Double-strand break repair deficiency in NONO knockout murine embryonic fibroblasts and compensation by spontaneous upregulation of the PSPC1 paralog.

abstract：:The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant hu...

journal_title：Nucleic acids research

authors： Martínez-Fundichely A,Casillas S,Egea R,Ràmia M,Barbadilla A,Pantano L,Puig M,Cáceres M

更新日期：2014-01-01 00:00:00

abstract：:Chromatin modulation at various cis-acting elements is critical for V(D)J recombination during T and B cell development. MARbeta, a matrix-associated region (MAR) located upstream of the T cell receptor beta (TCRbeta) enhancer (Ebeta), serves a crucial role in silencing Ebeta-mediated TCR activation. By DNaseI hyperse...

journal_title：Nucleic acids research

authors： Kaul-Ghanekar R,Jalota A,Pavithra L,Tucker P,Chattopadhyay S

更新日期：2004-09-15 00:00:00

abstract：:We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...

journal_title：Nucleic acids research

authors： Stanke M,Steinkamp R,Waack S,Morgenstern B

更新日期：2004-07-01 00:00:00

abstract：:The intrinsic stiffness of DNA limits its ability to be bent and twisted over short lengths, but such deformations are required for gene regulation. One classic paradigm is DNA looping in the regulation of the Escherichia coli lac operon. Lac repressor protein binds simultaneously to two operator sequences flanking th...

journal_title：Nucleic acids research

authors： Becker NA,Kahn JD,Maher LJ 3rd

更新日期：2007-01-01 00:00:00

abstract：:Hexokinase 2 is an essential factor for signalling repression through the Saccharomyces cerevisiae high-glucose sensing pathway. The main regulatory mechanism that controls the HXK2 gene expression in yeast is mediated by the Rgt1 and Med8 transcription factors, which repress HXK2 expression in low-glucose containing ...

journal_title：Nucleic acids research

authors： Palomino A,Herrero P,Moreno F

更新日期：2006-03-09 00:00:00

abstract：:Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown struct...

journal_title：Nucleic acids research

authors： Terribilini M,Sander JD,Lee JH,Zaback P,Jernigan RL,Honavar V,Dobbs D

更新日期：2007-07-01 00:00:00

abstract：:The oncogenic transformation of normal cells into malignant, rapidly proliferating cells requires major alterations in cell physiology. For example, the transformed cells remodel their metabolic processes to supply the additional demand for cellular building blocks. We have recently demonstrated essential metabolic pr...

journal_title：Nucleic acids research

authors： Shaul YD,Yuan B,Thiru P,Nutter-Upham A,McCallum S,Lanzkron C,Bell GW,Sabatini DM

更新日期：2016-01-04 00:00:00

abstract：:SMILE (small heterodimer partner interacting leucine zipper protein) has been identified as a coregulator in ER signaling. In this study, we have examined the effects of SMILE on other NRs (nuclear receptors). SMILE inhibits GR, CAR and HNF4 alpha-mediated transactivation. Knockdown of SMILE gene expression increases ...

journal_title：Nucleic acids research

authors： Xie YB,Nedumaran B,Choi HS

更新日期：2009-07-01 00:00:00

abstract：:Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formatio...

journal_title：Nucleic acids research

authors： Casar Tena T,Maerz LD,Szafranski K,Groth M,Blätte TJ,Donow C,Matysik S,Walther P,Jeggo PA,Burkhalter MD,Philipp M

更新日期：2019-01-10 00:00:00

abstract：:Translin is a single-stranded RNA- and DNA-binding protein, which has been highly conserved in eukaryotes, from man to Schizosaccharomyces pombe. TRAX is a Translin paralog associated with Translin, which has coevolved with it. We generated structural models of the S. pombe Translin (spTranslin), based on the solved 3...

journal_title：Nucleic acids research

authors： Eliahoo E,Ben Yosef R,Pérez-Cano L,Fernández-Recio J,Glaser F,Manor H

更新日期：2010-05-01 00:00:00

abstract：:Thermophilic viruses represent a novel source of genetic material and enzymes with great potential for use in biotechnology. We have isolated a number of thermophilic viruses from geothermal areas in Iceland, and by combining high throughput genome sequencing and state of the art bioinformatics we have identified a nu...

journal_title：Nucleic acids research

authors： Blondal T,Hjorleifsdottir SH,Fridjonsson OF,Aevarsson A,Skirnisdottir S,Hermannsdottir AG,Hreggvidsson GO,Smith AV,Kristjansson JK

更新日期：2003-12-15 00:00:00

abstract：:The metazoan cell cycle-regulated histone mRNAs are the only known cellular mRNAs that do not terminate in a poly(A) tall. Instead, mammalian histone mRNAs terminate in a highly conserved stem-loop structure which is required for 3'-end processing and regulates mRNA stability. The poly(A) tail not only regulates trans...

journal_title：Nucleic acids research

authors： Gallie DR,Lewis NJ,Marzluff WF

更新日期：1996-05-15 00:00:00

abstract：:In 4M NaCl solutions (dC-dG)n (n = 3,4; approximately 9 mM) exist as a mixture o +/- B and Z forms. The low and high field components of two 31P NMR resonances originating from internal phosphodiester groups are assigned to the GpC and CpG linkages, respectively. Low temperatures stabilize the Z-forms, which completel...

journal_title：Nucleic acids research

authors： Holak TA,Borer PN,Levy GC,van Boom JH,Wang AH

更新日期：1984-06-11 00:00:00

abstract：:Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts th...

journal_title：Nucleic acids research

authors： Wang J,Lunyak VV,Jordan IK

更新日期：2012-01-01 00:00:00

abstract：:Homing endonucleases recognize long target DNA sequences generating an accurate double-strand break that promotes gene targeting through homologous recombination. We have modified the homodimeric I-CreI endonuclease through protein engineering to target a specific DNA sequence within the human RAG1 gene. Mutations in ...

journal_title：Nucleic acids research

authors： Muñoz IG,Prieto J,Subramanian S,Coloma J,Redondo P,Villate M,Merino N,Marenchino M,D'Abramo M,Gervasio FL,Grizot S,Daboussi F,Smith J,Chion-Sotinel I,Pâques F,Duchateau P,Alibés A,Stricher F,Serrano L,Blanco FJ,Mo

更新日期：2011-01-01 00:00:00

abstract：:The three CD3 genes on human chromosome 11q23 encode proteins (gamma, delta and epsilon) which form part of the antigen receptor on T lymphocytes. All three genes are clustered within 50 kb and are activated approximately contemporaneously during the early stages of T cell ontogeny. In order to pinpoint potential regu...

journal_title：Nucleic acids research

authors： Tunnacliffe A

更新日期：1990-02-11 00:00:00

abstract：:Serine integrases are emerging as core tools in synthetic biology and have applications in biotechnology and genome engineering. We have designed a split-intein serine integrase-based system with potential for regulation of site-specific recombination events at the protein level in vivo. The ϕC31 integrase was split i...

journal_title：Nucleic acids research

authors： Olorunniji FJ,Lawson-Williams M,McPherson AL,Paget JE,Stark WM,Rosser SJ

更新日期：2019-12-02 00:00:00

abstract：:Thyroglobulin (Tg), the precursor of thyroid hormones, is a 660.000 Da dimeric glycoprotein synthesized exclusively in the thyroid gland. We have cloned the human thyroglobulin gene from cosmid and phage libraries and constructed a complete restriction map. The gene encodes an 8.7 kb mRNA, covers at least 300 kb DNA a...

journal_title：Nucleic acids research

authors： Baas F,van Ommen GJ,Bikker H,Arnberg AC,de Vijlder JJ

更新日期：1986-07-11 00:00:00

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：:The rDNA cluster in Saccharomyces cerevisiae is located 450 kb from the left end and 610 kb from the right end of chromosome XII and consists of approximately 150 tandemly repeated copies of a 9.1 kb rDNA unit. To explore the biological significance of this specific chromosomal context, chromosome XII was split at bot...

journal_title：Nucleic acids research

authors： Kim YH,Ishikawa D,Ha HP,Sugiyama M,Kaneko Y,Harashima S

更新日期：2006-05-31 00:00:00

abstract：:DNA3'pp5'G caps synthesized by the 3'-PO4/5'-OH ligase RtcB have a strong impact on enzymatic reactions at DNA 3'-OH ends. Aprataxin, an enzyme that repairs A5'pp5'DNA ends formed during abortive ligation by classic 3'-OH/5'-PO4 ligases, is also a DNA 3' de-capping enzyme, converting DNAppG to DNA3'p and GMP. By takin...

journal_title：Nucleic acids research

authors： Chauleau M,Jacewicz A,Shuman S

更新日期：2015-07-13 00:00:00

abstract：:Infection of cultured cells with herpes simplex virus (HSV) results in the transcriptional induction of a small number of cellular genes. Although the majority of such genes are dependent upon viral protein synthesis for their induction, a small minority are not. These genes are induced by events occurring prior to th...

journal_title：Nucleic acids research

authors： Kemp LM,Preston CM,Preston VG,Latchman DS

更新日期：1986-12-09 00:00:00

abstract：:The human gene for plasminogen activator inhibitor type-1 (PAI-1) has been isolated and its promoter region characterized. PAI-1 regulation by glucocorticoids, transforming growth factor-beta (TGF-beta) and the phorbol ester PMA is shown to be exerted at the promoter level. A fragment spanning 805 nucleotides of the 5...

journal_title：Nucleic acids research

authors： Riccio A,Lund LR,Sartorio R,Lania A,Andreasen PA,Danø K,Blasi F

更新日期：1988-04-11 00:00:00

abstract：:A series of unusual folding regions (UFR) immediately 3' to the cleavage site of the outer membrane protein (OMP) and transmembrane protein (TMP) were detected in the envelope gene RNA of the human immunodeficiency virus (HIV-1, HIV-2) and simian immunodeficiency virus (SIV) by an extensive Monte Carlo simulation. The...

journal_title：Nucleic acids research

authors： Le SY,Malim MH,Cullen BR,Maizel JV

更新日期：1990-03-25 00:00:00

abstract：:Spliceosomes are assembled in stages. The first stage forms complex E, which is characterized by the presence of U1 snRNPs base-paired to the 5' splice site, components recognizing the 3' splice site and proteins thought to connect them. The splice sites are held in close proximity and the pre-mRNA is committed to spl...

journal_title：Nucleic acids research

authors： Hodson MJ,Hudson AJ,Cherny D,Eperon IC

更新日期：2012-08-01 00:00:00

abstract：:PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...

journal_title：Nucleic acids research

authors： Jendele L,Krivak R,Skoda P,Novotny M,Hoksza D

更新日期：2019-07-02 00:00:00

abstract：:Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonom...

journal_title：Nucleic acids research

authors： Kautsar SA,Blin K,Shaw S,Weber T,Medema MH

更新日期：2021-01-08 00:00:00

abstract：:Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what types of complex mutation occur, and we cannot routinely characterize arbitrarily-complex mutations in a high-throughput, genome-wide manner. Long-read DNA sequencing m...

journal_title：Nucleic acids research

authors： Frith MC,Khan S

更新日期：2018-02-28 00:00:00

abstract：:Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nanodevice applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mecha...

journal_title：Nucleic acids research

authors： Li X,Peng Y,Qu X

更新日期：2006-08-02 00:00:00

abstract：:The chemical shifts of the well-resolved ring nitrogen protons of uracil and a series of substituted uracils, including pseudouridine (5-ribosyl-uracil) and uridine (1-ribosyl-uracil) were determined using nuclear magnetic resonance (NMR). The observed chemical shifts suggest the existence of an atypical syn conformat...

journal_title：Nucleic acids research

authors： Hurd RE,Reid BR

更新日期：1977-08-01 00:00:00