Activation of interferon-regulated, dsRNA-dependent enzymes by human immunodeficiency virus-1 leader RNA.

abstract：:Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks to identify contiguous regi...

journal_title：Nucleic acids research

authors： Collado-Torres L,Nellore A,Frazee AC,Wilks C,Love MI,Langmead B,Irizarry RA,Leek JT,Jaffe AE

更新日期：2017-01-25 00:00:00

abstract：:The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. In this biennial update, we present our new chemical-phenotype module that codes chemi...

journal_title：Nucleic acids research

authors： Davis AP,Grondin CJ,Johnson RJ,Sciaky D,McMorran R,Wiegers J,Wiegers TC,Mattingly CJ

更新日期：2019-01-08 00:00:00

abstract：:Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of tr...

journal_title：Nucleic acids research

authors： Too PH,Ma MK,Mak AN,Wong YT,Tung CK,Zhu G,Au SW,Wong KB,Shaw PC

更新日期：2009-02-01 00:00:00

abstract：:Gene rewiring is a common evolutionary phenomenon in nature that may lead to extinction for living organisms. Recent studies on synthetic biology demonstrate that cells can survive genetic rewiring. This survival (adaptation) is often linked to the stochastic expression of rewired genes with random transcriptional cha...

journal_title：Nucleic acids research

authors： Murakami Y,Matsumoto Y,Tsuru S,Ying BW,Yomo T

更新日期：2015-01-01 00:00:00

abstract：:The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrie...

journal_title：Nucleic acids research

authors： Shamimuzzaman M,Le Tourneau JJ,Unni DR,Diesh CM,Triant DA,Walsh AT,Tayal A,Conant GC,Hagen DE,Elsik CG

更新日期：2020-01-08 00:00:00

abstract：:Toxin-antitoxin systems are widespread in bacteria and archaea. They perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. Toxin-antitoxin systems have been divided into three types, depending on the nature of...

journal_title：Nucleic acids research

authors： Blower TR,Short FL,Rao F,Mizuguchi K,Pei XY,Fineran PC,Luisi BF,Salmond GP

更新日期：2012-07-01 00:00:00

abstract：:The 5'-cap of spliceosomal small nuclear RNAs, some small nucleolar RNAs and of telomerase RNA was found to be hypermethylated in vivo. The Trimethylguanosine Synthase 1 (TGS1) mediates this conversion of the 7-methylguanosine-cap to the 2,2,7-trimethylguanosine (m(3)G)-cap during maturation of the RNPs. For mammalian...

journal_title：Nucleic acids research

authors： Monecke T,Dickmanns A,Ficner R

更新日期：2009-07-01 00:00:00

abstract：:Ribosome biogenesis is a dynamic multistep process, many features of which are still incompletely documented. Here, we show that changes in this pathway can be captured and annotated by means of a graphic set of pre-rRNA ratios, a technique we call Ratio Analysis of Multiple Precursors (RAMP). We find that knocking do...

journal_title：Nucleic acids research

authors： Wang M,Anikin L,Pestov DG

更新日期：2014-01-01 00:00:00

abstract：:A complete nucleotide sequence of human aldolase B mRNA was determined with a recombinant cDNA (pHABL120-3). The cDNA insert was composed of 1,652 bases excluding poly(A) tail and the sequence was consistent with the previous results reported by others. However, S1 nuclease mapping and subsequent genomic analysis allo...

journal_title：Nucleic acids research

authors： Sakakibara M,Mukai T,Yatsuki H,Hori K

更新日期：1985-07-25 00:00:00

abstract：:As proteomics initiatives mature, the need will arise for the multiple visualization of proteins and supramolecular complexes within their true context, in situ. Single-stranded DNA and RNA aptamers can be used for low resolution imaging of cellular receptors and cytoplasmic proteins by light microscopy (LM). These te...

journal_title：Nucleic acids research

authors： Dellaire G,Nisman R,Eskiw CH,Bazett-Jones DP

更新日期：2004-11-23 00:00:00

abstract：:A key complication in comparative genomics for reliable gene function prediction is the existence of duplicated genes. To study the effect of gene duplication on function prediction, we analyze orthologs between pairs of genomes where in one genome the orthologous gene has duplicated after the speciation of the two ge...

journal_title：Nucleic acids research

authors： Notebaart RA,Huynen MA,Teusink B,Siezen RJ,Snel B

更新日期：2005-10-27 00:00:00

abstract：:MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome som...

journal_title：Nucleic acids research

authors： Sales G,Coppe A,Bicciato S,Bortoluzzi S,Romualdi C

更新日期：2010-04-01 00:00:00

abstract：:During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software ...

journal_title：Nucleic acids research

authors： Haas SA,Hild M,Wright AP,Hain T,Talibi D,Vingron M

更新日期：2003-10-01 00:00:00

abstract：:We have assessed the ability of nucleosomes to influence the formation of mammalian topoisomerase II-DNA complexes by mapping the sites of cleavage induced by four unrelated topoisomerase II inhibitors in naked versus nucleosome-reconstituted SV40 DNA. DNA fragments were reconstituted with histone octamers from HeLa c...

journal_title：Nucleic acids research

authors： Capranico G,Jaxel C,Roberge M,Kohn KW,Pommier Y

更新日期：1990-08-11 00:00:00

abstract：:The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less conservation with the corresponding region in RAD54. The biochemical roles of this region of RAD54B are not known, alth...

journal_title：Nucleic acids research

authors： Sarai N,Kagawa W,Fujikawa N,Saito K,Hikiba J,Tanaka K,Miyagawa K,Kurumizaka H,Yokoyama S

更新日期：2008-10-01 00:00:00

abstract：:The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute G...

journal_title：Nucleic acids research

authors： Chu A,Robertson G,Brooks D,Mungall AJ,Birol I,Coope R,Ma Y,Jones S,Marra MA

更新日期：2016-01-08 00:00:00

abstract：:While biallelic mutations in the PALB2 tumor suppressor cause Fanconi anemia subtype FA-N, monoallelic mutations predispose to breast and familial pancreatic cancer. Although hundreds of missense variants in PALB2 have been identified in patients to date, only a few have clear functional and clinical relevance. Herein...

journal_title：Nucleic acids research

authors： Rodrigue A,Margaillan G,Torres Gomes T,Coulombe Y,Montalban G,da Costa E Silva Carvalho S,Milano L,Ducy M,De-Gregoriis G,Dellaire G,Araújo da Silva W Jr,Monteiro AN,Carvalho MA,Simard J,Masson JY

更新日期：2019-11-18 00:00:00

abstract：:The ribosomal proteins L4 and L22 form part of the peptide exit tunnel in the large ribosomal subunit. In Escherichia coli, alterations in either of these proteins can confer resistance to the macrolide antibiotic, erythromycin. The structures of the 30S as well as the 50S subunits from each antibiotic resistant mutan...

journal_title：Nucleic acids research

authors： O'Connor M,Gregory ST,Dahlberg AE

更新日期：2004-10-27 00:00:00

abstract：:Four phage clones which hybridize with U1 small nuclear RNA were obtained from a rat gene library. Two clones contain a presumed pseudogene. A third clone includes two gene candidates that are co-linear with the rat U1-RNA, 3.6kb apart and in the opposite orientation. The two genes are surrounded by identical sequence...

journal_title：Nucleic acids research

authors： Watanabe-Nagasu N,Itoh Y,Tani T,Okano K,Koga N,Okada N,Ohshima Y

更新日期：1983-03-25 00:00:00

abstract：:This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in...

journal_title：Nucleic acids research

authors： Krzyzosiak WJ,Sobczak K,Wojciechowska M,Fiszer A,Mykowska A,Kozlowski P

更新日期：2012-01-01 00:00:00

abstract：:Friedreich ataxia (FRDA) is caused by hyperexpansion of GAA*TTC repeats located in the first intron of the FXN gene, which inhibits transcription leading to the deficiency of frataxin. The FXN gene is an excellent target for therapeutic intervention since (i) 98% of patients carry the same type of mutation, (ii) the m...

journal_title：Nucleic acids research

authors： Soragni E,Herman D,Dent SY,Gottesfeld JM,Wells RD,Napierala M

更新日期：2008-11-01 00:00:00

abstract：:The beta-globin gene of a patient with mRNA-deficient beta o-thalassemia has been sequenced. We find a single nucleotide deletion in amino acid codon 44 that produces a UGA terminator at codon 60. We have previously shown that the beta-globin mRNA of this patient is correctly spliced and polyadenylated, but rapidly tu...

journal_title：Nucleic acids research

authors： Kinniburgh AJ,Maquat LE,Schedl T,Rachmilewitz E,Ross J

更新日期：1982-09-25 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

authors： Matz MV,Lukyanov SA

更新日期：1998-12-15 00:00:00

abstract：:Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disorder caused by expansion of CTG triplet repeats in 3'-untranslated region of DMPK gene. The pathomechanism of DM1 is driven by accumulation of toxic transcripts containing expanded CUG repeats (CUG(exp)) in nuclear foci which sequester several ...

journal_title：Nucleic acids research

authors： Wojtkowiak-Szlachcic A,Taylor K,Stepniak-Konieczna E,Sznajder LJ,Mykowska A,Sroka J,Thornton CA,Sobczak K

更新日期：2015-03-31 00:00:00

abstract：:Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters...

journal_title：Nucleic acids research

authors： van Heel AJ,de Jong A,Song C,Viel JH,Kok J,Kuipers OP

更新日期：2018-07-02 00:00:00

abstract：:A frequently used method of comparing large RNA molecules employs the two-dimensional display of oligonucleotides generated through the action of specific RNases (oligonucleotide mapping, fingerprinting). Using computer simulations and simple analytic expressions the number of large RNase T1-resistant oligonucleotides...

journal_title：Nucleic acids research

authors： Aaronson RP,Young JF,Palese P

更新日期：1982-01-11 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

authors： Dietz A,Kay V,Schlake T,Landsmann J,Bode J

更新日期：1994-07-25 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

authors： Lin Y,May GE,Kready H,Nazzaro L,Mao M,Spealman P,Creeger Y,McManus CJ

更新日期：2019-09-26 00:00:00

abstract：:HOX11 is a homeobox-containing oncogene of specific T-cell leukemias. We determined the DNA binding specificity of the Hox11 protein by using a novel technique of random oligonucleotide selection developed in this study. The optimal Hox11 binding sequence, GGCGGTAAGTGG, contained a core TAAGTG motif that is consistent...

journal_title：Nucleic acids research

authors： Tang S,Breitman ML

更新日期：1995-06-11 00:00:00

abstract：:Many enzymes acting on DNA require Mg(2+) ions not only for catalysis but also to bind DNA. Binding studies often employ Ca(2+) as a substitute for Mg(2+), to promote DNA binding whilst disallowing catalysis. The SfiI endonuclease requires divalent metal ions to bind DNA but, in contrast to many systems where Ca(2+) m...

journal_title：Nucleic acids research

authors： Bellamy SR,Kovacheva YS,Zulkipli IH,Halford SE

更新日期：2009-09-01 00:00:00