Abstract：
:Yeast two-hybrid (Y2H) screenings result in identification of many out-of-frame (OOF) clones that code for short (2-100 amino acids) peptides with no sequence homology to known proteins. We hypothesize that these peptides can reveal common short linear motifs (SLiMs) responsible for their selection. We present a new protocol to address this issue, using an existing SLIM detector (TEIRESIAS) as a base method, and applying filters derived from a mathematical model of SLiM selection in OOF clones. The model allows for initial analysis of likely presence of SLiM(s) in a collection of OOF sequences, assisting investigators with the decision of whether to invest resources in further analysis. If SLiM presence is detected, it estimates the length and number of amino acid residues involved in binding specificity and the amount of noise in the Y2H screen. We demonstrate that our model can double the prediction sensitivity of TEIRESIAS and improve its specificity from 0 to 1.0 on simulated data and apply the model to seven sets of experimentally derived OOF clones. Finally, we experimentally validate one SLiM found by our method, demonstrating its utility.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Liu Y,Woods NT,Kim D,Sweet M,Monteiro AN,Karchin Rdoi
10.1093/nar/gkr600subject
Has Abstractpub_date
2011-10-01 00:00:00pages
e128issue
19eissn
0305-1048issn
1362-4962pii
gkr600journal_volume
39pub_type
杂志文章abstract：:Understanding the molecular mechanisms that influence transposable element target site preferences is a fundamental challenge in functional and evolutionary genomics. Large-scale transposon insertion projects provide excellent material to study target site preferences in the absence of confounding effects of post-inse...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn563
更新日期：2008-11-01 00:00:00
abstract：:We report the consensus sequence of members of a new dispersed middle-repetitive DNA family, MT, which is present in mouse and rat genomes. This family is shown to be as abundant as the described rodent B1 and B2 families. Hybridization experiments with radioactive single-stranded cDNAs from different tissues indicate...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.16.6403
更新日期：1986-08-26 00:00:00
abstract：:Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1003
更新日期：2013-01-07 00:00:00
abstract：:We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.521
更新日期：1984-01-11 00:00:00
abstract：:Ribosome biogenesis (RiBi) is an extremely energy intensive process that is critical for gene expression. It is thus highly regulated, including through the tightly coordinated expression of over 200 RiBi genes by positive and negative transcriptional regulators. We investigated RiBi regulation as cells initiated meio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz231
更新日期：2019-06-04 00:00:00
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
doi：10.1093/nar/19.19.5363
更新日期：1991-10-11 00:00:00
abstract：:The isolation and characterization of deletion mutants of the bacteriocinogenic plasmid Clo DF13 is described. To construct these deletion mutants, DNA of Clo DF13::Tn901 and Clo DF13-rep3::Tn901 plasmids was digested with restriction endonucleases, ligated with T4 ligase and introduced by transformation into Escheric...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.6.1801
更新日期：1978-06-01 00:00:00
abstract：:The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA duplex with no specific binding site were determined under varying conditions of potassium chloride concentration using a surface plasmonresonance biosensor. Association and dissociation rate constants were measured enabling calculation of the di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.4.1063
更新日期：1999-02-15 00:00:00
abstract：:Invertebrate RNA viruses are targets of the host RNA interference (RNAi) pathway, which limits virus infection by degrading viral RNA substrates. Several insect RNA viruses encode suppressor proteins to counteract this antiviral response. We recently demonstrated that the dsDNA virus Invertebrate iridescent virus 6 (I...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku910
更新日期：2014-10-29 00:00:00
abstract：:We present a simple and highly accurate computational method for operon prediction, based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database (Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq254
更新日期：2010-07-01 00:00:00
abstract：:DEAD, DEAH and DExH proteins are involved in almost every facet of RNA biochemistry. Members of these protein families exhibit an RNA-dependent ATPase activity and some possess an ATP-dependent RNA helicase activity. Although genetic studies have identified specific functions for certain DEx(D)/(H)proteins from which ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.19.3811
更新日期：1999-10-01 00:00:00
abstract：:MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1239
更新日期：2011-04-01 00:00:00
abstract：:The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this inform...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1036
更新日期：2019-01-08 00:00:00
abstract：:A cross index is presented for using the improved selectivity offered by the Hung and Wensink (Nucl. Acids Res. 12, 1863-1874, 1984) method of partially filling in 5'-extensions produced by type II restriction endonucleases. After this treatment, DNA fragments which normally cannot be ligated to one another, can be jo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.8.3199
更新日期：1987-04-24 00:00:00
abstract：:Antisense oligodeoxynucleotides targeted to Ha-ras mRNA have been designed to discriminate between the codon 12-mutated oncogene and the normal proto-oncogene. An in vitro assay using two different sources of RNase H (rabbit reticulocyte lysates and nuclear extract from HeLa cells) was used to characterize oligonucleo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.17.3411
更新日期：1995-09-11 00:00:00
abstract：:LTR-IS elements are middle repetitive sequences in the mouse genome with structural features of solitary retroviral LTRs. In order to get some insight in the possible functional role of these sequences the promotor activity of two LTR-IS representatives differing by 105 bp in their U3 region was investigated. Gene fus...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.7.2631
更新日期：1985-04-11 00:00:00
abstract：:The nuclear suppressor allele NSM3 in strain FF1210-6C/170-E22 (E22), which suppresses a mutation of the yeast mitochondrial tRNA(Asp)gene in Saccharomyces cerevisiae, was cloned and identified. To isolate the NSM3 allele, a genomic DNA library using the vector YEp13 was constructed from strain E22. Nine YEp13 recombi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.7.1542
更新日期：2000-04-01 00:00:00
abstract：:FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger stand...
journal_title：Nucleic acids research
pub_type： 历史文章,杂志文章,评审
doi：10.1093/nar/gkp1137
更新日期：2010-04-01 00:00:00
abstract：:The three CD3 genes on human chromosome 11q23 encode proteins (gamma, delta and epsilon) which form part of the antigen receptor on T lymphocytes. All three genes are clustered within 50 kb and are activated approximately contemporaneously during the early stages of T cell ontogeny. In order to pinpoint potential regu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.3.459
更新日期：1990-02-11 00:00:00
abstract：:Two types of different repetitive DNA sequences called RepMP1 and RepMP2 were identified in the genome of Mycoplasma pneumoniae. The number of these repeated elements, their nucleotide sequence and their localization on a physical map of the M. pneumoniae genome were determined. The results show that RepMP1 appears at...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.17.8337
更新日期：1988-09-12 00:00:00
abstract：:Hippo pathway is involved in tumorigenesis, and its regulation in cytosol has been extensively studied, but its regulatory mechanisms in the nuclear are not clear. In the current study, using a FBS-inducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1317
更新日期：2019-03-18 00:00:00
abstract：:The lesion bypass pathway, which is regulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), is essential for resolving replication stalling due to DNA lesions. This process is important for preventing genomic instability and cancer development. Previously, it was shown that cells deficient in tum...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1337
更新日期：2011-05-01 00:00:00
abstract：:Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itse...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1167
更新日期：2019-02-20 00:00:00
abstract：:The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn846
更新日期：2008-12-01 00:00:00
abstract：:A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw786
更新日期：2017-01-25 00:00:00
abstract：:Leishmania species are protozoan parasites whose remarkably plastic genome limits the establishment of effective genetic manipulation and leishmaniasis treatment. The strategies used by Leishmania to maintain its genome while allowing variability are not fully understood. Here, we used DiCre-mediated conditional gene ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1017
更新日期：2018-12-14 00:00:00
abstract：:The nucleotide sequence of Neurospora crassa 5.8 S rDNA and adjacent regions has been determined. The deduced 5.8 S rRNA sequence of Neurospora differs from the 5.8 S rRNA sequence of Saccharomyces cerevisiae at 13 of 158 residues. Nine of these differences are clustered in a segment capable of forming a short hairpin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.7.2561
更新日期：1979-06-11 00:00:00
abstract：:A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part1.101
更新日期：1984-01-11 00:00:00
abstract：:The pattern of preferential DNA repair of UV-induced pyrimidine dimers was studied in repair-deficient Chinese hamster ovary (CHO) cells transfected with the human excision repair gene, ERCC-1. Repair efficiency was measured in the active dihydrofolate reductase (DHFR) gene and in its flanking, non-transcribed sequenc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.15.7397
更新日期：1988-08-11 00:00:00
abstract：:Genomic DNA methylation profiles exhibit substantial variation within the human population, with important functional implications for gene regulation. So far little is known about the characteristics and determinants of DNA methylation variation among healthy individuals. We performed bioinformatic analysis of high-r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn122
更新日期：2008-06-01 00:00:00
