RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins.

abstract：:To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the fi...

journal_title：Nucleic acids research

authors： Wiwatwattana N,Kumar A

更新日期：2005-01-01 00:00:00

abstract：:A mutation in a gene dicA of Escherichia coli leads to temperature-sensitive cell division, by allowing expression of a nearby division inhibition gene dicB (1). We have now established the sequence of the DicA region and identified DicA as a 15.5 KD protein. A second gene dicC transcribed divergently from dicA and co...

journal_title：Nucleic acids research

authors： Béjar S,Cam K,Bouché JP

更新日期：1986-09-11 00:00:00

abstract：:Overexpressed in colon carcinoma-1 (OCC-1) is one of the earliest annotated long noncoding RNAs (lncRNAs) in colorectal cancer (CRC); however, its function remains largely unknown. Here, we revealed that OCC-1 plays a tumor suppressive role in CRC. OCC-1 knockdown by RNA interference promotes cell growth both in vitro...

journal_title：Nucleic acids research

authors： Lan Y,Xiao X,He Z,Luo Y,Wu C,Li L,Song X

更新日期：2018-06-20 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：:DNA swivel (nicking-rejoining) enzyme activity has been studied in various cell fractions of a human lymphoid cell line. Swivel activity is found only in chromatin and in a nuclear membrane fraction containing DNA and possessing endogenous DNA synthesizing activity. Twenty percent of the total swivel activity and less...

journal_title：Nucleic acids research

authors： Yoshida S,Ungers G,Rosenberg BH

更新日期：1977-01-01 00:00:00

abstract：:Aberration within the p53 tumor suppressor gene is the most frequently identified genetic damage in human cancer. Regulatory functions proposed for the p53 protein include modulation of the cell cycle, cellular differentiation, signal transduction, and gene expression. Additionally, the p53 gene product may guard the ...

journal_title：Nucleic acids research

authors： Hulla JE,Schneider RP

更新日期：1993-02-11 00:00:00

abstract：:Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5'-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured...

journal_title：Nucleic acids research

authors： Cang X,Šponer J,Cheatham TE 3rd

更新日期：2011-05-01 00:00:00

abstract：:PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes s...

journal_title：Nucleic acids research

authors： Dutreix M,Bäckman A,Célérier J,Bagdasarian MM,Sommer S,Bailone A,Devoret R,Bagdasarian M

更新日期：1988-11-25 00:00:00

abstract：:We have located and sequenced the murine homologue of the hst/k-FGF oncogene in genomic DNA clones that extend 3' from int-2 on mouse chromosome 7. The two genes are in the same transcriptional orientation, less than 20 kilobase pairs (kb) apart, and presumably evolved by tandem duplication of a common ancestral gene....

journal_title：Nucleic acids research

authors： Brookes S,Smith R,Thurlow J,Dickson C,Peters G

更新日期：1989-06-12 00:00:00

abstract：:Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells w...

journal_title：Nucleic acids research

authors： Melançon P,Lemieux C,Brakier-Gingras L

更新日期：1988-10-25 00:00:00

abstract：:Naturally occurring hammerhead ribozymes are produced by rolling circle replication followed by self-cleavage. This results in monomer-length catalytic RNAs which have self-complementary sequences that can occupy their trans -binding domains and potentially block their ability to cleave other RNA strands. Here we show...

journal_title：Nucleic acids research

authors： Ohmichi T,Kool ET

更新日期：2000-02-01 00:00:00

abstract：:A physical map is presented for the 1200 kb genome of Mycoplasma mycoides subsp. mycoides Y, locating 32 cleavage sites for 8 restriction endonucleases. The large restriction fragments involved were separated and sized by pulsed-field agarose gel electrophoresis. Their locations on the map were determined by probing S...

journal_title：Nucleic acids research

authors： Pyle LE,Finch LR

更新日期：1988-07-11 00:00:00

abstract：:DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 880 115 entries or 1 134 086 245 bases in the period from July 2006 to June 2007. The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others. Our computer system has been upgraded since March 2007. Anoth...

journal_title：Nucleic acids research

authors： Sugawara H,Ogasawara O,Okubo K,Gojobori T,Tateno Y

更新日期：2008-01-01 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 results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathwa...

journal_title：Nucleic acids research

authors： D'Andrea D,Grassi L,Mazzapioda M,Tramontano A

更新日期：2013-07-01 00:00:00

abstract：:We have developed a new method for analysis of complex genetic systems by a combination of the Amplification Refractory Mutation System (ARMS) and Single-Strand Conformation Polymorphism (SSCP) analysis: ARMS-SSCP. Thus, a complex allelic series is subdivided into a number of groups by ARMS followed by the identificat...

journal_title：Nucleic acids research

authors： Lo YM,Patel P,Mehal WZ,Fleming KA,Bell JI,Wainscoat JS

更新日期：1992-03-11 00:00:00

abstract：:We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...

journal_title：Nucleic acids research

authors： Dans PD,Balaceanu A,Pasi M,Patelli AS,Petkevičiūtė D,Walther J,Hospital A,Bayarri G,Lavery R,Maddocks JH,Orozco M

更新日期：2019-12-02 00:00:00

abstract：:Highly conserved sequences present at an identical position near the 3' ends of eukaryotic and prokaryotic 5S rRNAs are complementary to the 5' strand of the m2(6)A hairpin structure near the 3' ends of 18S rRNA and 16S rRNA, respectively. The extent of base-pairing and the calculated stabilities of the hybrids that c...

journal_title：Nucleic acids research

authors： Azad AA

更新日期：1979-12-11 00:00:00

abstract：:One-Block CYRCA is an automated procedure for identifying multiple-block alignments from single block queries (http://bioinfo.weizmann.ac.il/blocks/OneCYRCA). It is based on the LAMA and CYRCA block-to-block alignment methods. The procedure identifies whether the query blocks can form new multiple-block alignments (bl...

journal_title：Nucleic acids research

authors： Frenkel-Morgenstern M,Singer A,Bronfeld H,Pietrokovski S

更新日期：2005-07-01 00:00:00

abstract：:The complete mitochondrial (mt) genome of Crossostoma lacustre, a freshwater loach from mountain stream of Taiwan, has been cloned and sequenced. This fish mt genome, consisting of 16558 base-pairs, encodes genes for 13 proteins, two rRNAs, and 22 tRNAs, in addition to a regulatory sequence for replication and transcr...

journal_title：Nucleic acids research

authors： Tzeng CS,Hui CF,Shen SC,Huang PC

更新日期：1992-09-25 00:00:00

abstract：:Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrates are transpositionally inactive due to the accumulation of mutations in their transposase genes. A novel open reading frame-trapping method was used to isolate uninterrupted transposase coding regions from the genome of the frog s...

journal_title：Nucleic acids research

authors： Miskey C,Izsvák Z,Plasterk RH,Ivics Z

更新日期：2003-12-01 00:00:00

abstract：:Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We hav...

journal_title：Nucleic acids research

authors： Dai L,Toor N,Olson R,Keeping A,Zimmerly S

更新日期：2003-01-01 00:00:00

abstract：:The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Proje...

journal_title：Nucleic acids research

authors： Mukherjee S,Stamatis D,Bertsch J,Ovchinnikova G,Katta HY,Mojica A,Chen IA,Kyrpides NC,Reddy T

更新日期：2019-01-08 00:00:00

abstract：:Regulation of CLB2 is important both for completion of the normal vegetative cell cycle in Saccharomyces cerevisiae and for departure from the vegetative cell cycle upon nitrogen deprivation. Cell cycle-regulated transcription of CLB2 in the G2/M phase is known to be brought about by a set of proteins including Mcm1p,...

journal_title：Nucleic acids research

authors： Van Slyke C,Grayhack EJ

更新日期：2003-08-01 00:00:00

abstract：:Human stem cells are promising sources for regenerative therapy. To ensure safety of future therapeutic applications, the differentiation potency of stem cells has to be tested and be widely opened to the public. The potency is generally assessed by teratoma formation comprising differentiated cells from all three ger...

journal_title：Nucleic acids research

authors： Park SJ,Komiyama Y,Suemori H,Umezawa A,Nakai K

更新日期：2016-01-04 00:00:00

abstract：:Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomi...

journal_title：Nucleic acids research

authors： Lee J,Hong WY,Cho M,Sim M,Lee D,Ko Y,Kim J

更新日期：2016-07-08 00:00:00

abstract：:The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling val...

journal_title：Nucleic acids research

authors： Ringwald M,Eppig JT,Begley DA,Corradi JP,McCright IJ,Hayamizu TF,Hill DP,Kadin JA,Richardson JE

更新日期：2001-01-01 00:00:00

abstract：:We analysed the basic mechanisms of signal transmission in DNA and the origins of the allostery exhibited by systems such as the ternary complex BAMHI-DNA-GRDBD. We found that perturbation information generated by a primary protein binding event travels as a wave to distant regions of DNA following a hopping mechanism...

journal_title：Nucleic acids research

authors： Balaceanu A,Pérez A,Dans PD,Orozco M

更新日期：2018-09-06 00:00:00

abstract：:Diastereomeric dithymidine methanephosphonamidates (TnpmT) were synthesized by reaction of 3'-amino-3'-deoxythymidine with 3'- O -acetylthymidin-5-yl-methanephosphonochloridate. Separated dinucleotide TnpmT(fast) and TnpmT(slow) diastereomers were used as building blocks to prepare chimeric dodecathy-midylates, posses...

journal_title：Nucleic acids research

authors： Nawrot B,Boczkowska M,Wójcik M,Sochacki M,Kazmierski S,Stec WJ

更新日期：1998-06-01 00:00:00

abstract：:Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the...

journal_title：Nucleic acids research

authors： Zoppoli G,Douarre C,Dalla Rosa I,Liu H,Reinhold W,Pommier Y

更新日期：2011-08-01 00:00:00