Rabbit muscle creatine kinase: genomic cloning, sequencing, and analysis of upstream sequences important for expression in myocytes.

abstract：:Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available s...

journal_title：Nucleic acids research

authors： Parameswaran P,Jalili R,Tao L,Shokralla S,Gharizadeh B,Ronaghi M,Fire AZ

更新日期：2007-01-01 00:00:00

abstract：:In the known monoclinic crystals the 3-dimensional structure of the hexameric, replicative helicase RepA encoded by plasmid RSF1010 shows 6-fold rotational symmetry. In contrast, in the cubic crystal form at 2.55 A resolution described here RepA has 3-fold symmetry and consists of a trimer of dimers. To study structur...

journal_title：Nucleic acids research

authors： Ziegelin G,Niedenzu T,Lurz R,Saenger W,Lanka E

更新日期：2003-10-15 00:00:00

abstract：:In most bacteria, two tRNAs decode the four arginine CGN codons. One tRNA harboring a wobble inosine (tRNA(Arg)ICG) reads the CGU, CGC and CGA codons, whereas a second tRNA harboring a wobble cytidine (tRNA(Arg)CCG) reads the remaining CGG codon. The reduced genomes of Mycoplasmas and other Mollicutes lack the gene en...

journal_title：Nucleic acids research

authors： Yokobori S,Kitamura A,Grosjean H,Bessho Y

更新日期：2013-07-01 00:00:00

abstract：:The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, ...

journal_title：Nucleic acids research

authors： Kapushesky M,Emam I,Holloway E,Kurnosov P,Zorin A,Malone J,Rustici G,Williams E,Parkinson H,Brazma A

更新日期：2010-01-01 00:00:00

abstract：:CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR inter...

journal_title：Nucleic acids research

authors： Xue C,Seetharam AS,Musharova O,Severinov K,Brouns SJ,Severin AJ,Sashital DG

更新日期：2015-12-15 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：:Bovine mitochondrial (mt) phenylalanine tRNA (tRNA(Phe)), which lacks the 'conserved' GG and T psi YCG sequences, was efficiently purified by the selective hybridization method using a solid phase DNA probe. The entire nucleotide sequence of the tRNA, including modified nucleotides, was determined and its higher-order...

journal_title：Nucleic acids research

authors： Wakita K,Watanabe Y,Yokogawa T,Kumazawa Y,Nakamura S,Ueda T,Watanabe K,Nishikawa K

更新日期：1994-02-11 00:00:00

abstract：:More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of re...

journal_title：Nucleic acids research

authors： Braun CM,Hackert P,Schmid CE,Bohnsack MT,Bohnsack KE,Perez-Fernandez J

更新日期：2020-01-10 00:00:00

abstract：:Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse...

journal_title：Nucleic acids research

authors： Nguyen TM,Kabotyanski EB,Reineke LC,Shao J,Xiong F,Lee JH,Dubrulle J,Johnson H,Stossi F,Tsoi PS,Choi KJ,Ellis AG,Zhao N,Cao J,Adewunmi O,Ferreon JC,Ferreon ACM,Neilson JR,Mancini MA,Chen X,Kim J,Ma L,Li W,Ro

更新日期：2020-03-18 00:00:00

abstract：:Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteri...

journal_title：Nucleic acids research

authors： Wilson KA,Kellie JL,Wetmore SD

更新日期：2014-06-01 00:00:00

abstract：:The kinetics of PaeR7 endonuclease-catalysed cleavage reactions of fluorophor-labeled oligonucleotide substrates have been examined using fluorescence resonance energy transfer (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7 recognition site and donor (fluorescein) and acceptor (rh...

journal_title：Nucleic acids research

authors： Ghosh SS,Eis PS,Blumeyer K,Fearon K,Millar DP

更新日期：1994-08-11 00:00:00

abstract：:In mammalian cells, DNA double-strand breaks (DSBs) are repaired by three pathways, nonhomologous end-joining (NHEJ), gene conversion (GC) and single-strand annealing (SSA). These pathways are distinct with regard to repair efficiency and mutagenic potential and must be tightly controlled to preserve viability and gen...

journal_title：Nucleic acids research

authors： Mansour WY,Schumacher S,Rosskopf R,Rhein T,Schmidt-Petersen F,Gatzemeier F,Haag F,Borgmann K,Willers H,Dahm-Daphi J

更新日期：2008-07-01 00:00:00

abstract：:RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived ...

journal_title：Nucleic acids research

authors： Chu Y,Wang T,Dodd D,Xie Y,Janowski BA,Corey DR

更新日期：2015-06-23 00:00:00

abstract：:The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased th...

journal_title：Nucleic acids research

authors： Okamura Y,Aoki Y,Obayashi T,Tadaka S,Ito S,Narise T,Kinoshita K

更新日期：2015-01-01 00:00:00

abstract：:Two dimensional PEI-cellulose thin layer chromatography can resolve sequentially degraded oligonucleotide fragments of tRNA. This technique entails the sequential degradation of the oligonucleotide with snake venom phosphodiesterase in the presence of bacterial alkaline phosphatase, and periodate oxidation followed by...

journal_title：Nucleic acids research

authors： Chen EY,Roe BA

更新日期：1977-10-01 00:00:00

abstract：:We report the synthesis of new phosphoramidite building blocks and their use for the modification of oligonucleotides with hydrazides. The reaction of these hydrazide oligonucleotides with active esters and aldehydes is demonstrated for solution conjugation and immobilization. Compared with the established amino modif...

journal_title：Nucleic acids research

authors： Raddatz S,Mueller-Ibeler J,Kluge J,Wäss L,Burdinski G,Havens JR,Onofrey TJ,Wang D,Schweitzer M

更新日期：2002-11-01 00:00:00

abstract：:Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...

journal_title：Nucleic acids research

authors： Chung CZ,Jaramillo JE,Ellis MJ,Bour DYN,Seidl LE,Jo DHS,Turk MA,Mann MR,Bi Y,Haniford DB,Duennwald ML,Heinemann IU

更新日期：2019-04-08 00:00:00

abstract：:We have constructed vectors from bacteriophage lambda and from plasmid pBR322 having a single EcoRI restriction site which is immediately downstream from the lac UV5 promotor. Each vector allows the fusion of a cloned gene to the lac Z gene in a different phase relative to the translation initiation codon of the lac Z...

journal_title：Nucleic acids research

authors： Charnay P,Perricaudet M,Galibert F,Tiollais P

更新日期：1978-12-01 00:00:00

abstract：:The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although sing...

journal_title：Nucleic acids research

authors： Voet T,Kumar P,Van Loo P,Cooke SL,Marshall J,Lin ML,Zamani Esteki M,Van der Aa N,Mateiu L,McBride DJ,Bignell GR,McLaren S,Teague J,Butler A,Raine K,Stebbings LA,Quail MA,D'Hooghe T,Moreau Y,Futreal PA,Stratton MR

更新日期：2013-07-01 00:00:00

abstract：:The 'POU' (acronym of Pit-1, Oct-1, Unc-86) family of transcription factors share a common DNA-binding domain of approximately 160 residues, comprising so-called 'POUs' and 'POUh' sub-domains connected by a flexible linker. The importance of POU proteins as developmental regulators and tumor-promoting agents is due to...

journal_title：Nucleic acids research

authors： Alazard R,Mourey L,Ebel C,Konarev PV,Petoukhov MV,Svergun DI,Erard M

更新日期：2007-01-01 00:00:00

abstract：:Two forms of post-transcriptional control direct differential expression of the Saccharomyces cerevisiae genes encoding the AP1-like transcription factors Yap1p and Yap2p. The mRNAs of these genes contain respectively one (YAP1 uORF) and two (YAP2 uORF1 and uORF2) upstream open reading frames. uORF-mediated modulation...

journal_title：Nucleic acids research

authors： Vilela C,Linz B,Rodrigues-Pousada C,McCarthy JE

更新日期：1998-03-01 00:00:00

abstract：:Protein-RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number of available protein-RNA complex 3D structures has increased, it is now possible to statistically examine protein-RNA inter...

journal_title：Nucleic acids research

authors： Kim OT,Yura K,Go N

更新日期：2006-01-01 00:00:00

abstract：:Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacin...

journal_title：Nucleic acids research

authors： McCauley MJ,Rueter EM,Rouzina I,Maher LJ 3rd,Williams MC

更新日期：2013-01-07 00:00:00

abstract：:Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined t...

journal_title：Nucleic acids research

authors： Hinrichs W,Steifa M,Saenger W,Eckstein F

更新日期：1987-06-25 00:00:00

abstract：:The convergently transcribed restriction (R) and methylase (M) genes of the Restriction-Modification system Esp1396I are tightly regulated by a controller (C) protein that forms part of the CR operon. We have mapped the transcriptional start sites from each promoter and examined the regulatory role of C.Esp1396I in vi...

journal_title：Nucleic acids research

authors： Bogdanova E,Zakharova M,Streeter S,Taylor J,Heyduk T,Kneale G,Severinov K

更新日期：2009-06-01 00:00:00

abstract：:A long-range physical map of the centromeric region of human chromosome 7 has been constructed in order to define the region containing sequences with potential involvement in centromere function. The map is centered around alpha satellite DNA, a family of tandemly repeated DNA forming arrays of hundreds to thousands ...

journal_title：Nucleic acids research

authors： Wevrick R,Willard HF

更新日期：1991-05-11 00:00:00

abstract：:Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analy...

journal_title：Nucleic acids research

authors： Arimondo PB,Angenault S,Halby L,Boutorine A,Schmidt F,Monneret C,Garestier T,Sun JS,Bailly C,Hélène C

更新日期：2003-07-15 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：:The beta-globin gene of a patient with mRNA-deficient beta o-thalassemia has been sequenced. We find a single nucleotide deletion in amino acid codon 44 that produces a UGA terminator at codon 60. We have previously shown that the beta-globin mRNA of this patient is correctly spliced and polyadenylated, but rapidly tu...

journal_title：Nucleic acids research

authors： Kinniburgh AJ,Maquat LE,Schedl T,Rachmilewitz E,Ross J

更新日期：1982-09-25 00:00:00

abstract：:Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...

journal_title：Nucleic acids research

authors： Iwamura Y,Sakai M,Muramatsu M

更新日期：1982-07-24 00:00:00