Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions.

abstract：:In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in...

journal_title：Nucleic acids research

authors： Piper PW,Lockheart A,Patel N

更新日期：1984-05-25 00:00:00

abstract：:The Chinese hamster cell line, DC-3F, is heterozygous at the DHFR locus, and each allele can be distinguished on the basis of a unique DNA restriction pattern, protein isoelectric profile and in the abundancy of the DHFR mRNAs it expresses. Although each allele produces four transcripts, 1000, 1650 and 2150 nucleotide...

journal_title：Nucleic acids research

authors： Scotto KW,Yang H,Davide JP,Melera PW

更新日期：1992-12-25 00:00:00

abstract：:The non-essential MGS1 gene of Saccharomyces cerevisiae is highly conserved in eukaryotes and encodes an enzyme containing both DNA-dependent ATPase and DNA annealing activities. MGS1 appears to function in post-replicational repair processes that contribute to genome stability. In this study, we identified MGS1 as a ...

journal_title：Nucleic acids research

authors： Kim JH,Kang YH,Kang HJ,Kim DH,Ryu GH,Kang MJ,Seo YS

更新日期：2005-10-26 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：:Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori. We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial ...

journal_title：Nucleic acids research

authors： Arnion H,Korkut DN,Masachis Gelo S,Chabas S,Reignier J,Iost I,Darfeuille F

更新日期：2017-05-05 00:00:00

abstract：:Rad51 protein promotes homologous recombination in eukaryotes. Recombination activities are activated by Rad51 filament assembly on ssDNA. Previous studies of yeast Rad51 showed that His352 occupies an important position at the filament interface, where it could relay signals between subunits and active sites. To inve...

journal_title：Nucleic acids research

authors： Chen J,Villanueva N,Rould MA,Morrical SW

更新日期：2010-08-01 00:00:00

abstract：:Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active in such a process. To estimate the impact of uORFs on the regulation of translation in humans, we first circumscribed the universe ...

journal_title：Nucleic acids research

authors： McGillivray P,Ault R,Pawashe M,Kitchen R,Balasubramanian S,Gerstein M

更新日期：2018-04-20 00:00:00

abstract：:The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...

journal_title：Nucleic acids research

authors： Hain J,Reiter WD,Hüdepohl U,Zillig W

更新日期：1992-10-25 00:00:00

abstract：:The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription factors whose binding sites are tightly clustered and form cis-regulatory modules. In this paper, we present a web serve...

journal_title：Nucleic acids research

authors： Sharan R,Ben-Hur A,Loots GG,Ovcharenko I

更新日期：2004-07-01 00:00:00

abstract：:The modified nucleoside, 7-(4,5-cis-dihydroxy-1-cyclopenten-3-yl-aminomethyl)-7-deazaguanosine, designated as Q, and its derivative, Q*, were found in tRNA's from various organisms, including several mammalian tissues, other animals such as starfish, lingula and hagfish, and wheat germ. Q isolated from rat liver tRNA ...

journal_title：Nucleic acids research

authors： Kasai H,Kuchino Y,Nihei K,Nishimura S

更新日期：1975-10-01 00:00:00

abstract：:Lytic infection with polyoma virus leads in Go-arrested primary mouse kidney cell cultures to a mitotic host response. In the present work we focused our attention on cellular RNA synthesis shortly after onset of polyoma T-antigen synthesis. Onset of polyoma-induced stimulation of 45S pre-rRNA synthesis was determined...

journal_title：Nucleic acids research

authors： Matter JM,Tiercy JM,Weil R

更新日期：1983-10-11 00:00:00

abstract：:Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3'-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA-DNA, LNA-LNA, LNA-R...

journal_title：Nucleic acids research

authors： Pande V,Nilsson L

更新日期：2008-03-01 00:00:00

abstract：:By introduction of recombinant plasmids into monkey CV1 cells, we have unambiguously demonstrated that sequences entirely within the 72 bp repeat, which is located upstream of the SV40 early region, are crucial for T-antigen expression in vivo. We have also shown that a DNA fragment containing the 72 bp repeat, insert...

journal_title：Nucleic acids research

authors： Moreau P,Hen R,Wasylyk B,Everett R,Gaub MP,Chambon P

更新日期：1981-11-25 00:00:00

abstract：:Phenotype analysis is commonly recognized to be of great importance for gaining insight into genetic interaction underlying inherited diseases. However, few computational contributions have been proposed for this purpose, mainly owing to lack of controlled clinical information easily accessible and structured for comp...

journal_title：Nucleic acids research

authors： Masseroli M,Galati O,Pinciroli F

更新日期：2005-07-01 00:00:00

abstract：:The -1 ribosomal frameshifting requires the existence of an in cis RNA slippery sequence and is promoted by a downstream stimulator RNA. An atypical RNA pseudoknot with an extra stem formed by complementary sequences within loop 2 of an H-type pseudoknot is characterized in the severe acute respiratory syndrome corona...

journal_title：Nucleic acids research

authors： Su MC,Chang CT,Chu CH,Tsai CH,Chang KY

更新日期：2005-07-29 00:00:00

abstract：:The chemical synthesis of backbone deuterium labelled [r(CGCGAAU*U*CGCG)]2 (U* = [5'-2H]U) is described. An efficient purification procedure was developed using a polymeric reverse phase (PRP) HPLC column at 60 degrees C. This procedure provided pure RNA dodecamer in the multi-milligram quantities (39% overall yield) ...

journal_title：Nucleic acids research

authors： Khare D,Orban J

更新日期：1992-10-11 00:00:00

abstract：:We developed an integrated method to identify aptamers with only 10 fixed nucleotides through ligation and removal of primer binding sites within the systematic evolution of ligands by exponential enrichment (SELEX) process. This Tailored-SELEX approach was validated by identifying a Spiegelmer ('mirror-image aptamer'...

journal_title：Nucleic acids research

authors： Vater A,Jarosch F,Buchner K,Klussmann S

更新日期：2003-11-01 00:00:00

abstract：:Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloS...

journal_title：Nucleic acids research

authors： Huang Z,Zhu L,Cao Y,Wu G,Liu X,Chen Y,Wang Q,Shi T,Zhao Y,Wang Y,Li W,Li Y,Chen H,Chen G,Zhang J

更新日期：2011-01-01 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：:Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Exi...

journal_title：Nucleic acids research

authors： Ito J,Tabei Y,Shimizu K,Tsuda K,Tomii K

更新日期：2012-01-01 00:00:00

abstract：:A human telomere ends in a single-stranded 3' tail, composed of repeats of T2AG3. G-quadruplexes (GQs) formed from four consecutive repeats have been shown to possess high-structural and mechanical diversity. In principle, a GQ can form from any four repeats that are not necessarily consecutive. To understand the dyna...

journal_title：Nucleic acids research

authors： Mitra J,Ha T

更新日期：2019-12-02 00:00:00

abstract：:DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core o...

journal_title：Nucleic acids research

authors： Li H,Chang YY,Lee JY,Bahar I,Yang LW

更新日期：2017-07-03 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

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：:HORMA domain-containing proteins (HORMADs) play an essential role in meiosis in many organisms. The meiotic HORMADs, including yeast Hop1, mouse HORMAD1 and HORMAD2, and Arabidopsis ASY1, assemble along chromosomes at early prophase and the closure motif at their C-termini has been hypothesized to be instrumental for ...

journal_title：Nucleic acids research

authors： Yang C,Hu B,Portheine SM,Chuenban P,Schnittger A

更新日期：2020-11-18 00:00:00

abstract：:In nematodes, the 22 nucleotide (nt) spliced leader (SL) is normally encoded by a multi-copy, tandemly reiterated SL gene and is trans-spliced from SL-RNA onto the 5' end of a subset of mRNAs. We have found that the SL is also encoded at multiple (> 100) orphon genomic sites in the parasitic nematode Angiostrongylus c...

journal_title：Nucleic acids research

authors： Joshua GW,Perler FB,Wang CC

更新日期：1995-03-25 00:00:00

abstract：:Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoure...

journal_title：Nucleic acids research

authors： Yeoh LM,Goodman CD,Hall NE,van Dooren GG,McFadden GI,Ralph SA

更新日期：2015-05-19 00:00:00

abstract：:The HhaI methyltransferase recognizes the sequence GCGC and transfers a methyl group to C5 of the first cytosine residue. All m5C-methyltransferases contain a highly conserved sequence motif called the P-C motif. The cysteine residue of this motif is involved in catalysis by forming a covalent bond with the 6-position...

journal_title：Nucleic acids research

authors： Mi S,Roberts RJ

更新日期：1993-05-25 00:00:00

abstract：:Expansions of (GAA)n repeats within the first intron of the frataxin gene reduce its expression, resulting in a hereditary neurodegenerative disorder, Friedreich's ataxia. While it is generally believed that expanded (GAA)n repeats block transcription elongation, fine mechanisms responsible for gene repression are not...

journal_title：Nucleic acids research

authors： Krasilnikova MM,Kireeva ML,Petrovic V,Knijnikova N,Kashlev M,Mirkin SM

更新日期：2007-01-01 00:00:00

abstract：:In Saccharomyces cerevisiae, RNA polymerase II assembly is probably initiated by the formation of the RPB3-RPB11 heterodimer. RPB3 is encoded by a single copy gene in the yeast, mouse and human genomes. The RPB11 gene is also unique in yeast and mouse, but in humans a gene family has been identified that potentially e...

journal_title：Nucleic acids research

authors： Benga WJ,Grandemange S,Shpakovski GV,Shematorova EK,Kedinger C,Vigneron M

更新日期：2005-06-24 00:00:00