Open complex formation during transcription initiation at the Escherichia coli galP1 promoter: the role of the RNA polymerase alpha subunit at promoters lacking an UP-element.

abstract：:A search of sequence information in the GenBank files shows that tracts of 15-30 contiguous purines are greatly overrepresented in all eukaryotic species examined, ranging from yeast to human. Such an overabundance does not occur in prokaryotic sequences. The large increase in the number of oligopurine tracts cannot b...

journal_title：Nucleic acids research

authors： Behe MJ

更新日期：1995-02-25 00:00:00

abstract：:We describe the unique features of an aberrantly rearranged mu immunoglobulin heavy chain gene isolated from MPC-11 cells (a gamma 2b producing Balb/c plasmacytoma). A novel rearrangement has occurred 1.5 Kb 5' of the MPC-11 mu gene (denoted 18b mu) resulting in the deletion of the majority of the repetitive switch re...

journal_title：Nucleic acids research

authors： Greenberg R,Lang RB,Diamond MS,Marcu KB

更新日期：1982-12-11 00:00:00

abstract：:Many lists containing biological identifiers, such as gene lists, have been generated in various genomics projects. Identifying the overlap among gene lists can enable us to understand the similarities and differences between the data sets. Here, we present an interactome network-based web application platform named N...

journal_title：Nucleic acids research

authors： Wang Y,Thilmony R,Gu YQ

更新日期：2014-07-01 00:00:00

abstract：:RBD-1 is the Caenorhabditis elegans homolog of Mrd1p, which was recently shown to be required for 18S ribosomal RNA (rRNA) processing in yeast. To gain insights into the relationship between ribosome biogenesis and the development of multicellular organisms, we examined the expression and function of RBD-1. Maternal R...

journal_title：Nucleic acids research

authors： Saijou E,Fujiwara T,Suzaki T,Inoue K,Sakamoto H

更新日期：2004-02-10 00:00:00

abstract：:Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the repl...

journal_title：Nucleic acids research

authors： Spenkelink LM,Lewis JS,Jergic S,Xu ZQ,Robinson A,Dixon NE,van Oijen AM

更新日期：2019-05-07 00:00:00

abstract：:We have formed complexes of relaxed closed circular Col E1 DNA with various combinations of histones, and examined the effects of treating the complexes with nicking-closing enzyme. Germond et al (1) have shown that when a mixture of the four core histones of the nucleosome (HIA, H2B, H3 and H4) is used in such an exp...

journal_title：Nucleic acids research

authors： Camerini-Otero RD,Felsenfeld G

更新日期：1977-01-01 00:00:00

abstract：:Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets with a methyl thioether group (-SCH(3)). Members of two of the four known subgroups of MTTases...

journal_title：Nucleic acids research

authors： Anton BP,Russell SP,Vertrees J,Kasif S,Raleigh EA,Limbach PA,Roberts RJ

更新日期：2010-10-01 00:00:00

abstract：:A high molecular weight reticulocyte protein factor, named Co-eIF-2, contains Co-eIF-2A, Co-eIF-2B, and Co-eIF-2C activities and stimulates Met-tRNAf binding to eIF-2 both in the presence and absence of Mg2+. Some characteristics of this stimulation in the absence of Mg2+ are: (1) Stimulation is most pronounced at low...

journal_title：Nucleic acids research

authors： Bagchi MK,Banerjee AC,Roy R,Chakrabarty I,Gupta NK

更新日期：1982-10-25 00:00:00

abstract：:During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication i...

journal_title：Nucleic acids research

authors： Newman TJ,Mamun MA,Nieduszynski CA,Blow JJ

更新日期：2013-11-01 00:00:00

abstract：:Rad54 protein is a key member of the RAD52 epistasis group required for homologous recombination in eukaryotes. Rad54 is a duplex DNA translocase that remodels both DNA and protein-DNA complexes, and functions at multiple steps in the recombination process. Here we use biochemical criteria to demonstrate the existence...

journal_title：Nucleic acids research

authors： Haseltine CA,Kowalczykowski SC

更新日期：2009-05-01 00:00:00

abstract：:Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5'-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcr...

journal_title：Nucleic acids research

authors： Eggenhofer F,Tafer H,Stadler PF,Hofacker IL

更新日期：2011-07-01 00:00:00

abstract：:Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently av...

journal_title：Nucleic acids research

authors： Cahan P,Godfrey LE,Eis PS,Richmond TA,Selzer RR,Brent M,McLeod HL,Ley TJ,Graubert TA

更新日期：2008-04-01 00:00:00

abstract：:The GeneSpeed database (http://genespeed.uchsc.edu/) is an online database and resource tool facilitating the detailed study of protein domain homology in the transcriptomes of Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. The population schema for the GeneSpeed database takes advanta...

journal_title：Nucleic acids research

authors： Kutchma A,Quayum N,Jensen J

更新日期：2007-01-01 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：:A 34 base-pair (bp) fragment spanning sequences -154 to -120 of the promoter of the CHO1 gene (structural gene for phosphatidylserine synthase) from the yeast Saccharomyces cerevisiae has been shown to place transcription of a promoter-less Escherichia coli lacZ gene under control of the phospholipid precursors inosit...

journal_title：Nucleic acids research

authors： Bailis AM,Lopes JM,Kohlwein SD,Henry SA

更新日期：1992-03-25 00:00:00

abstract：:Message-specific translational regulation mechanisms shape the biogenesis of multimeric oxidative phosphorylation (OXPHOS) enzyme in mitochondria from the yeast Saccharomyces cerevisiae. These mechanisms, driven mainly by the action of mRNA-specific translational activators, help to coordinate synthesis of OXPHOS cata...

journal_title：Nucleic acids research

authors： Mays JN,Camacho-Villasana Y,Garcia-Villegas R,Perez-Martinez X,Barrientos A,Fontanesi F

更新日期：2019-06-20 00:00:00

abstract：:Re-sequencing, the identification of the specific variants in a sequence of interest compared with a known genomic sequence, is a ubiquitous task in today's biology. Universal arrays, which interrogate all possible oligonucleotides of a certain length in a target sequence, have been suggested for computationally deter...

journal_title：Nucleic acids research

authors： Pe'er I,Arbili N,Liu Y,Enck C,Gelfand CA,Shamir R

更新日期：2003-10-01 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：: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：:UHRF1 plays multiple roles in regulating DNMT1-mediated DNA methylation maintenance during DNA replication. The UHRF1 C-terminal RING finger functions as an ubiquitin E3 ligase to establish histone H3 ubiquitination at Lys18 and/or Lys23, which is subsequently recognized by DNMT1 to promote its localization onto repli...

journal_title：Nucleic acids research

authors： Li T,Wang L,Du Y,Xie S,Yang X,Lian F,Zhou Z,Qian C

更新日期：2018-04-06 00:00:00

abstract：:The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the...

journal_title：Nucleic acids research

authors： Galata V,Fehlmann T,Backes C,Keller A

更新日期：2019-01-08 00:00:00

abstract：:Segments of SV40 DNA having homologous overlapping termini recombine to produce viable genomes in monkey cells. Frequencies of recombination on either side of a deletion marker are non-random; replication and palindromes do not appear to be essential. Since recombination involves host enzymes, a suitable system has be...

journal_title：Nucleic acids research

authors： Upcroft P,Carter B,Kidson C

更新日期：1980-06-25 00:00:00

abstract：:We have sequenced the Escherichia coli grpE gene and shown that it encodes a 197-amino acid residue protein of 21,668-Mr. The predicted N-terminal amino acid sequence, as well as the overall amino acid composition agree well with that of the purified protein. From Northern analysis, we have shown that transcription of...

journal_title：Nucleic acids research

authors： Lipinska B,King J,Ang D,Georgopoulos C

更新日期：1988-08-11 00:00:00

abstract：:A computer program has been developed which aids in the determination of restriction enzyme recognition sequences. This is achieved by cleaving DNAs of known sequence with a restriction endonuclease and comparing the fragmentation pattern with a computer-generated set of patterns. The feasibility of this approach has ...

journal_title：Nucleic acids research

authors： Gingeras TR,MIlazzo JP,Roberts RJ

更新日期：1978-11-01 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：:Beta-thalassemia is a genetic disorder caused by mutations in the beta-globin gene. Triplex-forming oligonucleotides and triplex-forming peptide nucleic acids (PNAs) have been shown to stimulate recombination in mammalian cells via site-specific binding and creation of altered helical structures that provoke DNA repai...

journal_title：Nucleic acids research

authors： Lonkar P,Kim KH,Kuan JY,Chin JY,Rogers FA,Knauert MP,Kole R,Nielsen PE,Glazer PM

更新日期：2009-06-01 00:00:00

abstract：:Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translato...

journal_title：Nucleic acids research

authors： Liu W,Xiang L,Zheng T,Jin J,Zhang G

更新日期：2018-01-04 00:00:00

abstract：:Prokaryotes evolved numerous systems that defend against predation by bacteriophages. In addition to well-known restriction-modification and CRISPR-Cas immunity systems, many poorly characterized systems exist. One class of such systems, named BREX, consists of a putative phosphatase, a methyltransferase and four othe...

journal_title：Nucleic acids research

authors： Gordeeva J,Morozova N,Sierro N,Isaev A,Sinkunas T,Tsvetkova K,Matlashov M,Truncaite L,Morgan RD,Ivanov NV,Siksnys V,Zeng L,Severinov K

更新日期：2019-01-10 00:00:00

abstract：:PCAF and hGCN5 are distinct human genes that encode proteins related to the yeast histone acetyltransferase and transcriptional adapter GCN5. The PCAF protein shares extensive similarity with the 439 amino acids of yGCN5, but it has an approximately 350 amino acid N-terminal extension that interacts with the transcrip...

journal_title：Nucleic acids research

authors： Smith ER,Belote JM,Schiltz RL,Yang XJ,Moore PA,Berger SL,Nakatani Y,Allis CD

更新日期：1998-06-15 00:00:00

abstract：:Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on ...

journal_title：Nucleic acids research

authors： Mount DW,Conrad B

更新日期：1984-01-11 00:00:00