Abstract:
:In many eukaryotic mRNAs one or more short 'upstream' open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and to amplify the signals likely explains their occurrence in most polyamine pathway mRNAs. The uORF-mediated polyamine responsive autoregulatory circuits found in polyamine pathway mRNAs exemplify the translationally regulated dynamic interface between components of the proteome and metabolism.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Ivanov IP,Atkins JF,Michael AJdoi
10.1093/nar/gkp1037subject
Has Abstractpub_date
2010-01-01 00:00:00pages
353-9issue
2eissn
0305-1048issn
1362-4962pii
gkp1037journal_volume
38pub_type
杂志文章,评审abstract::Liquid-liquid phase separation plays an important role in a variety of cellular processes, including the formation of membrane-less organelles, the cytoskeleton, signalling complexes, and many other biological supramolecular assemblies. Studies on the molecular basis of phase separation in cells have focused on protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz978
更新日期:2019-12-16 00:00:00
abstract::We have reported previously (1) two unexpected consequences of the microinjection into fertilized mouse eggs of a recombinant plasmid designated p12B1, carrying a 343 bp insert of non-repetitive mouse DNA. Injected at very low concentrations, this plasmid could be established as an extrachromosomal genetic element. Wh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.25.7243
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abstract::The targeted adduction of aflatoxin B1- exo -8,9-epoxide (AFB1- exo -8,9-epoxide) to a specific guanine within an oligodeoxyribonucleotide containing multiple guanines was achieved using a DNA triplex to control sequence selectivity. The oligodeoxyribonucleotide d(AGAGAAGATTTTCTTCTCTTTTTTTTCTCTT), designated '3G', spo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.4.1070
更新日期:1998-02-15 00:00:00
abstract::The Trypanosoma brucei exoribonuclease, TbDSS-1, has been implicated in multiple aspects of mitochondrial RNA metabolism. Here, we investigate the role of TbDSS-1 in RNA processing and surveillance by analyzing 12S rRNA processing intermediates in TbDSS-1 RNAi cells. RNA fragments corresponding to leader sequence upst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm690
更新日期:2008-01-01 00:00:00
abstract::Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloS...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1022
更新日期:2011-01-01 00:00:00
abstract::We have examined the expression and structure of several genes belonging to two classes of vegetative specific genes of the simple eukaryote, Dictyostelium discoideum. In amebae grown on bacteria, deactivation of all vegetative specific genes occurred at the onset of development and very little mRNA exists by 8 to 10 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.23.9679
更新日期:1989-12-11 00:00:00
abstract::GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm929
更新日期:2008-01-01 00:00:00
abstract::High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku370
更新日期:2014-07-01 00:00:00
abstract::TcruziDB (http://TcruziDB.org) is an integrated genome database for the parasitic organism Trypanosoma cruzi, the causative agent of Chagas' disease. The database currently incorporates all available sequence data (Genomic, BAC, EST) in a single user-friendly location. The database contains a variety of tools specific...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh049
更新日期:2004-01-01 00:00:00
abstract::Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-indep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw620
更新日期:2016-11-02 00:00:00
abstract::We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar struc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa629
更新日期:2020-09-04 00:00:00
abstract::Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1009
更新日期:2013-01-07 00:00:00
abstract::The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3'-5' exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv260
更新日期:2015-04-30 00:00:00
abstract::Despite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to dele...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku576
更新日期:2014-09-01 00:00:00
abstract::Numerous RNA-binding proteins have modular structures, comprising one or several copies of a selective RNA-binding domain generally coupled to an auxiliary domain that binds RNA non-specifically. We have built and compared homology-based models of the cold-shock domain (CSD) of the Xenopus protein, FRGY2, and of the t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.11.2223
更新日期:2001-06-01 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::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::Regulatory T-cells (Treg) play an essential role in the negative regulation of immune answers by developing an attenuated cytokine response that allows suppressing proliferation and effector function of T-cells (CD4(+) Th). The transcription factor FoxP3 is responsible for the regulation of many genes involved in the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr444
更新日期:2011-10-01 00:00:00
abstract::SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp281
更新日期:2009-07-01 00:00:00
abstract::High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2017-02-28 00:00:00
abstract::We studied fluorescence intensity, polarization and lifetime of some commonly used fluorophores conjugated to oligodeoxyribonucleotides with different primary and secondary structures. We found that fluorescence intensity can increase or decrease upon hybridization of the labeled strand to its complement depending on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.9.2089
更新日期:2002-05-01 00:00:00
abstract::EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade i...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2013-01-01 00:00:00
abstract::This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with ov...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa417
更新日期:2020-07-09 00:00:00
abstract::p73, the p53 homologue, exists as a transactivation-domain-proficient TAp73 or deficient deltaN(DN)p73 form. Expectedly, the oncogenic DNp73 that is capable of inactivating both TAp73 and p53 function, is over-expressed in cancers. However, the role of TAp73, which exhibits tumour-suppressive properties in gain or los...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn414
更新日期:2008-08-01 00:00:00
abstract::Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.7.1685
更新日期:1992-04-11 00:00:00
abstract::The NCBI has introduced two new web resources-LocusLink and RefSeq-that facilitate retrieval of gene-based information and provide reference sequence standards. These resources are designed to provide a non-redundant view of current knowledge about human genes, transcripts and proteins. Additional information about th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.126
更新日期:2000-01-01 00:00:00
abstract::In order to examine the nature of the complex formation between the ribosomal protein S1 and nucleic acids three methods were used: Inhibition of the reaction of n-ethyl[2.3 14C]-maleimide with S1 by the addition of oligonucleotides; adsorption of the complexes to nitrocellulose filters; and equilibrium dialysis. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.10.3627
更新日期:1977-10-01 00:00:00
abstract::Cis-elements (-933 to -641) upstream of the human M creatine kinase gene cap site contain an enhancer that confers developmental and tissue-specific expression to the chloramphenicol acetyltransferase gene in C2C12 myogenic cells transfected in culture. Division of the enhancer at -770 into a 5' fragment that includes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.9.2313
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abstract::Based on parameters governing promoter activity and using regulatory elements of the lac, ara and tet operon transcription control sequences were composed which permit the regulation in Escherichia coli of several gene activities independently and quantitatively. The novel promoter PLtetO-1 allows the regulation of ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.6.1203
更新日期:1997-03-15 00:00:00
abstract::The beta protein encoded by the Streptococcus pyogenes plasmid pSM19035 is a site-specific recombinase involved in both resolution of plasmid multimers into monomers and DNA inversion. It has been proposed that the DNA region to which the beta recombinase binds to mediate recombination includes a promoter from which o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.10.1855
更新日期:1994-05-25 00:00:00