EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes.

abstract：:We describe the structure (3840 bp) of a novel Euglena gracilis chloroplast ribosomal protein operon that encodes the five genes rpl16-rpl14-rpl5-rps8-rpl36. The gene organization resembles the spc and the 3'-end of the S10 ribosomal protein operons of E. coli. The rpl5 is a new chloroplast gene not previously reporte...

journal_title：Nucleic acids research

authors： Christopher DA,Hallick RB

更新日期：1989-10-11 00:00:00

abstract：:Remodelling protein nucleic acid interfaces is an important biological task, which is often carried out by nucleic acid stimulated ATPases of the Swi2/Snf2 superfamily. Here we study the mechano-chemical cycle of such an ATPase, namely the catalytic domain of the Sulfolobus solfataricus Rad54 homologue (SsoRad54cd), b...

journal_title：Nucleic acids research

authors： Lewis R,Dürr H,Hopfner KP,Michaelis J

更新日期：2008-04-01 00:00:00

abstract：:Using cyanoethyldiisopropylamino phosphoramidite chemistry, four oligonucleotides constituting a part of the sequence of the initiator t-RNA from B. subtilis were synthesized. For the protection of the exocyclic amino functions of bases, phenoxyacetyl group was used for adenine and guanine, and acetyl group was prefer...

journal_title：Nucleic acids research

authors： Chaix C,Duplaa AM,Molko D,Téoule R

更新日期：1989-09-25 00:00:00

abstract：:Meiotic cells possess surveillance mechanisms that monitor critical events such as recombination and chromosome synapsis. Meiotic defects resulting from the absence of the synaptonemal complex component Zip1 activate a meiosis-specific checkpoint network resulting in delayed or arrested meiotic progression. Pch2 is an...

journal_title：Nucleic acids research

authors： Herruzo E,Ontoso D,González-Arranz S,Cavero S,Lechuga A,San-Segundo PA

更新日期：2016-09-19 00:00:00

abstract：:The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super-s...

journal_title：Nucleic acids research

authors： Espadaler J,Fernandez-Fuentes N,Hermoso A,Querol E,Aviles FX,Sternberg MJ,Oliva B

更新日期：2004-01-01 00:00:00

abstract：:The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and 9 archaeal homologs) and a total of 20 protein sequences representing SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72. The o...

journal_title：Nucleic acids research

authors： Zwieb C,Larsen N

更新日期：1994-09-01 00:00:00

abstract：:p53 as an effector of nucleolar stress is well defined, but p53 independent mechanisms are largely unknown. Like p53, the NF-κB transcription factor plays a critical role in maintaining cellular homeostasis under stress. Many stresses that stimulate NF-κB also disrupt nucleoli. However, the link between nucleolar func...

journal_title：Nucleic acids research

authors： Chen J,Lobb IT,Morin P,Novo SM,Simpson J,Kennerknecht K,von Kriegsheim A,Batchelor EE,Oakley F,Stark LA

更新日期：2018-07-06 00:00:00

abstract：:DNA primase has been partially purified from wheat germ. This enzyme, like DNA primases characterized from many procaryotic and eucaryotic sources, catalyses the synthesis of primers involved in DNA replication. However, the wheat enzyme differs from animal DNA primase in that it is found partially associated with a D...

journal_title：Nucleic acids research

authors： Laquel P,Castroviejo M,Litvak S

更新日期：1990-08-25 00:00:00

abstract：:ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be s...

journal_title：Nucleic acids research

authors： Parkinson H,Sarkans U,Shojatalab M,Abeygunawardena N,Contrino S,Coulson R,Farne A,Lara GG,Holloway E,Kapushesky M,Lilja P,Mukherjee G,Oezcimen A,Rayner T,Rocca-Serra P,Sharma A,Sansone S,Brazma A

更新日期：2005-01-01 00:00:00

abstract：:In non-malignant RWPE-1 prostate epithelial cells signaling by the nuclear receptor Vitamin D Receptor (VDR, NR1I1) induces cell cycle arrest through targets including CDKN1A (encodes p21((waf1/cip1))). VDR dynamically induced individual histone modification patterns at three VDR binding sites (R1, 2, 3) on the CDKN1A...

journal_title：Nucleic acids research

authors： Thorne JL,Maguire O,Doig CL,Battaglia S,Fehr L,Sucheston LE,Heinaniemi M,O'Neill LP,McCabe CJ,Turner BM,Carlberg C,Campbell MJ

更新日期：2011-03-01 00:00:00

abstract：:Translesion DNA synthesis (TLS) by the Y-family DNA polymerases Polη, Polι and Polκ, mediated via interaction with proliferating cell nuclear antigen (PCNA), is a crucial pathway that protects human cells against DNA damage. We report that Polη has three PCNA-interacting protein (PIP) boxes (PIP1, 2, 3) that contribut...

journal_title：Nucleic acids research

authors： Masuda Y,Kanao R,Kaji K,Ohmori H,Hanaoka F,Masutani C

更新日期：2015-09-18 00:00:00

abstract：:Alternative splicing constitutes a major mechanism creating protein diversity in humans. This diversity can result from the alternative skipping of entire exons or by alternative selection of the 5' or 3' splice sites that define the exon boundaries. In this study, we analyze the sequence and evolutionary characterist...

journal_title：Nucleic acids research

authors： Akerman M,Mandel-Gutfreund Y

更新日期：2007-01-01 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：:Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes and maintains telomeric DNA. Studies of telomeres and telomerase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as Tetrahymena thermophila. To examine the expression of telomerase, we investigated the...

journal_title：Nucleic acids research

authors： Hargrove BW,Bhattacharyya A,Domitrovich AM,Kapler GM,Kirk K,Shippen DE,Kunkel GR

更新日期：1999-11-01 00:00:00

abstract：:We have determined the nucleotide sequence of the major species of E. coli tRNASer and of a minor species having the same GGA anticodon. These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E. coli. The two sequences differ in only one positio...

journal_title：Nucleic acids research

authors： Grosjean H,Nicoghosian K,Haumont E,Söll D,Cedergren R

更新日期：1985-08-12 00:00:00

abstract：:Variable (diversity) joining [V(D)J] recombination of immune gene loci proceeds in an ordered manner with D to J portions recombining first and then an upstream V joins that recombinant. We present evidence that the non-core domain of recombination activating gene (RAG) protein 2 is involved in the regulation of recom...

journal_title：Nucleic acids research

authors： Curry JD,Schlissel MS

更新日期：2008-10-01 00:00:00

abstract：:Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanis...

journal_title：Nucleic acids research

authors： Yamakawa N,Okuyama K,Ogata J,Kanai A,Helwak A,Takamatsu M,Imadome K,Takakura K,Chanda B,Kurosaki N,Yamamoto H,Ando K,Matsui H,Inaba T,Kotani A

更新日期：2014-04-01 00:00:00

abstract：:The bacteriophage Mu A and B genes, which lie adjacent to each other and are colinear on the phage genome, encode proteins that catalyze efficient transposition of Mu DNA. We show that the molar ratio of A and B proteins is approximately 1:20 in extracts prepared after induction of cells containing a Mu lysogen or a p...

journal_title：Nucleic acids research

authors： Parsons RL,Harshey R

更新日期：1988-12-09 00:00:00

abstract：:ID elements comprise a rodent SINE (short interspersed DNA repetitive element) family that has amplified by retroposition of a few master genes. In order to understand the important factors of SINE amplification, we investigated the transcription of rat ID elements. Three different size classes of ID transcripts, BC1,...

journal_title：Nucleic acids research

authors： Kim J,Kass DH,Deininger PL

更新日期：1995-06-25 00:00:00

abstract：:A filter binding assay was developed that allows measurement of specific binding of trp repressor to operator DNA. The most important feature of this procedure is the concentration and type of salt present in the binding buffer. Using this assay the dissociation constant of the repressor-operator complex was determine...

journal_title：Nucleic acids research

authors： Klig LS,Crawford IP,Yanofsky C

更新日期：1987-07-10 00:00:00

abstract：:E. coli genes for tRNAasp and tRNAtrp are transcribed by eukaryotic RNA polymerase III upon injection into nuclei of Xenopus oocytes. This indicates that some bacterial tRNA genes contain RNA polymerase III promoter sequences. We discuss evolutionary aspects of this finding. ...

journal_title：Nucleic acids research

authors： Folk WR,Hofstetter H,Birnstiel ML

更新日期：1982-11-25 00:00:00

abstract：:The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...

journal_title：Nucleic acids research

authors： Bee L,Marini S,Pontarin G,Ferraro P,Costa R,Albrecht U,Celotti L

更新日期：2015-02-27 00:00:00

abstract：:Advances in genomic sequencing have enormous potential to revolutionize personalized medicine, however distinguishing disease-causing from benign variants remains a challenge. The increasing number of human genome and exome sequences available has revealed areas where unfavourable variation is removed through purifyin...

journal_title：Nucleic acids research

authors： Silk M,Petrovski S,Ascher DB

更新日期：2019-07-02 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：:R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied ...

journal_title：Nucleic acids research

authors： Antonov AV,Schmidt EE,Dietmann S,Krestyaninova M,Hermjakob H

更新日期：2010-07-01 00:00:00

abstract：:Aberrant Notch signaling plays a pivotal role in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL). Amplitude and duration of the Notch response is controlled by ubiquitin-dependent proteasomal degradation of the Notch1 intracellular domain (NICD1), a hallmark of the leukemogenic proce...

journal_title：Nucleic acids research

authors： Ferrante F,Giaimo BD,Bartkuhn M,Zimmermann T,Close V,Mertens D,Nist A,Stiewe T,Meier-Soelch J,Kracht M,Just S,Klöble P,Oswald F,Borggrefe T

更新日期：2020-04-17 00:00:00

abstract：:p16INK4a and p21WAF1, two major cyclin-dependent kinase inhibitors, are the products of two tumor suppressor genes that play important roles in various cellular metabolic pathways. p21WAF1 is up-regulated in response to different DNA damaging agents. While the activation of p21WAF1 is p53-dependent following -rays, th...

journal_title：Nucleic acids research

authors： Al-Mohanna MA,Al-Khalaf HH,Al-Yousef N,Aboussekhra A

更新日期：2007-01-01 00:00:00

abstract：:By subtractive screening of a library made from mRNA of lipopolysaccharide (LPS)-stimulated mouse B lymphocytes we isolated cDNA-clones encoding the ribosomal protein L7. Human L7 mRNA was cloned from activated T-lymphocytes. Although no specific function of L7 in the translation apparatus is known as yet, it should b...

journal_title：Nucleic acids research

authors： Hemmerich P,von Mikecz A,Neumann F,Sözeri O,Wolff-Vorbeck G,Zoebelein R,Krawinkel U

更新日期：1993-01-25 00:00:00

abstract：:Digestion of isolated Friend erythroleukemic cell nuclei with DNase I under conditions which selectively destroy the DNA of transcriptionally "active" genes releases into the supernatant fraction proteins of the non-histone "High Mobility Group" (HMGs). Two of these, HMG-14 and HMG-17(identified by solubility in trich...

journal_title：Nucleic acids research

authors： Reeves R,Candido EP

更新日期：1980-05-10 00:00:00

abstract：:For the isolation of single stranded plasmid DNA, various E. coli and E. coli-Streptomyces shuttle plasmids were equipped with the phage f1 replication origin. The transformation of some representative Streptomyces species with plasmid vectors occurred irrespective of whether single or double stranded DNA was used. In...

journal_title：Nucleic acids research

authors： Hillemann D,Pühler A,Wohlleben W

更新日期：1991-02-25 00:00:00