Abstract：
: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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wildschutte JH,Baron A,Diroff NM,Kidd JMdoi
10.1093/nar/gkv1089subject
Has Abstractpub_date
2015-12-02 00:00:00pages
10292-307issue
21eissn
0305-1048issn
1362-4962pii
gkv1089journal_volume
43pub_type
杂志文章abstract：:A 5',7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa743
更新日期：2020-10-09 00:00:00
abstract：:CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa705
更新日期：2020-09-25 00:00:00
abstract：:Analysis of the human VK (ref. 2) gene locus led to the detection of a new sequence family (L sequences). Its copy number is in the range of 10(2). The L sequences, which are about 500 bp long, are found as part of the 3' flanking regions of a clustered set of human VKI genes but they occur also separate from the gene...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.13.5265
更新日期：1984-07-11 00:00:00
abstract：:Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq590
更新日期：2010-11-01 00:00:00
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
doi：10.1093/nar/14.1.31
更新日期：1986-01-10 00:00:00
abstract：:HIV-1 reverse transcriptase (RT) is a primary target for anti-AIDS drugs. Structures of HIV-1 RT, usually determined at approximately 2.5-3.0 A resolution, are important for understanding enzyme function and mechanisms of drug resistance in addition to being helpful in the design of RT inhibitors. Despite hundreds of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn464
更新日期：2008-09-01 00:00:00
abstract：:The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and distant evolutionary relationships; the third, fold...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.257
更新日期：2000-01-01 00:00:00
abstract：:Pancreatic DNase requires both Ca2+ and Mg2+ for its activity as measured by formation of an activated DNA template for in vitro DNA polymerase alpha assay and by the hyperchromic shift. Mn2+ can partially satisfy the Mg2+ requirement of the DNase for activation of DNA but the resulting template is only 50% as active ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.8.2641
更新日期：1977-08-01 00:00:00
abstract：:Pairing of a given E3 ubiquitin ligase with different E2s allows synthesis of ubiquitin conjugates of different topologies. While this phenomenon contributes to functional diversity, it remains largely unknown how a single E3 ubiquitin ligase recognizes multiple E2s, and whether identical structural requirements deter...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr655
更新日期：2012-01-01 00:00:00
abstract：:Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw374
更新日期：2016-07-08 00:00:00
abstract：:Homeodomains appear to be one of the most frequently employed DNA-binding domains in a superfamily of transacting factors. It is likely that during evolution several sub-types of homeodomain have evolved from a common ancestral domain, resulting in distinct but closely related DNA-binding preferences. Here we describe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.7.1202
更新日期：1994-04-11 00:00:00
abstract：:Detailed models are presented for the triple-stranded polynucleotide helices of poly (U)-poly (A)-poly (U) (two forms), poly (U)-poly d (A) -poly (U), poly d(C)-poly d(I)-poly d(C), poly d(T)-polyd(A)-poly d(T) and poly (I)-poly (A)-poly (I). The models were genrated using a computerized, linked-atom procedure which p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.10.2459
更新日期：1976-10-01 00:00:00
abstract：:TAP/hNXF1 is a key factor that mediates general cellular mRNA export from the nucleus, and its orthologs are structurally and functionally conserved from yeast to humans. Metazoans encode additional proteins that share homology and domain organization with TAP/hNXF1, suggesting their participation in mRNA metabolism; ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki706
更新日期：2005-07-13 00:00:00
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
doi：10.1093/nar/gkx198
更新日期：2017-06-02 00:00:00
abstract：:PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not 5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35 Å resolution. Although the protein has bee...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku186
更新日期：2014-05-01 00:00:00
abstract：:We present evidence that the splice sites in mammalian pre-mRNAs are brought together via a three dimensional diffusion mechanism. We tested two mechanisms for splice site pairing: a lateral diffusion ('scanning') model and the currently favored three dimensional diffusion ('jumping') model. Two lines of evidence that...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.9.1638
更新日期：1996-05-01 00:00:00
abstract：:The Rhizobium trifolii nod genes required for host-specific nodulation of clovers are located on 14 kb of Sym (symbiotic) plasmid DNA. Analysis of the nucleotide sequence of a 3.7 kb portion of this region has revealed open reading frames corresponding to the nodABCDEF genes. A DNA sequencing technique, using primer e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.7.2891
更新日期：1986-04-11 00:00:00
abstract：:Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.24.4940
更新日期：1997-12-15 00:00:00
abstract：:Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and transla...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg161
更新日期：2003-01-15 00:00:00
abstract：:Full-length cDNA of the 6.3 kb turnip yellow mosaic virus (TYMV) genome was placed between a T7 promoter and a unique Hind III site. In vitro transcription of Hind III-linearized DNA of clone pTYMC yielded full-length RNA transcripts. In inoculations of Chinese cabbage protoplasts and plants, capped transcripts and vi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.12.4675
更新日期：1989-06-26 00:00:00
abstract：:Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.6.1485
更新日期：1999-03-15 00:00:00
abstract：:Transcriptional repression and activation by nuclear receptors (NRs) are brought about by coregulator complexes. These complexes modify the chromatin environment of target genes and affect the activity of the basal transcription machinery. We have previously implicated the yeast ADA3 protein in transcriptional activat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.11.2508
更新日期：2002-06-01 00:00:00
abstract：:Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a subset of these proteins. SDPMOD addresses this deficit in structural information by providing a freely available automated...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh394
更新日期：2004-07-01 00:00:00
abstract：:Most RNA molecules collapse rapidly and reach the native state through a pathway that contains numerous traps and unproductive intermediates. The D135 group II intron ribozyme is unusual in that it can fold slowly and directly to the native state, despite its large size and structural complexity. Here we use hydroxyl ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki973
更新日期：2005-11-27 00:00:00
abstract：:Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from many phyla. Pnkp is composed of three catalytic modules: an N-terminal polynucleotide 5' kinase, a central 2',3' phosphatase and a C-terminal ligase. The phosphatase module is a Mn(2+)-dependent phosphodiesterase...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt221
更新日期：2013-06-01 00:00:00
abstract：:Herpes simplex type 1 virus (HSV-1) and bacteriophage λ capsids undergo considerable structural changes during self-assembly and DNA packaging. The initial steps of viral capsid self-assembly require weak, non-covalent interactions between the capsid subunits to ensure free energy minimization and error-free assembly....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku634
更新日期：2014-08-01 00:00:00
abstract：:Mutations of the KRAS proto-oncogene are associated with several tumor types, which is why it is being considered as a target for anti-cancer drug development. The human KRAS promoter contains a nuclease hypersensitive element (NHE), which can bind to nuclear proteins and is believed to form G-quadruplex structures. P...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1359
更新日期：2016-01-29 00:00:00
abstract：:U1 snRNP plays a crucial role in the 5' splice site recognition during splicing. Here we report the first example of naturally occurring U1-independent U2-type splicing in humans. The U1 components were not included in the pre-spliceosomal E complex formed on the human F1gamma (hF1gamma) intron 9 in vitro. Moreover, h...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp050
更新日期：2009-04-01 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：:The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1154
更新日期：2018-01-04 00:00:00
