Gene-regulatory interactions in embryonic stem cells represent cell-type specific gene regulatory programs.

abstract：:Genomic DNA methylation profiles exhibit substantial variation within the human population, with important functional implications for gene regulation. So far little is known about the characteristics and determinants of DNA methylation variation among healthy individuals. We performed bioinformatic analysis of high-r...

journal_title：Nucleic acids research

authors： Bock C,Walter J,Paulsen M,Lengauer T

更新日期：2008-06-01 00:00:00

abstract：:PKR is a doubled-stranded RNA-dependent protein kinase which is implicated in the regulation of several cellular processes, including cell proliferation. PKR undergoes phosphorylation and activation in mouse embryonic 3T3-F442A cells in response to endogenous RNA(s). Activation of PKR is related to growth and differen...

journal_title：Nucleic acids research

authors： Petryshyn RA,Ferrenz AG,Li J

更新日期：1997-07-01 00:00:00

abstract：:The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on ...

journal_title：Nucleic acids research

authors： Kogure H,Handa Y,Nagata M,Kanai N,Güntert P,Kubota K,Nameki N

更新日期：2014-03-01 00:00:00

abstract：:Xenopus laevis 5S rRNA isolated from 7S particles or transcribed in vitro is found to adopt two alternative conformations. These two conformers contain different structural elements within the major TF III A binding domain, which, when isolated as RNA fragments, still interact with the transcription factor. Chemical m...

journal_title：Nucleic acids research

authors： Pieler T,Guddat U,Oei SL,Erdmann VA

更新日期：1986-08-11 00:00:00

abstract：:2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-cont...

journal_title：Nucleic acids research

authors： Sochacka E,Szczepanowski RH,Cypryk M,Sobczak M,Janicka M,Kraszewska K,Bartos P,Chwialkowska A,Nawrot B

更新日期：2015-03-11 00:00:00

abstract：:A small cloned DNA segment previously shown to contain all genetic information for the expression of the tRNA1met gene of Xenopus laevis was cleaved into an anterior and posterior portion by Hae III restriction. Both restriction fragments were cloned in pCR1 using EcoRI linkers. Starting from these tDNA subclones, a s...

journal_title：Nucleic acids research

authors： Kressmann A,Hofstetter H,Di Capua E,Grosschedl R,Birnstiel ML

更新日期：1979-12-11 00:00:00

abstract：:The titration viscometric investigation of the multi-mode interaction of netropsin (Nt) with (A.T) clusters of NaDNA12 and NH4DNA10 has been extended to different temperatures. The position of two boundaries on the r-scale (r= [Nt]bound/[DNA-P]) with increasing temperature steadily (rI/II) or more abruptly (rO/I) shif...

journal_title：Nucleic acids research

authors： Reinert KE,Geller D,Stutter E

更新日期：1981-05-25 00:00:00

abstract：:The DNA photosensitisers m-iodo Hoechst and m-iodo, p-methoxy Hoechst have been co-crystallised with the oligonucleotide d(CGCGAATTCGCG)(2)and their crystal structures determined. The crystals were then subjected to slow dehydration, which reduced their solvent contents from 40 (normal) to 30 (partially dehydrated) an...

journal_title：Nucleic acids research

authors： Squire CJ,Baker LJ,Clark GR,Martin RF,White J

更新日期：2000-03-01 00:00:00

abstract：:The loss of the tumour suppressor E-cadherin (Cdh1) is a key event during tumourigenesis and epithelial-mesenchymal transition (EMT). Transforming growth factor-β (TGFβ) triggers EMT by inducing the expression of non-histone chromatin protein High Mobility Group A2 (HMGA2). We have previously shown that HMGA2, togethe...

journal_title：Nucleic acids research

authors： Tan EJ,Kahata K,Idås O,Thuault S,Heldin CH,Moustakas A

更新日期：2015-01-01 00:00:00

abstract：:A single base change in 16S rRNA (C726 to G) has previously been shown to have a dramatic effect on protein synthesis in E. coli (1). This paper more specifically details the effects of the mutation on mRNA binding and translation-termination. The in vitro technique of toeprinting (2) was used to demonstrate that 30S ...

journal_title：Nucleic acids research

authors： Prescott CD,Göringer HU

更新日期：1990-09-25 00:00:00

abstract：:Initiation of σ(54)-dependent transcription requires assistance to melt DNA at the promoter site but is impeded by numerous protein-protein and nucleo-protein interactions. To alleviate these inhibitory interactions, hexameric bacterial enhancer binding proteins (bEBP), a subset of the ATPases associated with various ...

journal_title：Nucleic acids research

authors： Zhang N,Joly N,Buck M

更新日期：2012-10-01 00:00:00

abstract：:Prostatic steroid binding protein, whose expression is stimulated by androgens, consists of two subunits: one containing the polypeptides C1 and C3 and the other containing C2 and C3. We have characterised genomic clones containing the C1 and C2 genes by restriction enzyme analysis and DNA sequencing. Both genes are 3...

journal_title：Nucleic acids research

authors： Parker M,Needham M,White R,Hurst H,Page M

更新日期：1982-09-11 00:00:00

abstract：:We have identified cDNAs encoding Mel-N1, the mouse homologue of a human nervous system-specific RNA-binding protein, Hel-N1. Two major mRNA transcripts of Mel-N1 were detected predominantly in the adult mouse brain by Northern blot analysis. To gain insight into the RNA binding specificity of Mel-N1, we performed ite...

journal_title：Nucleic acids research

authors： Abe R,Yamamoto K,Sakamoto H

更新日期：1996-06-01 00:00:00

abstract：:The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main nove...

journal_title：Nucleic acids research

authors： Floden EW,Tommaso PD,Chatzou M,Magis C,Notredame C,Chang JM

更新日期：2016-07-08 00:00:00

abstract：:Insertion of microRNA target sequences into the flavivirus genome results in selective tissue-specific attenuation and host-range restriction of live attenuated vaccine viruses. However, previous strategies for miRNA-targeting did not incorporate a mechanism to prevent target elimination under miRNA-mediated selective...

journal_title：Nucleic acids research

authors： Tsetsarkin KA,Liu G,Shen K,Pletnev AG

更新日期：2016-04-20 00:00:00

abstract：:Ribosomal RNA (rRNA) in intact ribosomes is cleaved into discrete products on incubation of reticulocyte lysates or L-cell extracts with ppp(A2'p)3A. Cleavage of rRNA may, therefore, provide a useful assay for 2-5A (ppp)A2'p)nA; n = 2 to 4) or for the presence of a 2-5A-dependent nuclease. The results with reticulocyt...

journal_title：Nucleic acids research

authors： Wreschner DH,James TC,Silverman RH,Kerr IM

更新日期：1981-04-10 00:00:00

abstract：:DNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higher-order G4 structure more stable in sodium than in potassium. Repeats o...

journal_title：Nucleic acids research

authors： Saintomé C,Amrane S,Mergny JL,Alberti P

更新日期：2016-04-07 00:00:00

abstract：:We report the complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1, as 6633 base pairs of composition 79.5% G+C. This contains immediate early gene 3, encoding the IE175 protein, an important transcriptional activator of later virus genes. The IE175 coding region was identified...

journal_title：Nucleic acids research

authors： McGeoch DJ,Dolan A,Donald S,Brauer DH

更新日期：1986-02-25 00:00:00

abstract：:Adaptation of the P1 phage-derived Cre /loxP site- specific recombination system to the gene targeting technique allows for the conditional deletion of genes in mice. To selectively modify genes in B lymphocytes, we have generated mice (designated CD19-Cre) which express cre under the transcriptional control of the B ...

journal_title：Nucleic acids research

authors： Rickert RC,Roes J,Rajewsky K

更新日期：1997-03-15 00:00:00

abstract：:Previously we identified Rrp1 and Rrp2 as two proteins required for the Sfr1/Swi5-dependent branch of homologous recombination (HR) in Schizosaccharomyces pombe. Here we use a yeast two-hybrid approach to demonstrate that Rrp1 and Rrp2 can interact with each other and with Swi5, an HR mediator protein. Rrp1 and Rrp2 f...

journal_title：Nucleic acids research

authors： Dziadkowiec D,Kramarz K,Kanik K,Wisniewski P,Carr AM

更新日期：2013-09-01 00:00:00

abstract：:Resonances of the water exchangeable iminoprotons of the acceptor and D stem of yeast tRNAPhe have been assigned by means of Nuclear Overhauser Effects (NOE's). Assignments were made for spectra recorded from tRNA dialysed against a buffer with 110 mM sodium and 5 mM magnesium ions and against a buffer with 430 mM sod...

journal_title：Nucleic acids research

authors： Heerschap A,Haasnoot CA,Hilbers CW

更新日期：1982-11-11 00:00:00

abstract：:Base specificity in the interaction of ethidium with double stranded synthetic RNA homopolymers has been studied by means of spectroscopic (UV-visible absorption and fluorescence), microcalorimetric and dilatometric techniques. The results show a strong base specificity in this interaction, the association constant wi...

journal_title：Nucleic acids research

authors： Babayan Y,Manzini G,Xodo LE,Quadrifoglio F

更新日期：1987-07-24 00:00:00

abstract：:We describe conditions for producing uninterrupted expanded CTG repeats consisting of up to 2000 repeats using 29 DNA polymerase. Previously, generation of such repeats was hindered by CTG repeat instability in plasmid vectors maintained in Escherichia coli and poor in vitro ligation of CTG repeat concatemers due to s...

journal_title：Nucleic acids research

authors： Osborne RJ,Thornton CA

更新日期：2008-03-01 00:00:00

abstract：:Rotaviruses are a major cause of acute, often fatal, gastroenteritis in infants and young children world-wide. Virions contain an 11 segment double-stranded RNA genome. Little is known about the cis-acting sequences and structural elements of the viral RNAs. Using a database of 1621 full-length sequences of mammalian ...

journal_title：Nucleic acids research

authors： Li W,Manktelow E,von Kirchbach JC,Gog JR,Desselberger U,Lever AM

更新日期：2010-11-01 00:00:00

abstract：:HBV genotypes differ in pathogenicity. In addition, genotype-specific differences in the regulation of transcription and virus replication exist in HBV, but the underlying mechanisms are unknown. Here, we show the presence of a G-quadruplex motif in the promoter of the preS2/S gene; this G-quadruplex is highly conserv...

journal_title：Nucleic acids research

authors： Biswas B,Kandpal M,Vivekanandan P

更新日期：2017-11-02 00:00:00

abstract：:The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here P...

journal_title：Nucleic acids research

authors： Hernández-de-Diego R,Tarazona S,Martínez-Mira C,Balzano-Nogueira L,Furió-Tarí P,Pappas GJ Jr,Conesa A

更新日期：2018-07-02 00:00:00

abstract：:Single-stranded guanosine-rich oligodeoxyribonucleotides (GROs) have a propensity to form quadruplex structures that are stabilized by G-quartets. In addition to intense speculation about the role of G-quartet formation in vivo, there is considerable interest in the therapeutic potential of quadruplex oligonucleotides...

journal_title：Nucleic acids research

authors： Dapić V,Abdomerović V,Marrington R,Peberdy J,Rodger A,Trent JO,Bates PJ

更新日期：2003-04-15 00:00:00

abstract：:TERC is an RNA component of telomerase. However, TERC is also ubiquitously expressed in most human terminally differentiated cells, which don't have telomerase activity. The function of TERC in these cells is largely unknown. Here, we report that TERC enhances the expression and secretion of inflammatory cytokines by ...

journal_title：Nucleic acids research

authors： Liu H,Yang Y,Ge Y,Liu J,Zhao Y

更新日期：2019-09-05 00:00:00

abstract：:MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and va...

journal_title：Nucleic acids research

authors： Davis IW,Leaver-Fay A,Chen VB,Block JN,Kapral GJ,Wang X,Murray LW,Arendall WB 3rd,Snoeyink J,Richardson JS,Richardson DC

更新日期：2007-07-01 00:00:00

abstract：:The class II genes of the major histocompatibility complex (MHC) encode a family of cell surface glycoproteins that present processed antigen to the T cell receptor. Class II genes are regulated coordinately, responding to both immunologic and developmental signals. Conserved sequence elements 5' to class II genes hav...

journal_title：Nucleic acids research

authors： Hasegawa SL,Sloan JH,Reith W,Mach B,Boss JM

更新日期：1991-03-25 00:00:00