Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers.

abstract：:Alternative splicing (AS) of pre-mRNAs is an important regulatory mechanism shaping the transcriptome. In plants, only few RNA-binding proteins are known to affect AS. Here, we show that the glycine-rich RNA-binding protein AtGRP7 influences AS in Arabidopsis thaliana. Using a high-resolution RT-PCR-based AS panel, we...

journal_title：Nucleic acids research

authors： Streitner C,Köster T,Simpson CG,Shaw P,Danisman S,Brown JW,Staiger D

更新日期：2012-12-01 00:00:00

abstract：:A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of...

journal_title：Nucleic acids research

authors： Weinel C,Tümmler B,Hilbert H,Nelson KE,Kiewitz C

更新日期：2001-11-15 00:00:00

abstract：:Selected groups of isolated 14C-labelled proteins from E. coli 30S ribosomal subunits were reconstituted with 32P-labelled 16S RNA, and the reconstituted complexes were partially digested with ribonuclease A. RNA fragments protected by the proteins were separated by gel electrophoresis and subjected to sequence analys...

journal_title：Nucleic acids research

authors： Wiener L,Schüler D,Brimacombe R

更新日期：1988-02-25 00:00:00

abstract：:Two models have been proposed for triggering release of the lagging strand polymerase at the replication fork, enabling cycling to the primer for the next Okazaki fragment--either collision with the 5'-end of the preceding fragment (collision model) or synthesis of a new primer by primase (signaling model). Specific p...

journal_title：Nucleic acids research

authors： Yuan Q,McHenry CS

更新日期：2014-02-01 00:00:00

abstract：:The heterodimeric subunit, SRP9/14, of the signal recognition particle (SRP) has previously been found to bind to scAlu and scB1 RNAs in vitro and to exist in large excess over SRP in anthropoid cells. Here we show that human and mouse SRP9/14 bind with high affinities to other Alu-like RNAs of different evolutionary ...

journal_title：Nucleic acids research

authors： Bovia F,Wolff N,Ryser S,Strub K

更新日期：1997-01-15 00:00:00

abstract：:We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effe...

journal_title：Nucleic acids research

authors： Staden R

更新日期：1984-01-11 00:00:00

abstract：:The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...

journal_title：Nucleic acids research

authors： Nguyen DT,Mathias S,Bologa C,Brunak S,Fernandez N,Gaulton A,Hersey A,Holmes J,Jensen LJ,Karlsson A,Liu G,Ma'ayan A,Mandava G,Mani S,Mehta S,Overington J,Patel J,Rouillard AD,Schürer S,Sheils T,Simeonov A,Sklar L

更新日期：2017-01-04 00:00:00

abstract：:We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain ...

journal_title：Nucleic acids research

authors： Barik A,Mishra A,Bahadur RP

更新日期：2012-07-01 00:00:00

abstract：:Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of hig...

journal_title：Nucleic acids research

authors： Werner A

更新日期：2011-02-01 00:00:00

abstract：:The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...

journal_title：Nucleic acids research

authors： Freistadt MS,Cross GA,Branch AD,Robertson HD

更新日期：1987-12-10 00:00:00

abstract：:RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept o...

journal_title：Nucleic acids research

authors： Novichkov PS,Rodionov DA,Stavrovskaya ED,Novichkova ES,Kazakov AE,Gelfand MS,Arkin AP,Mironov AA,Dubchak I

更新日期：2010-07-01 00:00:00

abstract：:Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...

journal_title：Nucleic acids research

authors： Jiricny J,Martin D

更新日期：1986-03-11 00:00:00

abstract：:Identification of MHC-binding peptides is a prerequisite in rational design of T-cell based peptide vaccines. During the past decade a number of computational approaches have been introduced for the prediction of MHC-binding peptides, efficiently reducing the number of candidate binders that need to be experimentally ...

journal_title：Nucleic acids research

authors： Dönnes P,Kohlbacher O

更新日期：2006-07-01 00:00:00

abstract：:PrimPol is a primase-polymerase involved in nuclear and mitochondrial DNA replication in eukaryotic cells. Although PrimPol is predicted to possess an archaeo-eukaryotic primase and a UL52-like zinc finger domain, the role of these domains has not been established. Here, we report that the proposed zinc finger domain ...

journal_title：Nucleic acids research

authors： Keen BA,Jozwiakowski SK,Bailey LJ,Bianchi J,Doherty AJ

更新日期：2014-05-01 00:00:00

abstract：:Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome v...

journal_title：Nucleic acids research

authors： Welch JD,Hu Y,Prins JF

更新日期：2016-05-05 00:00:00

abstract：:A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase has been investigated. Gene mapping and complementation experiments placed the mutation to temperature-sensitivity within the alpha operon at 72 min. on the bacterial chromosome. The rate of RNA synthesis in vivo and the...

journal_title：Nucleic acids research

authors： Mehrpouyan M,Champney WS

更新日期：1990-06-25 00:00:00

abstract：:We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as 'H'). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-R...

journal_title：Nucleic acids research

authors： Peng CG,Damha MJ

更新日期：2005-12-23 00:00:00

abstract：:An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by...

journal_title：Nucleic acids research

authors： Paccanaro A,Casbon JA,Saqi MA

更新日期：2006-03-17 00:00:00

abstract：:Characterization of the epigenetic status of individual cells remains a challenge. Current sequencing approaches have limited coverage, and it is difficult to assign an epigenetic status to the transcription state of individual gene alleles in the same cell. To address these limitations, a targeted microscopy-based ep...

journal_title：Nucleic acids research

authors： Kint S,Van Criekinge W,Vandekerckhove L,De Vos WH,Bomsztyk K,Krause DS,Denisenko O

更新日期：2021-01-28 00:00:00

abstract：:We have used a polymerase chain reaction (PCR) procedure to analyse low abundance complementary sense RNAs of Digitaria streak virus (DSV) from infected leaves of Digitaria setigera. This study has confirmed that both spliced and unspliced RNAs are synthesised by the same transcription unit. The position of the intron...

journal_title：Nucleic acids research

authors： Mullineaux PM,Guerineau F,Accotto GP

更新日期：1990-12-25 00:00:00

abstract：:We have investigated loop-induced structural perturbation of the stem structure in hairpins d(GAATTCXnGAATTC) (X = A, T and n = 3, 4, 5 and 6) that contain an EcoRI restriction site in close proximity to the hairpin loop. Oligonucleotides containing either a T3 or a A3 loop were not hydrolyzed by the restriction enzym...

journal_title：Nucleic acids research

authors： Germann MW,Kalisch BW,Lundberg P,Vogel HJ,van de Sande JH

更新日期：1990-03-25 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：:We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains...

journal_title：Nucleic acids research

authors： Kröger M,Wahl R,Rice P

更新日期：1993-07-01 00:00:00

abstract：:Cleavage of phosphodiester bonds by small ribonuclease mimics within different bulge-loops of RNA was investigated. Bulge-loops of different size (1-7 nt) and sequence composition were formed in a 3' terminal fragment of influenza virus M2 RNA (96 nt) by hybridization of complementary oligodeoxynucleotides. Small bulg...

journal_title：Nucleic acids research

authors： Kuznetsova IL,Zenkova MA,Gross HJ,Vlassov VV

更新日期：2005-02-24 00:00:00

abstract：:The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.ed...

journal_title：Nucleic acids research

authors： Cole JR,Chai B,Farris RJ,Wang Q,Kulam SA,McGarrell DM,Garrity GM,Tiedje JM

更新日期：2005-01-01 00:00:00

abstract：:We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Uniqu...

journal_title：Nucleic acids research

authors： Csank C,Taylor FM,Martindale DW

更新日期：1990-09-11 00:00:00

abstract：:We have developed an end-labelling approach to map the positions of nucleosomes and protein binding sites at nucleotide resolution by footprinting micrococcal nuclease (MNase)-sensitive sites. Using this approach we determined that the MFA2 gene and its upstream control regions have four positioned nucleosomes when tr...

journal_title：Nucleic acids research

authors： Teng Y,Yu S,Waters R

更新日期：2001-07-01 00:00:00

abstract：:The generalized mismatch repair system of Streptococcus pneumoniae (the Hex system) can eliminate base pair mismatches arising in heteroduplex DNA during transformation or by DNA polymerase errors during replication. Mismatch repair is most likely initiated at nicks or gaps. The present work was started to examine the...

journal_title：Nucleic acids research

authors： Méjean V,Devedjian JC,Rives I,Alloing G,Claverys JP

更新日期：1991-10-25 00:00:00

abstract：:The HIV RT and Protease Sequence Database is an online relational database that catalogs evolutionary and drug-related human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease sequence variation (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protea...

journal_title：Nucleic acids research

authors： Shafer RW,Jung DR,Betts BJ,Xi Y,Gonzales MJ

更新日期：2000-01-01 00:00:00

abstract：:PAX6 is a transcription factor that plays a major role in ocular morphogenesis. PAX6 is expressed in the eye, central nervous system and pancreas. Two alternative promoters, P0 and P1, which are differentially regulated during development, drive PAX6 transcription. We identified a 57 bp cis-regulatory element in exon ...

journal_title：Nucleic acids research

authors： Zheng JB,Zhou YH,Maity T,Liao WS,Saunders GF

更新日期：2001-10-01 00:00:00