Abstract：
:Previous work in predicting protein localization to the chloroplast organelle in plants led to the development of an artificial neural network-based approach capable of remarkable accuracy in its prediction (ChloroP). A common criticism against such neural network models is that it is difficult to interpret the criteria that are used in making predictions. We address this concern with several new prediction methods that base predictions explicitly on the abundance of different amino acid types in the N-terminal region of the protein. Our successful prediction accuracy suggests that ChloroP uses little positional information in its decision-making; an unexpected result given the elaborate ChloroP input scheme. By removing positional information, our simpler methods allow us to identify those amino acids that are useful for successful prediction. The identification of important sequence features, such as amino acid content, is advantageous if one of the goals of localization predictors is to gain an understanding of the biological process of chloroplast localization. Our most accurate predictor combines principal component analysis and logistic regression. Web-based prediction using this method is available online at http://apicoplast.cis.upenn.edu/pclr/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schein AI,Kissinger JC,Ungar LHdoi
10.1093/nar/29.16.e82keywords:
subject
Has Abstractpub_date
2001-08-15 00:00:00pages
E82issue
16eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章abstract：:Human Ape2 protein has 3' phosphodiesterase activity for processing 3'-damaged DNA termini, 3'-5' exonuclease activity that supports removal of mismatched nucleotides from the 3'-end of DNA, and a somewhat weak AP-endonuclease activity. However, very little is known about the role of Ape2 in DNA repair processes. Here...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp357
更新日期：2009-07-01 00:00:00
abstract：:In vivo and in vitro RNA splicing experiments have demonstrated that the intron splicing machineries are not interchangeable in all organisms. These differences have prevented the efficient in vivo expression of monocot genes containing introns in dicot plants and the in vitro excision of some plant introns in HeLa ce...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.14.7159
更新日期：1988-07-25 00:00:00
abstract：:DNA binding of heat shock factor 2 (HSF2) is induced during hemin-induced differentiation of human erythroleukemia cell line K562. To identify the transcriptional activation and the regulatory domains of HSF2, we constructed a series of deletion derivatives fused to the yeast GAL4 DNA binding domain and analyzed their...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.11.2580
更新日期：1998-06-01 00:00:00
abstract：:Gene expression profiling has gradually become a routine procedure for disease diagnosis and classification. In the past decade, many computational methods have been proposed, resulting in great improvements on various levels, including feature selection and algorithms for classification and clustering. In this study,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt343
更新日期：2013-08-01 00:00:00
abstract：:Approximately 2% of the Dictyostelium discoideum genome consists of multiple copies of a retrotransposable element termed DRE (Dictyostelium Repetitive Element). These elements have always been found integrated in a position and orientation-specific manner 50 +/- 4 nucleotides upstream of the coding region of tRNA gen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.23.6247
更新日期：1992-12-11 00:00:00
abstract：:A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.1.221
更新日期：1978-01-01 00:00:00
abstract：:In plants, nuclear multisubunit RNA polymerases IV and V are RNA Polymerase II-related enzymes that synthesize non-coding RNAs for RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Here, we tested the importance of the C-terminal domain (CTD) of Pol IV's largest subunit given that the Pol II CTD ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz615
更新日期：2019-09-26 00:00:00
abstract：:A class of heterogeneous nuclear RNA (hnRNA) molecules contain an internal transcribed poly A sequence of close to 25 uninterrupted AMP residues. HnRNA molecules containing this sequence are separable from those containing the large 3' terminal poly A sequence on the basis of their differential affinity for oligo dT c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.3.1097
更新日期：1979-03-01 00:00:00
abstract：:Bacillus subtilis plasmid pGR71 is a promoter-probe shuttle vector derived from pUB110. The expression of the cat gene on pGR71 in B. subtilis requires the insertion of a Bacillus promoter and a ribosomal binding site (RBS) into the HindIII cloning site immediately upstream from the cat gene. A recombinant plasmid of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.4.739
更新日期：1990-02-25 00:00:00
abstract：:Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interact...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1260
更新日期：2021-01-25 00:00:00
abstract：:A novel approach for the amplification of cDNA ends is described. It requires only minimal amounts of material, a simple cDNA synthesis reaction and a single PCR reaction to amplify the desired 5'- or 3'-ends of a certain cDNA of interest. It combines the so called CapFinder approach with solid phase cDNA synthesis, t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.22.e96
更新日期：2000-11-15 00:00:00
abstract：:TATA-binding protein (TBP) is central to the regulation of eukaryotic transcription initiation. Recruitment of TBP to target genes can be positively regulated by one of two basal transcription factor complexes: SAGA or TFIID. Negative regulation of TBP promoter association can be performed by Mot1p or the NC2 complex....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr784
更新日期：2012-02-01 00:00:00
abstract：:DNA double-strand breaks are repaired by end-joining or homologous recombination. A key-committing step of recombination is DNA end resection. In resection, phosphorylated CtIP first promotes the endonuclease of MRE11-RAD50-NBS1 (MRN). Subsequently, CtIP also stimulates the WRN/BLM-DNA2 pathway, coordinating thus both...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa273
更新日期：2020-06-04 00:00:00
abstract：:Synthetic deoxyoligonucleotides have been 5'-aminoalkylated at the end of step-wise synthesis on the polymer support. This was achieved through the activation of the 5'-hydroxyl group as its 5'-imidazolyl derivative using carbonyldiimidazole, which was subsequently displaced with hexamethylene diamine to yield the tit...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.20.7985
更新日期：1986-10-24 00:00:00
abstract：:Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx752
更新日期：2017-10-13 00:00:00
abstract：:Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx037
更新日期：2017-05-05 00:00:00
abstract：:MicroRNA (miRNA) 5'-isoforms, or 5'-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5' ends shifted from the 5' ends of the miRNAs by a few nucleotides. Although 5'-isomiRs have been reported, their origins, properties and potential functions remain to be examine...
journal_title：Nucleic acids research
pub_type： 杂志文章,meta分析
doi：10.1093/nar/gkt967
更新日期：2014-02-01 00:00:00
abstract：:Toxicogenomics focuses on assessing the safety of compounds using gene expression profiles. Gene expression signatures from large toxicogenomics databases are expected to perform better than small databases in identifying biomarkers for the prediction and evaluation of drug safety based on a compound's toxicological m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku955
更新日期：2015-01-01 00:00:00
abstract：:Constitutive expression of major histocompatibility complex class II (MHC II) antigens normally occurs in B-lymphocytes and antigen presenting cells of the monocyte/macrophage lineage. However, many malignant tumours and transformed cells express these proteins aberrantly. We demonstrate here that the MHC II DR alpha ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.18.4881
更新日期：1992-09-25 00:00:00
abstract：:Uracil may occur in DNA due to either cytosine deamination or thymine replacing incorporation. Its quantitative characterization is important in assessing DNA damages in cells with perturbed thymidylate metabolism or within different DNA segments involved in immunoglobulin gene diversification. The archaeal DNA polyme...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq815
更新日期：2010-11-01 00:00:00
abstract：:Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1146
更新日期：2018-01-25 00:00:00
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
doi：10.1093/nar/gku747
更新日期：2014-01-01 00:00:00
abstract：:A 14 kb maize DNA fragment carrying nuclear rRNA genes and spacer regions was isolated and characterised by restriction enzyme mapping. A complete 3020 bp long external spacer region was sequenced and revealed 9 tandemly arranged 200 bp long repeat units with high homology. The repeat units lie upstream from two promi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.12.4969
更新日期：1986-06-25 00:00:00
abstract：:The hammerhead self-cleaving motif occurs in a variety of RNAs that infect plants and consists of three non-conserved helices connected by a highly conserved central core. A variant hammerhead, called the extended hammerhead, is found in satellite 2 transcripts from a variety of caudate amphibians. The extended hammer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.11.2189
更新日期：1997-06-01 00:00:00
abstract：:Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA's 5'-terminal 'cap'. The minimal 'cap0' consists of N7-methylguanosine linked to the first nucleotide via a 5'-5' triphosphate (ppp) bridge. Cap0 is further modified by 2'-O-methylation of the next two riboses, yielding 'cap1' (m7GpppNmN) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1321
更新日期：2014-03-01 00:00:00
abstract：:Although the thermophilic bacterium Thermus aquaticus grows optimally at 70 degrees C and cannot grow at moderate temperatures, its DNA polymerase I has significant activity at 20-37 degrees C. This activity is a bane to some PCRs, since it catalyzes non-specific priming. We report mutations of Klentaq (an N-terminal ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg813
更新日期：2003-11-01 00:00:00
abstract：:Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa896
更新日期：2020-11-18 00:00:00
abstract：:We report here the different ways in which four subunits of the basal transcription/repair factor TFIIH (XPB, XPD, p62 and p44) and the damage recognition XPC repair protein can enter the nucleus. We examined their nuclear localization by transiently expressing the gene products tagged with the enhanced green fluoresc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.7.1574
更新日期：2001-04-01 00:00:00
abstract：:Zinc finger protein with KRAB and SCAN domains 3 (ZKSCAN3) has long been known as a master transcriptional repressor of autophagy. Here, we identify a novel role for ZKSCAN3 in alleviating senescence that is independent of its autophagy-related activity. Downregulation of ZKSCAN3 is observed in aged human mesenchymal ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa425
更新日期：2020-06-19 00:00:00
abstract：:The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hy...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.18.7007
更新日期：1984-09-25 00:00:00
