Abstract:
:Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; however, they have limitations in detecting insertions in complex repetitive genomic regions. Here, we developed a computational tool (PALMER) and used it to identify 203 non-reference L1Hs insertions in the NA12878 benchmark genome. Using PacBio long-read sequencing data, we identified L1Hs insertions that were absent in previous short-read studies (90/203). Approximately 81% (73/90) of the L1Hs insertions reside within endogenous LINE-1 sequences in the reference assembly and the analysis of unique breakpoint junction sequences revealed 63% (57/90) of these L1Hs insertions could be genotyped in 1000 Genomes Project sequences. Moreover, we observed that amplification biases encountered in single-cell WGS experiments led to a wide variation in L1Hs insertion detection rates between four individual NA12878 cells; under-amplification limited detection to 32% (65/203) of insertions, whereas over-amplification increased false positive calls. In sum, these data indicate that L1Hs insertions are often missed using standard short-read sequencing approaches and long-read sequencing approaches can significantly improve the detection of L1Hs insertions present in individual genomes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zhou W,Emery SB,Flasch DA,Wang Y,Kwan KY,Kidd JM,Moran JV,Mills REdoi
10.1093/nar/gkz1173subject
Has Abstractpub_date
2020-02-20 00:00:00pages
1146-1163issue
3eissn
0305-1048issn
1362-4962pii
5680708journal_volume
48pub_type
杂志文章abstract::RJ2.2.5, a mutant derived from the human B-lymphoma cell, Raji, is unable to express the MHC class II genes because of a recessive transcriptional defect attributed to the lack of an activator function. We report the isolation of a RJ2.2.5 revertant, namely AR, in which the expression of the mRNAs encoded by these gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.3.381
更新日期:1993-02-11 00:00:00
abstract::The novel deoxyribonucleotide alpha-[d(CpCpTpTpCpC)] and its complement beta-[d(GpGpApApGpG)] were synthesized by the phosphotriester method. 1H-NMR-NOE examination of the alpha-hexamer revealed that the cytosine and thymine bases appear to adopt anti conformations in this strand. In addition the deoxyribose of the th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.12.5019
更新日期:1986-06-25 00:00:00
abstract::We have determined the nucleotide sequence at the 3' end of the vesicular stomatitis virus (VSV) polymerase or L gene and compared it to that obtained from a defective interfering particle (DI) RNA generated by this virus. The latter (DI 0.50) contains a large internal deletion within this gene. The deletion begins ex...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.21.6919
更新日期:1982-11-11 00:00:00
abstract::Synthetic DNA fragments were constructed to determine the effect of G tracts, in conjunction with periodically spaced A tracts, on DNA bends. Relative length measurements showed that the G tracts spaced at the half helical turn enhanced the DNA bend. When the G tract was interrupted with a thymine or shortened to one ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.4.817
更新日期:1990-02-25 00:00:00
abstract::Restriction endonucleases are highly specific in recognizing the particular DNA sequence they act on. However, their activity is affected by sequence context, enzyme concentration and buffer composition. Changes in these factors may lead to either ineffective cleavage at the cognate restriction site or relaxed specifi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt257
更新日期:2013-06-01 00:00:00
abstract::Partial acid cleavage, comparative HPLC tryptic peptide mapping and amino acid sequencing of the C1 and C2 proteins of HeLa heterogeneous nuclear ribonucleoprotein (hnRNP) particles demonstrate that proteins C1 and C2 differ in primary structure by the presence of a 13 amino acid insert sequence in C2. This C2 insert ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.21.8441
更新日期:1989-11-11 00:00:00
abstract::By putting heterologous genomic regulatory systems into contact, chromosome addition lines derived from interspecific or intergeneric crosses allow the investigation of transcriptional regulation in new genomic environments. Here, we report the transcriptional and epigenetic adaptation of stably inherited alien maize ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky209
更新日期:2018-06-01 00:00:00
abstract::We have characterized elongation complexes (ECs) of RNA polymerase from the extremely thermophilic bacterium, Thermus thermophilus. We found that complexes assembled on nucleic acid scaffolds are transcriptionally competent at high temperature (50-80 degrees C) and, depending upon the organization of the scaffold, pos...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl559
更新日期:2006-01-01 00:00:00
abstract::We present evidence of formation of an intramolecular parallel triple helix with T*A.T and G*G.C base triplets (where * represents the hydrogen bonding interaction between the third strand and the duplex while. represents the Watson-Crick interactions which stabilize the duplex). The third GT strand, containing seven ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.18.3511
更新日期:2000-09-15 00:00:00
abstract::KUPS (The University of Kansas Proteomics Service) provides high-quality protein-protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NI...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq943
更新日期:2011-01-01 00:00:00
abstract::Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv469
更新日期:2015-06-23 00:00:00
abstract::The far upstream region of herpes simplex virus (HSV) immediate early (IE) gene 3 has previously been shown to increase gene expression in an enhancer-like manner, and to contain sequences which respond to stimulation of transcription by a virion polypeptide, Vmw65. To analyse the specific DNA sequences which mediate ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.2.929
更新日期:1986-01-24 00:00:00
abstract::A new series of DNA bis-intercalators is reported in which acridine moieties are connected by rigid and extended pyridine-based linkers of varied length. Cross-linking of DNA by bis-intercalation is inferred from the unwinding and folding of linear DNA induced by the compounds; after ligation and removal of the bis-in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.5.983
更新日期:1992-03-11 00:00:00
abstract::The heterodimeric subunit, SRP9/14, of the signal recognition particle (SRP) has previously been found to bind to scAlu and scB1 RNAs in vitro and to exist in large excess over SRP in anthropoid cells. Here we show that human and mouse SRP9/14 bind with high affinities to other Alu-like RNAs of different evolutionary ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.2.318
更新日期:1997-01-15 00:00:00
abstract::A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand cleavage at an occupied PNA strand displacement binding site, and under optimized conditions complete cleavage can be obtaine...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.9.2103
更新日期:1993-05-11 00:00:00
abstract::A number of novel phosphate triester derivatives of the anti-cancer nucleoside analogue araC have been prepared by a rapid 2-step procedure, not necessitating prior sugar protection. Spectroscopic and lipophilicity data have been collected on these compounds. An in vitro assay indicated inhibition of thymidine incorpo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.18.7195
更新日期:1989-09-25 00:00:00
abstract::The transcription factor Sox5 has previously been shown in chicken to be expressed in early neural crest cells and neural crest-derived peripheral glia. Here, we show in mouse that Sox5 expression also continues after neural crest specification in the melanocyte lineage. Despite its continued expression, Sox5 has litt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn527
更新日期:2008-10-01 00:00:00
abstract::The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.3075
更新日期:1994-08-11 00:00:00
abstract::Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku463
更新日期:2014-07-01 00:00:00
abstract::Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1236
更新日期:2016-01-04 00:00:00
abstract::Recent studies employing genome-wide approaches have provided an unprecedented view of the scope of L1 activities on structural variations in the human genome, and further reinforced the role of L1s as one of the major driving forces behind human genome evolution. The rapid identification of novel L1 elements by these...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1076
更新日期:2011-02-01 00:00:00
abstract::The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.23.4698
更新日期:2000-12-01 00:00:00
abstract::The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog map...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa936
更新日期:2021-01-08 00:00:00
abstract::The main goal of this review is to provide some guide-lines for choosing a proper method when searching for differentially expressed transcripts. The choice of an approach should depend upon particular features of the experiment and project requirements. We outline some general considerations to help decide between di...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/26.24.5537
更新日期:1998-12-15 00:00:00
abstract::The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1044
更新日期:2012-01-01 00:00:00
abstract::JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister's Millennium Project. The aim of this undertaking is to identify and collate up to 150 000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.158
更新日期:2002-01-01 00:00:00
abstract::A small cloned DNA segment previously shown to contain all genetic information for the expression of the tRNA1met gene of Xenopus laevis was cleaved into an anterior and posterior portion by Hae III restriction. Both restriction fragments were cloned in pCR1 using EcoRI linkers. Starting from these tDNA subclones, a s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.7.1749
更新日期:1979-12-11 00:00:00
abstract::Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m(7)G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku580
更新日期:2014-07-01 00:00:00
abstract::Neuroserpin is an axonally secreted serine protease inhibitor expressed in the nervous system that protects neurons from ischemia-induced apoptosis. Mutant neuroserpin forms have been found polymerized in inclusion bodies in a familial autosomal encephalopathy causing dementia, or associated with epilepsy. Regulation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.10.2202
更新日期:2002-05-15 00:00:00
abstract::Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg582
更新日期:2003-07-01 00:00:00