Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease.

abstract：:The mitochondrial DNA (mtDNA) control regions for common chimpanzee, pygmy chimpanzee and gorilla were sequenced and the lengths and termini of their D-loop DNA's characterized. In these and all other species for which there are data, 5' termini map to sequences that contain the trinucleotide YAY. 3' termini are 25-51...

journal_title：Nucleic acids research

authors： Foran DR,Hixson JE,Brown WM

更新日期：1988-07-11 00:00:00

abstract：:Mutations in mammalian and Drosophila Hel308 and PolQ paralogues cause genome instability but their helicase functions are mysterious. By in vivo and in vitro analysis, we show that Hel308 from archaea (Hel308a) may act at stalled replication forks. Introducing hel308a into Escherichia coli dnaE strains that condition...

journal_title：Nucleic acids research

authors： Guy CP,Bolt EL

更新日期：2005-06-30 00:00:00

abstract：:Non-selenocysteine-containing phospholipid hydroperoxide glutathione peroxidase (NPGPx or GPx7) is an oxidative stress sensor that modulates the antioxidative activity of its target proteins through intermolecular disulfide bond formation. Given NPGPx's role in protecting cells from oxidative damage, identification of...

journal_title：Nucleic acids research

authors： Chen PJ,Weng JY,Hsu PH,Shew JY,Huang YS,Lee WH

更新日期：2015-10-30 00:00:00

abstract：:Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA's 5'-terminal 'cap'. The minimal 'cap0' consists of N7-methylguanosine linked to the first nucleotide via a 5'-5' triphosphate (ppp) bridge. Cap0 is further modified by 2'-O-methylation of the next two riboses, yielding 'cap1' (m7GpppNmN) ...

journal_title：Nucleic acids research

authors： Kumar P,Sweeney TR,Skabkin MA,Skabkina OV,Hellen CU,Pestova TV

更新日期：2014-03-01 00:00:00

abstract：:Most type II restriction-modification (R-M) systems produce separate endonuclease (REase) and methyltransferase (MTase) proteins. After R-M genes enter a new cell, MTase activity must appear before REase or the host chromosome will be cleaved. Temporal control of these genes thus has life-or-death consequences. PvuII ...

journal_title：Nucleic acids research

authors： Mruk I,Blumenthal RM

更新日期：2009-02-01 00:00:00

abstract：:We have sequenced the external transcribed spacer (ETS) of a ribosomal transcription unit from Xenopus laevis, together with sections of the preceding non-transcribed spacer. Our analysis was carried out on the same cloned transcription unit as that from which the internal transcribed spacers (ITS) were previously seq...

journal_title：Nucleic acids research

authors： Maden BE,Moss M,Salim M

更新日期：1982-04-10 00:00:00

abstract：:The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. We have synthesized a phosphoramidite building block of a cis-syn cyclobutane thymine-uracil dimer (T[]U), which is the deaminat...

journal_title：Nucleic acids research

authors： Takasawa K,Masutani C,Hanaoka F,Iwai S

更新日期：2004-03-12 00:00:00

abstract：:Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom availa...

journal_title：Nucleic acids research

authors： Azad RN,Zafiropoulos D,Ober D,Jiang Y,Chiu TP,Sagendorf JM,Rohs R,Tullius TD

更新日期：2018-03-16 00:00:00

abstract：:We recently compared the efficiency of six picornaviral internal ribosome entry segments (IRESes) and the hepatitis C virus (HCV) IRES for their ability to drive internal initiation of translationin vitro. Here we present the results of a similar comparison performed in six different cultured cell lines infected with ...

journal_title：Nucleic acids research

authors： Borman AM,Le Mercier P,Girard M,Kean KM

更新日期：1997-03-01 00:00:00

abstract：:Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algo...

journal_title：Nucleic acids research

authors： Pitt JN,Rajapakse I,Ferré-D'Amaré AR

更新日期：2010-12-01 00:00:00

abstract：:The identification of genes with specific patterns of change (e.g. down-regulated and methylated) as phenotype drivers or samples with similar profiles for a given gene set as drivers of clinical outcome, requires the integration of several genomic data types for which an 'integrate by intersection' (IBI) approach is ...

journal_title：Nucleic acids research

authors： Kowalski J,Dwivedi B,Newman S,Switchenko JM,Pauly R,Gutman DA,Arora J,Gandhi K,Ainslie K,Doho G,Qin Z,Moreno CS,Rossi MR,Vertino PM,Lonial S,Bernal-Mizrachi L,Boise LH

更新日期：2016-04-20 00:00:00

abstract：:We have investigated the mechanism of the electrophoresis-driven chromatin aggregation which had been described by Weintraub (1984, Cell 38, 17-27) as a putative mean for propagation of genetic repression in eukaryotes. We show that the oligonucleosome aggregates are assembled de novo at the starting zone of DNP elect...

journal_title：Nucleic acids research

authors： Grigoryev SA,Spirin KS,Krasheninnikov IA

更新日期：1990-12-25 00:00:00

abstract：:Gene trap vectors developed for genome-wide mutagenesis can be used to study factors governing the expression of exons inserted throughout the genome. For example, entrapment vectors consisting of a partial 3'-terminal exon [i.e. a neomycin resistance gene (Neo), a poly(A) site, but no 3' splice site] were typically e...

journal_title：Nucleic acids research

authors： Osipovich AB,White-Grindley EK,Hicks GG,Roshon MJ,Shaffer C,Moore JH,Ruley HE

更新日期：2004-05-20 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：:Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNA...

journal_title：Nucleic acids research

authors： Browner MF,Lawrence CB

更新日期：1985-12-09 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：:Aryldiazonium salts are shown to be useful as phototriggered structural probes for RNA mapping as well as for footprinting of RNA/protein interaction. In particular the yeast tRNA(Asp)/aspartyl-tRNA synthetase complex is shown to involve the variable loop face and the concave side of the L-shaped nucleic acid bound to...

journal_title：Nucleic acids research

authors： Garcia A,Giegé R,Behr JP

更新日期：1990-01-11 00:00:00

abstract：:The Human Gene and Protein Database (HGPD; http://www.HGPD.jp/) is a unique database that stores information on a set of human Gateway entry clones in addition to protein expression and protein synthesis data. The HGPD was launched in November 2008, and 33,275 human Gateway entry clones have been constructed from the ...

journal_title：Nucleic acids research

authors： Maruyama Y,Kawamura Y,Nishikawa T,Isogai T,Nomura N,Goshima N

更新日期：2012-01-01 00:00:00

abstract：:U1 snRNP plays a crucial role in the 5' splice site recognition during splicing. Here we report the first example of naturally occurring U1-independent U2-type splicing in humans. The U1 components were not included in the pre-spliceosomal E complex formed on the human F1gamma (hF1gamma) intron 9 in vitro. Moreover, h...

journal_title：Nucleic acids research

authors： Fukumura K,Taniguchi I,Sakamoto H,Ohno M,Inoue K

更新日期：2009-04-01 00:00:00

abstract：:Yeast two-hybrid (Y2H) screenings result in identification of many out-of-frame (OOF) clones that code for short (2-100 amino acids) peptides with no sequence homology to known proteins. We hypothesize that these peptides can reveal common short linear motifs (SLiMs) responsible for their selection. We present a new p...

journal_title：Nucleic acids research

authors： Liu Y,Woods NT,Kim D,Sweet M,Monteiro AN,Karchin R

更新日期：2011-10-01 00:00:00

abstract：:The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...

journal_title：Nucleic acids research

authors： Karp PD,Riley M,Paley SM,Pellegrini-Toole A,Krummenacker M

更新日期：1999-01-01 00:00:00

abstract：:Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of...

journal_title：Nucleic acids research

authors： Li Y,Hao P,Zheng S,Tu K,Fan H,Zhu R,Ding G,Dong C,Wang C,Li X,Thiesen HJ,Chen YE,Jiang H,Liu L,Li Y

更新日期：2008-11-01 00:00:00

abstract：:We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...

journal_title：Nucleic acids research

authors： Tsukahara T,Casciato C,Helfman DM

更新日期：1994-06-25 00:00:00

abstract：:The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.c...

journal_title：Nucleic acids research

authors： Carter P,Andersen CA,Rost B

更新日期：2003-07-01 00:00:00

abstract：:Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their circularity as well as biochemically enrich these transcripts, it has become standard in the field to use the 3'-5' exonuclease RNase R. Here, we demonst...

journal_title：Nucleic acids research

authors： Xiao MS,Wilusz JE

更新日期：2019-09-19 00:00:00

abstract：:The proportion of cytosines methylated in the DNA of nucleosome oligomers and of core particles appears indistinguishable from that of total nuclear DNA from CHO cells. However the DNA in nucleoprotein which is initially released from nuclei by treatment with very low levels of micrococcal nuclease and the first 10% o...

journal_title：Nucleic acids research

authors： Adams RL,McKay EL,Douglas JT,Burdon RH

更新日期：1977-09-01 00:00:00

abstract：:PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set com...

journal_title：Nucleic acids research

authors： Balaji S,Sujatha S,Kumar SS,Srinivasan N

更新日期：2001-01-01 00:00:00

abstract：:The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences are both eukaryotic and archaeal in origin. Several new histone fold-containing proteins have been identified, includin...

journal_title：Nucleic acids research

authors： Sullivan SA,Aravind L,Makalowska I,Baxevanis AD,Landsman D

更新日期：2000-01-01 00:00:00

abstract：:The topoisomerase I (TOP1) inhibitor irinotecan triggers cell death by trapping TOP1 on DNA, generating cytotoxic protein-linked DNA breaks (PDBs). Despite its wide application in a variety of solid tumors, the mechanisms of cancer cell resistance to irinotecan remains poorly understood. Here, we generated colorectal ...

journal_title：Nucleic acids research

authors： Meisenberg C,Ashour ME,El-Shafie L,Liao C,Hodgson A,Pilborough A,Khurram SA,Downs JA,Ward SE,El-Khamisy SF

更新日期：2017-02-17 00:00:00

abstract：:A cDNA encoding the 60 kDa subunit of mammalian splicing factor SF3a has been isolated. The deduced protein sequence reveals a 30% identity to the PRP9 splicing protein of the yeast S.cerevisiae. The highest homology is present in a zinc finger-like region in the C-terminal domain of both proteins. The PRP9 zinc finge...

journal_title：Nucleic acids research

authors： Krämer A,Legrain P,Mulhauser F,Gröning K,Brosi R,Bilbe G

更新日期：1994-12-11 00:00:00