Abstract:
:Eukaryotic genomes contain many endogenous retroviral sequences (ERVs). ERVs are often severely mutated, therefore difficult to detect. A platform independent (Java) program package, RetroTector (ReTe), was constructed. It has three basic modules: (i) detection of candidate long terminal repeats (LTRs), (ii) detection of chains of conserved retroviral motifs fulfilling distance constraints and (iii) attempted reconstruction of original retroviral protein sequences, combining alignment, codon statistics and properties of protein ends. Other features are prediction of additional open reading frames, automated database collection, graphical presentation and automatic classification. ReTe favors elements >1000-bp long due to its dependence on order of and distances between retroviral fragments. It detects single or low-copy-number elements. ReTe assigned a 'retroviral' score of 890-2827 to 10 exogenous retroviruses from seven genera, and accurately predicted their genes. In a simulated model, ReTe was robust against mutational decay. The human genome was analyzed in 1-2 days on a LINUX cluster. Retroviral sequences were detected in divergent vertebrate genomes. Most ReTe detected chains were coincident with Repeatmasker output and the HERVd database. ReTe did not report most of the evolutionary old HERV-L related and MalR sequences, and is not yet tailored for single LTR detection. Nevertheless, ReTe rationally detects and annotates many retroviral sequences.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sperber GO,Airola T,Jern P,Blomberg Jdoi
10.1093/nar/gkm515subject
Has Abstractpub_date
2007-01-01 00:00:00pages
4964-76issue
15eissn
0305-1048issn
1362-4962pii
gkm515journal_volume
35pub_type
杂志文章abstract::Numerous examples exist of how disrupting the actions of physiological regulators of blood cell development yields hematologic malignancies. The master regulator of hematopoietic stem/progenitor cells GATA-2 was cloned almost 20 years ago, and elegant genetic analyses demonstrated its essential function to promote hem...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gks281
更新日期:2012-07-01 00:00:00
abstract::Ribosomal protein (RP) genes must be coordinately expressed for proper assembly of the ribosome yet the mechanisms that control expression of RP genes in metazoans are poorly understood. Recently, TATA-binding protein-related factor 2 (TRF2) rather than the TATA-binding protein (TBP) was found to function in transcrip...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx676
更新日期:2017-10-13 00:00:00
abstract::Enzymes of intermediary metabolism are often reported to have moonlighting functions as RNA-binding proteins and have regulatory roles beyond their primary activities. Human serine hydroxymethyltransferase (SHMT) is essential for the one-carbon metabolism, which sustains growth and proliferation in normal and tumour c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz129
更新日期:2019-05-07 00:00:00
abstract::Base excision repair (BER), which is initiated by DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. The NTHL1 glycosylase, which excises DNA base damage caused by reactive oxygen species, is thought to be a tumor suppressor. However, in addition to NTHL1 loss-of-function...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky162
更新日期:2018-05-18 00:00:00
abstract::The Bovine Genome Database (BGD; http://BovineGenome.org) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1235
更新日期:2011-01-01 00:00:00
abstract::31P NMR chemical shifts of the selected mono- and oligonucleotide derivatives, including the compounds with P-N, P-C, P-S bonds and phosphite nucleotide analogues have been presented. The influence of substituents upon 31P chemical shifts has been discussed. The concrete examples of 31P chemical shifts data applicatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.14.5547
更新日期:1984-07-25 00:00:00
abstract::Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv311
更新日期:2015-05-19 00:00:00
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
doi:10.1093/nar/gku214
更新日期:2014-05-01 00:00:00
abstract::Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.3039
更新日期:1988-04-11 00:00:00
abstract::Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5' mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a mino...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz681
更新日期:2019-09-26 00:00:00
abstract::Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) predominantly induces non-homologous end joining (NHEJ), which generates random insertions or deletions, whereas homology-directed repair (HDR), which generates precise recombination products, is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky264
更新日期:2018-05-18 00:00:00
abstract::We have overproduced and purified wild type regA protein, a translational repressor encoded by bacteriophage T4. The repressor activity of the cloned regA protein has been tested on four known regA target genes (T4 genes: 44, 45, rpbA and regA) using in vitro coupled transcription-translation reactions. We have demons...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.23.10047
更新日期:1989-12-11 00:00:00
abstract::The HIV RT and Protease Sequence Database is an online relational database that catalogs evolutionary and drug-related human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease sequence variation (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.346
更新日期:2000-01-01 00:00:00
abstract::The rpoA gene, encoding the alpha subunit of RNA polymerase, was cloned from Streptomyces coelicolor A3(2). It is preceded by rpsK and followed by rplQ, encoding ribosomal proteins S11 and L17, respectively, similar to the gene order in Bacillus subtilis. The rpoA gene specifies a protein of 339 amino acids with deduc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.22.4565
更新日期:1996-11-15 00:00:00
abstract::DNA labeled for 15 minutes during UV induced repair synthesis is two-fold more sensitive to micrococcal nuclease than the bulk nuclear DNA. As the length of the labeling period increases from 15 minutes to 4 hours the nuclease sensitivity of repair labeled DNA approaches that of bulk chromatin. Pulse-chase experiments...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.1.203
更新日期:1981-01-10 00:00:00
abstract::Saccharomyces cerevisiae chl1 mutants have a significant increase in the rate of chromosome missegregation. CHL1 encodes a 99 kDa predicted protein with an ATP binding site consensus, a putative helix-turn-helix DNA binding motif, and homology to helicases. Using site-directed mutagenesis, I show that mutations that a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.16.3056
更新日期:2000-08-15 00:00:00
abstract::Unmodified tRNA molecules are useful for many purposes in cell-free protein biosynthesis, but there is little information about how the lack of tRNA post-transcriptional modifications affects the coding specificity for synonymous codons. In the present study, we prepared an unmodified form of Escherichia coli tRNA1Ser...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.15.2894
更新日期:1996-08-01 00:00:00
abstract::The DNA photosensitisers m-iodo Hoechst and m-iodo, p-methoxy Hoechst have been co-crystallised with the oligonucleotide d(CGCGAATTCGCG)(2)and their crystal structures determined. The crystals were then subjected to slow dehydration, which reduced their solvent contents from 40 (normal) to 30 (partially dehydrated) an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.5.1252
更新日期:2000-03-01 00:00:00
abstract::Bacterial genomics has revolutionized our understanding of the microbial tree of life; however, mapping and visualizing the distribution of functional traits across bacteria remains a challenge. Here, we introduce AnnoTree-an interactive, functionally annotated bacterial tree of life that integrates taxonomic, phyloge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz246
更新日期:2019-05-21 00:00:00
abstract::We have determined the genomic structure of the fosB gene and shown that it consists of 4 exons and 3 introns at positions also found in the c-fos gene. By deletion analysis we have characterized a region upstream of the TATA box which is the promoter region of the gene. Several consensus sequences have been identifie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.2.343
更新日期:1992-01-25 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 present the complete sequence of an mRNA which is induced by estrogen in the human breast cancer cell line MCF-7 [pS2 mRNA, Masiakowski et al., Nucleic Acids Res. 10, 7895-7903 (1982)]. Primer extension and cloning of double-stranded cDNA (ds-cDNA) into a vector designed to make full-length cDNA were used to determ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.6.2861
更新日期:1984-03-26 00:00:00
abstract::Strand Displacement Amplification (SDA) is an isothermal, in vitro method of amplifying a DNA target sequence prior to detection [Walker et al (1992) Nucleic Acids Res., 20, 1691-1693]. Here we describe a multiplex form of SDA that allows two target sequences and an internal amplification control to be co-amplified by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.13.2670
更新日期:1994-07-11 00:00:00
abstract::RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks289
更新日期:2012-08-01 00:00:00
abstract::Integration of foreign genes into plant genomes by the Agrobacterium T-DNA transfer system has been considered to occur at random. It has been speculated that the chromosomal structure of the integration site might affect the expression pattern of the introduced genes. To gain insight into the molecular structure of T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.14.2744
更新日期:1994-07-25 00:00:00
abstract::The Chinese hamster cell line, DC-3F, is heterozygous at the DHFR locus, and each allele can be distinguished on the basis of a unique DNA restriction pattern, protein isoelectric profile and in the abundancy of the DHFR mRNAs it expresses. Although each allele produces four transcripts, 1000, 1650 and 2150 nucleotide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.24.6597
更新日期:1992-12-25 00:00:00
abstract::Treatment of NIH 3T3 cells with trichostatin A (TSA), an inhibitor of histone deacetylase (HDAC), resulted in a dose-dependent increase in transcription from a rDNA reporter and from endogenous rRNA genes. Chromatin immunoprecipitation using anti-acetyl-histone H4 antibodies demonstrated a direct effect of TSA on the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.20.4114
更新日期:2001-10-15 00:00:00
abstract::A 34 base-pair (bp) fragment spanning sequences -154 to -120 of the promoter of the CHO1 gene (structural gene for phosphatidylserine synthase) from the yeast Saccharomyces cerevisiae has been shown to place transcription of a promoter-less Escherichia coli lacZ gene under control of the phospholipid precursors inosit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.6.1411
更新日期:1992-03-25 00:00:00
abstract::By means of titration viscometry a number of distinct modes could be resolved for the interaction between the antibiotic netropsin and DNA species of 50, 58, and 69 mole + (A+T) below r = 0.04 netropsin molecules bound per DNA phosphate group. The number of corresponding binding sites increases with a high power of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.5.1375
更新日期:1979-11-10 00:00:00
abstract::The alternation/deficiency in activation-3 (ADA3) is an essential component of the human p300/CBP-associated factor (PCAF) and yeast Spt-Ada-Gcn5-acetyltransferase (SAGA) histone acetyltransferase complexes. These complexes facilitate transactivation of target genes by association with transcription factors and modifi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq269
更新日期:2010-09-01 00:00:00