RNA editing in the acceptor stem of squid mitochondrial tRNA(Tyr).

abstract：:Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac s...

journal_title：Nucleic acids research

authors： Klein BJ,Ahmad S,Vann KR,Andrews FH,Mayo ZA,Bourriquen G,Bridgers JB,Zhang J,Strahl BD,Côté J,Kutateladze TG

更新日期：2018-01-09 00:00:00

abstract：:WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). WorfDB serves as a central ...

journal_title：Nucleic acids research

authors： Vaglio P,Lamesch P,Reboul J,Rual JF,Martinez M,Hill D,Vidal M

更新日期：2003-01-01 00:00:00

abstract：:Coralyne is a small crescent-shaped molecule known to intercalate duplex and triplex DNA. We report that coralyne can cause the complete and irreversible disproportionation of duplex poly(dT)*poly(dA). That is, coralyne causes the strands of duplex poly(dT)*poly(dA) to repartition into equal molar equivalents of tripl...

journal_title：Nucleic acids research

authors： Polak M,Hud NV

更新日期：2002-02-15 00:00:00

abstract：:The potency of the immune response has still to be harnessed effectively to combat human cancers. However, the discovery of T-cell targets in melanomas and other tumors has raised the possibility that cancer vaccines can be used to induce a therapeutically effective immune response against cancer. The targets, cancer-...

journal_title：Nucleic acids research

authors： Almeida LG,Sakabe NJ,deOliveira AR,Silva MC,Mundstein AS,Cohen T,Chen YT,Chua R,Gurung S,Gnjatic S,Jungbluth AA,Caballero OL,Bairoch A,Kiesler E,White SL,Simpson AJ,Old LJ,Camargo AA,Vasconcelos AT

更新日期：2009-01-01 00:00:00

abstract：:Myotonic dystrophy type 1 (DM1) is caused by the expansion of a (CTG).(CAG) repeat in the DMPK gene on chromosome 19q13.3. At least 17 neurological diseases have similar genetic mutations, the expansion of DNA repeats. In most of these disorders, the disease severity is related to the length of the repeat expansion, a...

journal_title：Nucleic acids research

authors： Hashem VI,Pytlos MJ,Klysik EA,Tsuji K,Khajavi M,Ashizawa T,Sinden RR

更新日期：2004-12-01 00:00:00

abstract：:Adaptation to the host cell environment to efficiently take-over the host cell's machinery is crucial in particular for small RNA viruses like picornaviruses that come with only small RNA genomes and replicate exclusively in the cytosol. Their Internal Ribosome Entry Site (IRES) elements are specific RNA structures th...

journal_title：Nucleic acids research

authors： Andreev DE,Hirnet J,Terenin IM,Dmitriev SE,Niepmann M,Shatsky IN

更新日期：2012-07-01 00:00:00

abstract：:Alu insertions have contributed to >11% of the human genome and ∼30-35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means...

journal_title：Nucleic acids research

authors： Wildschutte JH,Baron A,Diroff NM,Kidd JM

更新日期：2015-12-02 00:00:00

abstract：:Thermal elution poly(U)-Sepharose chromatography was utilized to fractionate yeast mRNA based on poly(A) size. Analysis of the in vitro translation products of the fractionated RNAs in a wheat-embryo cell-free protein synthesis system shows a heterogeneous but equal distribution of these abundant translatable mRNAs in...

journal_title：Nucleic acids research

authors： Saunders CA,Bostian KA,Halvorson HO

更新日期：1980-09-11 00:00:00

abstract：:RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept o...

journal_title：Nucleic acids research

authors： Novichkov PS,Rodionov DA,Stavrovskaya ED,Novichkova ES,Kazakov AE,Gelfand MS,Arkin AP,Mironov AA,Dubchak I

更新日期：2010-07-01 00:00:00

abstract：:Melanotransferrin (MTf) is a tumor associated antigen found in abundance on the surface of melanoma cells. It is a transferrin-like protein found in low amount in most adult tissues and whose gene is reminiscent of house-keeping genes. With the goal of understanding the regulatory mechanisms which might explain the en...

journal_title：Nucleic acids research

authors： Duchange N,Ochoa A,Plowman GD,Rozé A,Amdjadi M,Zakin MM

更新日期：1992-06-11 00:00:00

abstract：:DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through...

journal_title：Nucleic acids research

authors： Lee JY,Kim YJ,Lee C,Lee JG,Yagyu H,Tabata O,Kim DN

更新日期：2019-01-10 00:00:00

abstract：:The effect of UV-irradiation on the conversion of the single-stranded DNA of the parvovirus Minute-Virus-of-Mice (MVM) to duplex Replicative Forms (RF) was studied after infection of mouse A9 fibroblasts. UV-irradiation of the virus prior to infection of unirradiated cells resulted in a dose-dependent, single-hit, inh...

journal_title：Nucleic acids research

authors： Rommelaere J,Ward DC

更新日期：1982-04-24 00:00:00

abstract：:The exact sites at which a number of drugs inhibit the nick translation of DNA by E.coli DNA polymerase-I have been pinpointed. In order to do this, a method has been developed for sequencing double-stranded plasmid DNA from the site of a specifically induced nick. The initial experiments have concentrated on analysis...

journal_title：Nucleic acids research

authors： Wilkins RJ

更新日期：1982-11-25 00:00:00

abstract：:The p-n-butylphenyl- and p-n-butylanilino- substituted analogs of dGTP and dATP, respectively, were tested as inhibitors of purified human placental DNA polymerases alpha and delta. It was observed that DNA polymerase alpha activity was potently inhibited by these analogs with I0.5 values as low as the nanomolar range...

journal_title：Nucleic acids research

authors： Lee MY,Toomey NL,Wright GE

更新日期：1985-12-09 00:00:00

abstract：:Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists datab...

journal_title：Nucleic acids research

authors： Waghu FH,Gopi L,Barai RS,Ramteke P,Nizami B,Idicula-Thomas S

更新日期：2014-01-01 00:00:00

abstract：:The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here P...

journal_title：Nucleic acids research

authors： Hernández-de-Diego R,Tarazona S,Martínez-Mira C,Balzano-Nogueira L,Furió-Tarí P,Pappas GJ Jr,Conesa A

更新日期：2018-07-02 00:00:00

abstract：:Various oligonucleotides containing 8-methylguanine (m8G) have been synthesized and their structures and thermodynamic properties investigated. Introduction Of M8G into DNA sequences markedly stabilizes the Z conformation under low salt conditions. The hexamer d(CGC[M8G]CG)2 exhibits a CD spectrum characteristic of th...

journal_title：Nucleic acids research

authors： Sugiyama H,Kawai K,Matsunaga A,Fujimoto K,Saito I,Robinson H,Wang AH

更新日期：1996-04-01 00:00:00

abstract：:Resistance to androgen receptor (AR)-targeted therapies in prostate cancer (PC) is a major clinical problem. A key mechanism of treatment resistance in advanced PC is the generation of alternatively spliced forms of the AR termed AR variants (AR-Vs) that are refractory to targeted agents and drive tumour progression. ...

journal_title：Nucleic acids research

authors： Kounatidou E,Nakjang S,McCracken SRC,Dehm SM,Robson CN,Jones D,Gaughan L

更新日期：2019-06-20 00:00:00

abstract：:In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adap...

journal_title：Nucleic acids research

authors： Hardigan AA,Roberts BS,Moore DE,Ramaker RC,Jones AL,Myers RM

更新日期：2019-08-22 00:00:00

abstract：:Messenger RNAs homologous to a cDNA clone (pTOM 13) derived from a ripe-tomato-specific cDNA library are expressed during tomato fruit ripening and after the wounding of leaf and green fruit material. Both responses involve the synthesis of the hormone ethylene. Accumulation of the pTOM 13--homologous RNA during ripen...

journal_title：Nucleic acids research

authors： Holdsworth MJ,Bird CR,Ray J,Schuch W,Grierson D

更新日期：1987-01-26 00:00:00

abstract：:Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...

journal_title：Nucleic acids research

authors： Elati M,Nicolle R,Junier I,Fernández D,Fekih R,Font J,Képès F

更新日期：2013-02-01 00:00:00

abstract：:RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep Reg...

journal_title：Nucleic acids research

authors： Santos-Zavaleta A,Salgado H,Gama-Castro S,Sánchez-Pérez M,Gómez-Romero L,Ledezma-Tejeida D,García-Sotelo JS,Alquicira-Hernández K,Muñiz-Rascado LJ,Peña-Loredo P,Ishida-Gutiérrez C,Velázquez-Ramírez DA,Del Moral-Chávez V,Bonavid

更新日期：2019-01-08 00:00:00

abstract：:The binary Cre-lox conditional knockout system requires an essential part of the target gene to be flanked by loxP sites, enabling excision in vivo upon Cre expression. LoxP sites are introduced by homologous recombination, together with a selectable marker. However, this marker can disturb gene expression and should ...

journal_title：Nucleic acids research

authors： Leneuve P,Colnot S,Hamard G,Francis F,Niwa-Kawakita M,Giovannini M,Holzenberger M

更新日期：2003-03-01 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

authors： Horváth A,Vértessy BG

更新日期：2010-11-01 00:00:00

abstract：:The alternatively spliced RNA species of tumor suppressor gene p53, containing an additional 96 bases derived from intron 10, is present at approximately 25 to 30% the level of regularly spliced p53 RNA in both normal epidermal and carcinoma cells. The presence of this alternatively spliced RNA in 10T1/2 fibroblast ce...

journal_title：Nucleic acids research

authors： Han KA,Kulesz-Martin MF

更新日期：1992-04-25 00:00:00

abstract：:The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivati...

journal_title：Nucleic acids research

authors： Damante G,Fabbro D,Pellizzari L,Civitareale D,Guazzi S,Polycarpou-Schwartz M,Cauci S,Quadrifoglio F,Formisano S,Di Lauro R

更新日期：1994-08-11 00:00:00

abstract：:High-throughput sequencing technologies enable direct approaches to catalog and analyze snapshots of the total small RNA content of living cells. Characterization of high-throughput sequencing data requires bioinformatic tools offering a wide perspective of the small RNA transcriptome. Here we present SeqBuster, a hig...

journal_title：Nucleic acids research

authors： Pantano L,Estivill X,Martí E

更新日期：2010-03-01 00:00:00

abstract：:The synthetic DNA fragment (formula, see text) (corresponding to nucleotides 4299-4314 of the phi X DNA sequence) was cloned into either the AmpR gene or the KmR gene of plasmid pACYC 177. The DNA sequence of the KmR gene around the insertion site was determined by nucleotide sequence analysis of the pACYC 177 FnudII ...

journal_title：Nucleic acids research

authors： Heidekamp F,Baas PD,van Boom JH,Veeneman GH,Zipursky SL,Jansz HS

更新日期：1981-07-24 00:00:00

abstract：:Therapeutic oligonucleotides are often modified using the phosphorothioate (PS) backbone modification which enhances stability from nuclease mediated degradation. However, substituting oxygen in the phosphodiester backbone with sulfur introduce chirality into the backbone such that a full PS 16-mer oligonucleotide is ...

journal_title：Nucleic acids research

authors： Østergaard ME,De Hoyos CL,Wan WB,Shen W,Low A,Berdeja A,Vasquez G,Murray S,Migawa MT,Liang XH,Swayze EE,Crooke ST,Seth PP

更新日期：2020-02-28 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

authors： Fuchs A,Riegler S,Ayatollahi Z,Cavallari N,Giono LE,Nimeth BA,Mutanwad KV,Schweighofer A,Lucyshyn D,Barta A,Petrillo E,Kalyna M

更新日期：2021-01-25 00:00:00