Classification and energetics of the base-phosphate interactions in RNA.

abstract：:RBD-1 is the Caenorhabditis elegans homolog of Mrd1p, which was recently shown to be required for 18S ribosomal RNA (rRNA) processing in yeast. To gain insights into the relationship between ribosome biogenesis and the development of multicellular organisms, we examined the expression and function of RBD-1. Maternal R...

journal_title：Nucleic acids research

authors： Saijou E,Fujiwara T,Suzaki T,Inoue K,Sakamoto H

更新日期：2004-02-10 00:00:00

abstract：:We have compiled the DNA sequence data for E. coli K12 available from the GENBANK and EMBO databases and over a period of several years independently from the literature. We have introduced all available genetic map data and have arranged the sequences accordingly. As far as possible the overlaps are deleted and a tot...

journal_title：Nucleic acids research

authors： Kröger M

更新日期：1989-01-01 00:00:00

abstract：:A coiled-coil microtubule-bundling protein, p180, was originally identified as one of the ribosome receptor candidates on the rough endoplasmic reticulum (ER) and is highly expressed in secretory tissues. Recently, we reported that p180 plays crucial roles in upregulating collagen biosynthesis, mainly by facilitating ...

journal_title：Nucleic acids research

authors： Ueno T,Kaneko K,Sata T,Hattori S,Ogawa-Goto K

更新日期：2012-04-01 00:00:00

abstract：:8-Oxo-7,8-dihydroguanine (8-oxoGua) is produced in cells by reactive oxygen species normally formed during cellular metabolic processes. This oxidized base can pair with both adenine and cytosine, and thus the existence of this base in messenger RNA would cause translational errors. The MutT protein of Escherichia col...

journal_title：Nucleic acids research

authors： Ishibashi T,Hayakawa H,Ito R,Miyazawa M,Yamagata Y,Sekiguchi M

更新日期：2005-07-07 00:00:00

abstract：:The FALC-Loop web server provides an online interface for protein loop modeling by employing an ab initio loop modeling method called FALC (fragment assembly and analytical loop closure). The server may be used to construct loop regions in homology modeling, to refine unreliable loop regions in experimental structures...

journal_title：Nucleic acids research

authors： Ko J,Lee D,Park H,Coutsias EA,Lee J,Seok C

更新日期：2011-07-01 00:00:00

abstract：:The x-ray crystal structures of two new anti-HIV compounds, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-beta-D-threo- pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined at two temperatures. Both crystals are in the space group P2(1)2(1)2(1), and ...

journal_title：Nucleic acids research

authors： Liaw YC,Gao YG,Marquez VE,Wang AH

更新日期：1992-02-11 00:00:00

abstract：:To understand how potential for G-quadruplex formation might influence regulation of gene expression, we examined the 2 kb spanning the transcription start sites (TSS) of the 18 217 human RefSeq genes, distinguishing contributions of template and nontemplate strands. Regions both upstream and downstream of the TSS are...

journal_title：Nucleic acids research

authors： Eddy J,Maizels N

更新日期：2008-03-01 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

authors： Giglio M,Tauber R,Nadendla S,Munro J,Olley D,Ball S,Mitraka E,Schriml LM,Gaudet P,Hobbs ET,Erill I,Siegele DA,Hu JC,Mungall C,Chibucos MC

更新日期：2019-01-08 00:00:00

abstract：:Chelation of divalent cations by 5 mM EDTA and subsequent removal by dialysis from a cytoplasmic HeLa cell extract leads to a complete loss of 5S rRNA transcription without affecting tRNA synthesis. Transcription complexes for 5S RNA can no longer be assembled in such a zinc-depleted extract and this ability can be fu...

journal_title：Nucleic acids research

authors： Wingender E,Dilloo D,Seifart KH

更新日期：1984-12-11 00:00:00

abstract：:Poly(ADP-ribosyl)ation regulates numerous cellular processes like genome maintenance and cell death, thus providing protective functions but also contributing to several pathological conditions. Poly(ADP-ribose) (PAR) molecules exhibit a remarkable heterogeneity in chain lengths and branching frequencies, but the biol...

journal_title：Nucleic acids research

authors： Aberle L,Krüger A,Reber JM,Lippmann M,Hufnagel M,Schmalz M,Trussina IREA,Schlesiger S,Zubel T,Schütz K,Marx A,Hartwig A,Ferrando-May E,Bürkle A,Mangerich A

更新日期：2020-10-09 00:00:00

abstract：:A general approach for the synthesis of oligonucleotide-triplet phosphoramidites and the synthesis of four such blocks are described. A strategy was devised to minimize the number of dimer precursors needed for synthesis of a complete set of triplet-amidite blocks encoding all 20 amino acids. Whereas synthesis of 20 t...

journal_title：Nucleic acids research

authors： Ono A,Matsuda A,Zhao J,Santi DV

更新日期：1995-11-25 00:00:00

abstract：:The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and efficient transgenesis methods makes of this subphylum an ideal system for the investigation of vertebrate physiological and de...

journal_title：Nucleic acids research

authors： Sierro N,Kusakabe T,Park KJ,Yamashita R,Kinoshita K,Nakai K

更新日期：2006-01-01 00:00:00

abstract：:The RDM1 gene encodes a RNA recognition motif (RRM)-containing protein involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. We previously reported a cDNA encoding the full-length human RDM1 protein. Here, we describe the identification of 11 human cDNAs encoding RDM1 protein isoforms. Th...

journal_title：Nucleic acids research

authors： Messaoudi L,Yang YG,Kinomura A,Stavreva DA,Yan G,Bortolin-Cavaillé ML,Arakawa H,Buerstedde JM,Hainaut P,Cavaillé J,Takata M,Van Dyck E

更新日期：2007-01-01 00:00:00

abstract：:Protein domains are subunits of proteins that recur throughout the protein world. There are many definitions attempting to capture the essence of a protein domain, and several systems that identify protein domains and classify them into families. EVEREST, recently described in Portugaly et al. (2006) BMC Bioinformatic...

journal_title：Nucleic acids research

authors： Portugaly E,Linial N,Linial M

更新日期：2007-01-01 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

authors： Birzele F,Fauti T,Stahl H,Lenter MC,Simon E,Knebel D,Weith A,Hildebrandt T,Mennerich D

更新日期：2011-10-01 00:00:00

abstract：:Previous evidence indicates that telomeres resemble common fragile sites and present a challenge for DNA replication. The precise impediments to replication fork progression at telomeric TTAGGG repeats are unknown, but are proposed to include G-quadruplexes (G4) on the G-rich strand. Here we examined DNA synthesis and...

journal_title：Nucleic acids research

authors： Lormand JD,Buncher N,Murphy CT,Kaur P,Lee MY,Burgers P,Wang H,Kunkel TA,Opresko PL

更新日期：2013-12-01 00:00:00

abstract：:We have previously reported that transcription from a distal promoter (promoter B) of the estrogen receptor alpha (ERalpha) gene is responsible for the increased expression of ERalpha in human breast carcinomas. This paper first characterized the promoter B region in terms of transient transfection experiments with lu...

journal_title：Nucleic acids research

authors： Tanimoto K,Eguchi H,Yoshida T,Hajiro-Nakanishi K,Hayashi S

更新日期：1999-02-01 00:00:00

abstract：:Sets of genes expressed in the same tissue are believed to be under the regulation of a similar set of transcription factors, and can thus be assumed to contain similar structural patterns in their regulatory regions. Here we present a study of the structural patterns in promoters of genes expressed specifically in 26...

journal_title：Nucleic acids research

authors： Vandenbon A,Nakai K

更新日期：2010-01-01 00:00:00

abstract：:Hepatocyte Nuclear Factor 4 (HNF-4), a liver-enriched orphan receptor of the nuclear receptor superfamily, is required for the expression of a wide variety of liver-specific genes including apoAI. To explore the possibility that site A of the apoAI gene enhancer might also be the target for HNF-4 without the interfere...

journal_title：Nucleic acids research

authors： Fuernkranz HA,Wang Y,Karathanasis SK,Mak P

更新日期：1994-12-25 00:00:00

abstract：:The conditions under which Drosophila melanogaster are grown markedly influence the amount of the hypermodified nucleoside Q found in certain tRNAs. This effect on Q biosynthesis was found in both the wild-type and the suppressor of sable [su(s)2] mutant. Suppressed vermilion flies [su(s)2v; bw] with 78% of the tyrosi...

journal_title：Nucleic acids research

authors： Wosnick MA,White BN

更新日期：1977-11-01 00:00:00

abstract：:Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ...

journal_title：Nucleic acids research

authors： Qin Z,Stoilov P,Zhang X,Xing Y

更新日期：2018-05-04 00:00:00

abstract：:Enhancer-dependent transcription involving the promoter specificity factor σ(54) is widely distributed amongst bacteria and commonly associated with cell envelope function. For transcription initiation, σ(54)-RNA polymerase yields open promoter complexes through its remodelling by cognate AAA+ ATPase activators. Since...

journal_title：Nucleic acids research

authors： Schaefer J,Engl C,Zhang N,Lawton E,Buck M

更新日期：2015-09-03 00:00:00

abstract：:We have studied the regulation of DNA ligase I gene expression in UV-C irradiated human primary fibroblasts. An increase of approximately 6-fold both in DNA ligase I messenger and activity levels was observed 24 h after UV treatment, when nucleotide excision repair (NER) is no longer operating. DNA ligase I induction ...

journal_title：Nucleic acids research

authors： Montecucco A,Savini E,Biamonti G,Stefanini M,Focher F,Ciarrocchi G

更新日期：1995-03-25 00:00:00

abstract：:Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...

journal_title：Nucleic acids research

authors： Mourgues S,Lomax ME,O'Neill P

更新日期：2007-01-01 00:00:00

abstract：:The gene, rpb1, encoding the largest subunit of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB1, of Saccharomyces cerevisiae as a cross-hybridization probe. We have determined the complete sequence of this gene, and parts of PCR-amplified rpb1 cDNA. The predicted cod...

journal_title：Nucleic acids research

authors： Azuma Y,Yamagishi M,Ueshima R,Ishihama A

更新日期：1991-02-11 00:00:00

abstract：:The nucleobase modification 5-methylcytosine (m(5)C) is widespread both in DNA and different cellular RNAs. The functions and enzymatic mechanisms of DNA m(5)C-methylation were extensively studied during the last decades. However, the location, the mechanism of formation and the cellular function(s) of the same modifi...

journal_title：Nucleic acids research

authors： Motorin Y,Lyko F,Helm M

更新日期：2010-03-01 00:00:00

abstract：:The investigation of RNA structure, dynamics and biological function often requires the site-specific incorporation of non-natural moieties. Here we describe the functionalization of RNA transcripts by aldehyde-hydrazine chemistry using a simple initiator nucleotide that carries an acetal-protected aldehyde function. ...

journal_title：Nucleic acids research

authors： Pfander S,Fiammengo R,Kirin SI,Metzler-Nolte N,Jäschke A

更新日期：2007-01-01 00:00:00

abstract：:Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interacti...

journal_title：Nucleic acids research

authors： Kersey PJ,Allen JE,Allot A,Barba M,Boddu S,Bolt BJ,Carvalho-Silva D,Christensen M,Davis P,Grabmueller C,Kumar N,Liu Z,Maurel T,Moore B,McDowall MD,Maheswari U,Naamati G,Newman V,Ong CK,Paulini M,Pedro H,Perry E

更新日期：2018-01-04 00:00:00

abstract：:With the rapid accumulation of our knowledge on diseases, disease-related genes and drug targets, network-based analysis plays an increasingly important role in systems biology, systems pharmacology and translational science. The new release of VisANT aims to provide new functions to facilitate the convenient network ...

journal_title：Nucleic acids research

authors： Hu Z,Chang YC,Wang Y,Huang CL,Liu Y,Tian F,Granger B,Delisi C

更新日期：2013-07-01 00:00:00

abstract：:The sigma(54) factor associates with core RNA polymerase (RNAP) to form a holoenzyme that is unable to initiate transcription unless acted on by an activator protein. sigma(54) is closely involved in many steps of activator-dependent transcription, such as core RNAP binding, promoter recognition, activator interaction...

journal_title：Nucleic acids research

authors： Xiao Y,Wigneshweraraj SR,Weinzierl R,Wang YP,Buck M

更新日期：2009-07-01 00:00:00