ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes.

abstract：:RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functio...

journal_title：Nucleic acids research

authors： Charbonnel C,Niazi AK,Elvira-Matelot E,Nowak E,Zytnicki M,de Bures A,Jobet E,Opsomer A,Shamandi N,Nowotny M,Carapito C,Reichheld JP,Vaucheret H,Sáez-Vásquez J

更新日期：2017-11-16 00:00:00

abstract：:In small oocytes of Xenopus species, two sets of 5S RNA genes, oocyte-type and somatic-type, are fully activated. The 5S RNA transcripts are temporarily stored, half in association with TFIIIA to form a 7S particle, the other half in association with tRNA and two proteins (p48 and p43) to form a 42S particle. It has b...

journal_title：Nucleic acids research

authors： Barrett P,Sommerville J

更新日期：1987-11-11 00:00:00

abstract：:We have microinjected genomic DNA clones containing the Moloney murine leukemia virus (M-MuLV) proviral genome and flanking mouse sequences from Mov-3, Mov-7 and Mov-10 mice into Xenopus laevis oocytes and analyzed the virus-specific transcription and translation products. These mouse strains carry a proviral genome c...

journal_title：Nucleic acids research

authors： Breindl M,Kalthoff H,Jaenisch R

更新日期：1983-06-25 00:00:00

abstract：:The active and inactive state of transcription factors in growing cells is usually directed by allosteric physicochemical signals or metabolites, which are in turn either produced in the cell or obtained from the environment by the activity of the products of effector genes. To understand the regulatory dynamics and t...

journal_title：Nucleic acids research

authors： Janga SC,Salgado H,Martínez-Antonio A,Collado-Vides J

更新日期：2007-01-01 00:00:00

abstract：:Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploite...

journal_title：Nucleic acids research

authors： Huang Z,Wen Y,Shandilya R,Marks JR,Berchuck A,Murphy SK

更新日期：2006-01-23 00:00:00

abstract：:MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post...

journal_title：Nucleic acids research

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

更新日期：2012-07-01 00:00:00

abstract：:Chinese hamster genomic DNA sequences from the region downstream of the dihydrofolate reductase (DHFR) gene reported to contain a chromosomal origin of bidirectional DNA replication (OBR-1) were tested for their ability to support autonomous DNA replication in human cells. A 13.3 kilobase fragment containing OBR-1 and...

journal_title：Nucleic acids research

authors： Caddle MS,Calos MP

更新日期：1992-11-25 00:00:00

abstract：:Extracellular vesicles (EVs) are membranous vesicles that are released by both prokaryotic and eukaryotic cells into the extracellular microenvironment. EVs can be categorised as exosomes, ectosomes or shedding microvesicles and apoptotic bodies based on the mode of biogenesis. EVs contain biologically active cargo of...

journal_title：Nucleic acids research

authors： Pathan M,Fonseka P,Chitti SV,Kang T,Sanwlani R,Van Deun J,Hendrix A,Mathivanan S

更新日期：2019-01-08 00:00:00

abstract：:Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of informati...

journal_title：Nucleic acids research

authors： Gelfand Y,Rodriguez A,Benson G

更新日期：2007-01-01 00:00:00

abstract：:Automated fluorescence-based DNA sequence analysis offers the possibility to undertake very large scale sequencing projects. Directed strategies, such as the specific-primer-directed sequencing approach ('gene walking'), should prove useful in such projects. Described herein is a study involving the use of this approa...

journal_title：Nucleic acids research

authors： Kaiser RJ,MacKellar SL,Vinayak RS,Sanders JZ,Saavedra RA,Hood LE

更新日期：1989-08-11 00:00:00

abstract：:Onconase, a cytotoxic ribonuclease from Rana pipiens, possesses pyroglutamate (Pyr) at the N-terminus and has a substrate preference for uridine-guanine (UG). To identify residues responsible for onconase's cytotoxicity, we cloned the rpr gene from genomic DNA and expressed it in Escherichia coli BL21(DE3). The recomb...

journal_title：Nucleic acids research

authors： Liao YD,Wang SC,Leu YJ,Wang CF,Chang ST,Hong YT,Pan YR,Chen C

更新日期：2003-09-15 00:00:00

abstract：:The irradiation of native or unmodified yeast tRNA(Phe) by short wavelength UV light (260 nM) results in an intramolecular crosslink that has been mapped to occur between C48 in the variable loop and U59 in the T loop. Photo-reversibility of the crosslink and the absence of fluorescent photo adducts suggest that the c...

journal_title：Nucleic acids research

authors： Behlen LS,Sampson JR,Uhlenbeck OC

更新日期：1992-08-11 00:00:00

abstract：:High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interactio...

journal_title：Nucleic acids research

authors： Zhang H,Li F,Jia Y,Xu B,Zhang Y,Li X,Zhang Z

更新日期：2017-12-15 00:00:00

abstract：:Telomerase activity, not detectable in somatic cells but frequently activated during carcinogenesis, confers immortality to tumors. Mechanisms governing expression of the catalytic subunit hTERT, the limiting factor for telomerase activity, still remain unclear. We previously proposed a model in which the binding of t...

journal_title：Nucleic acids research

authors： Renaud S,Loukinov D,Alberti L,Vostrov A,Kwon YW,Bosman FT,Lobanenkov V,Benhattar J

更新日期：2011-02-01 00:00:00

abstract：:In this study, we show that silencing of CITED2 using small-hairpin RNA (shCITED2) induced DNA damage and reduction of ERCC1 gene expression in HEK293, HeLa and H1299 cells, even in the absence of cisplatin. In contrast, ectopic expression of ERCC1 significantly reduced intrinsic and induced DNA damage levels, and res...

journal_title：Nucleic acids research

authors： Liu YC,Chang PY,Chao CC

更新日期：2015-12-15 00:00:00

abstract：:Adjustable transgene expression is considered key for next-generation molecular interventions in gene therapy scenarios, therapeutic reprogramming of clinical cell phenotypes for tissue engineering and sophisticated gene-function analyses in the post-genomic era. We have designed a portfolio of latest generation self-...

journal_title：Nucleic acids research

authors： Mitta B,Weber CC,Rimann M,Fussenegger M

更新日期：2004-07-16 00:00:00

abstract：:Nuclear organization of chromatin is an important level of genome regulation with positional changes of genes occurring during reprogramming. Inherent variability of biological specimens, wide variety of sample preparation and imaging conditions, though pose significant challenges to data analysis and comparison. Here...

journal_title：Nucleic acids research

authors： Jost KL,Haase S,Smeets D,Schrode N,Schmiedel JM,Bertulat B,Herzel H,Cremer M,Cardoso MC

更新日期：2011-09-01 00:00:00

abstract：:Human minisatellite probes cross-hybridize to mouse DNA and detect multiple variable loci. The resulting DNA "fingerprints" vary substantially between inbred strains but relatively little within an inbred strain. By studying the segregation of variable DNA fragments in BXD recombinant inbred strains of mice, at least ...

journal_title：Nucleic acids research

authors： Jeffreys AJ,Wilson V,Kelly R,Taylor BA,Bulfield G

更新日期：1987-04-10 00:00:00

abstract：:Two fragments cloned from purified human satellite III DNA do not cross-react with each other. One fragment, for which a partial sequence is reported, hybridises to satellite II as well as III and is shown to originate on chromosome 1. The other cloned fragment originates from the Y chromosome. This fragment has under...

journal_title：Nucleic acids research

authors： Cooke HJ,Hindley J

更新日期：1979-07-25 00:00:00

abstract：:Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequen...

journal_title：Nucleic acids research

authors： Janissen R,Berghuis BA,Dulin D,Wink M,van Laar T,Dekker NH

更新日期：2014-10-01 00:00:00

abstract：:Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN...

journal_title：Nucleic acids research

authors： Aiello FA,Palma A,Malacaria E,Zheng L,Campbell JL,Shen B,Franchitto A,Pichierri P

更新日期：2019-07-26 00:00:00

abstract：:Thiol-activated neocarzinostatin chromophore abstracts tritium from the 5', but not from the 1' or 2' positions of deoxyribose in DNA and incorporates it into a stable, non-exchangeable form. The abstracted tritium remains covalently associated with the chromophore or its degradation product after treatment with acid ...

journal_title：Nucleic acids research

authors： Kappen LS,Goldberg IH

更新日期：1985-03-11 00:00:00

abstract：:The human beta-actin promoter, including its 5' flanking region and 5' untranslated region, is ubiquitously active in mammalian cells in culture. In this report we investigated the transcriptional activity of, and the protein-DNA interactions that occur within, the proximal region of the human beta-actin promoter. Eff...

journal_title：Nucleic acids research

authors： Danilition SL,Frederickson RM,Taylor CY,Miyamoto NG

更新日期：1991-12-25 00:00:00

abstract：:Glucocorticoid (GC) signaling synchronizes the circadian rhythm of individual peripheral cells and induces the expression of circadian genes, including Period1 (Per1) and Period2 (Per2). However, no GC response element (GRE) has been reported in the Per2 promoter region. Here we report the molecular mechanisms of Per2...

journal_title：Nucleic acids research

authors： Cheon S,Park N,Cho S,Kim K

更新日期：2013-07-01 00:00:00

abstract：:Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesion...

journal_title：Nucleic acids research

authors： Da LT,Yu J

更新日期：2018-06-20 00:00:00

abstract：:Type II restriction endonucleases Bam HI and Eco RI were covalently coupled to Sepharose. These insolubilized enzymes generated fragment patterns for several viral DNAs identical to those produced by the respective free enzymes. Conditions for optimal activity were similar for both bound and unbound forms of the enzym...

journal_title：Nucleic acids research

authors： Lee YH,Blakesley RW,Smith LA,Chirikjian JG

更新日期：1978-03-01 00:00:00

abstract：:Bacterial small regulatory RNAs (sRNAs) play a major role in the regulation of various cellular functions. Most sRNAs interact with mRNA targets via an antisense mechanism, modifying their translation and/or degradation. Despite considerable progresses in discovering sRNAs in Gram-positive bacteria, their functions, f...

journal_title：Nucleic acids research

authors： Ivain L,Bordeau V,Eyraud A,Hallier M,Dreano S,Tattevin P,Felden B,Chabelskaya S

更新日期：2017-05-05 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：: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

authors： Kierzek R,He L,Turner DH

更新日期：1992-04-11 00:00:00

abstract：:For the first time mosaic nucleic acids composed of 50% RNA and 50% DNA can be obtained as transcripts with T7 RNA polymerase. Two NTPs could be replaced simultaneously in a transcription reaction. This means more than 40 deoxynucleotides were inserted in one transcript. Previously, a maximum of two deoxynucleotides c...

journal_title：Nucleic acids research

authors： Conrad F,Hanne A,Gaur RK,Krupp G

更新日期：1995-06-11 00:00:00