J,Doherty AJ

    更新日期:2014-05-01 00:00:00