Nascent RNA length dictates opposing effects of NusA on antitermination.

abstract：:Upf1 is a highly conserved RNA helicase essential for nonsense-mediated mRNA decay (NMD), an mRNA quality-control mechanism that degrades aberrant mRNAs harboring premature termination codons (PTCs). For the activation of NMD, UPF1 interacts first with a translation-terminating ribosome and then with a downstream exon...

journal_title：Nucleic acids research

authors： Shigeoka T,Kato S,Kawaichi M,Ishida Y

更新日期：2012-08-01 00:00:00

abstract：:Transcriptional repression of pathogen defense-related genes is essential for plant growth and development. Several proteins are known to be involved in the transcriptional regulation of plant defense responses. However, mechanisms by which expression of defense-related genes are regulated by repressor proteins are po...

journal_title：Nucleic acids research

authors： Kim HS,Park HC,Kim KE,Jung MS,Han HJ,Kim SH,Kwon YS,Bahk S,An J,Bae DW,Yun DJ,Kwak SS,Chung WS

更新日期：2012-10-01 00:00:00

abstract：:The study of pathogenic mitochondrial DNA mutations has, in most cases, relied on the production of transmitochondrial cybrids. Although the procedure to produce such cybrids is well established, it is laborious and cumbersome. Moreover, the mechanical enucleation procedure is inefficient and different techniques have...

journal_title：Nucleic acids research

authors： Bayona-Bafaluy MP,Manfredi G,Moraes CT

更新日期：2003-08-15 00:00:00

abstract：:Nuclear DNA from liver cells of the kangaroo rat species Dipodomysordii was fractionated and characterized with the aid of buoyant density gradients in neutral and alkaline CsCl and in Ag(+)-Cs(2)SO(4). More than one-half of the DNA was present in three density satellites, a greater proportion than in any other specie...

journal_title：Nucleic acids research

authors： Hatch FT,Mazrimas JA

更新日期：1974-04-01 00:00:00

abstract：:We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed t...

journal_title：Nucleic acids research

authors： Zhu W,Lomsadze A,Borodovsky M

更新日期：2010-07-01 00:00:00

abstract：:We have developed an improved method for photofootprinting in vivo which utilizes the thermostable DNA polymerase from T. aquaticus (Taq) in a primer extension assay. UV light is used to introduce photoproducts into the genomic DNA of intact yeast cells. The photoproducts are then detected and mapped at the nucleotide...

journal_title：Nucleic acids research

authors： Axelrod JD,Majors J

更新日期：1989-01-11 00:00:00

abstract：:RNase E is a 472-kDa homo-tetrameric essential endoribonuclease involved in RNA processing and turnover in Escherichia coli. In its N-terminal half (NTH) is the catalytic active site, as also a substrate 5'-sensor pocket that renders enzyme activity maximal on 5'-monophosphorylated RNAs. The protein's non-catalytic C-...

journal_title：Nucleic acids research

authors： Ali N,Gowrishankar J

更新日期：2020-01-24 00:00:00

abstract：:We have examined the formation of alternate strand triple-helices at the target sequence A11(TC)6.(GA)6T11 using the oligonucleotides T11(AG)6 and T11(TG)6, by DNase I footprinting. These third strands were designed so as to form parallel T.AT triplets together with antiparallel G.GC and A.AT or T.AT triplets. We find...

journal_title：Nucleic acids research

authors： Washbrook E,Fox KR

更新日期：1994-09-25 00:00:00

abstract：:The active form of Escherichia coli DNA polymerase V responsible for damage-induced mutagenesis is a multiprotein complex (UmuD'(2)C-RecA-ATP), called pol V Mut. Optimal activity of pol V Mut in vitro is observed on an SSB-coated single-stranded circular DNA template in the presence of the β/γ complex and a transactiv...

journal_title：Nucleic acids research

authors： Vaisman A,Kuban W,McDonald JP,Karata K,Yang W,Goodman MF,Woodgate R

更新日期：2012-07-01 00:00:00

abstract：:The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these ...

journal_title：Nucleic acids research

authors： Bult CJ,Eppig JT,Blake JA,Kadin JA,Richardson JE,Mouse Genome Database Group.

更新日期：2016-01-04 00:00:00

abstract：:A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...

journal_title：Nucleic acids research

authors： Reimann V,Alkhnbashi OS,Saunders SJ,Scholz I,Hein S,Backofen R,Hess WR

更新日期：2017-01-25 00:00:00

abstract：:Chromatin organization and epigenetic markers influence splicing, though the magnitudes of these effects and the mechanisms are largely unknown. Here, we demonstrate that linker histone H1.5 influences mRNA splicing. We observed that linker histone H1.5 binds DNA over splice sites of short exons in human lung fibrobla...

journal_title：Nucleic acids research

authors： Glaich O,Leader Y,Lev Maor G,Ast G

更新日期：2019-07-09 00:00:00

abstract：:Two group I introns (CpSSU.1 and CpSSU.2) that each potentially encode a protein with two copies of the LAGLI-DADG motif were identified in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene. They both belong to subgroup IA3 and represent novel insertion positions in this gene (sites 508 and 793 i...

journal_title：Nucleic acids research

authors： Turmel M,Mercier JP,Côté V,Otis C,Lemieux C

更新日期：1995-07-11 00:00:00

abstract：:Insertion of DNA containing PR, the early rightward promoter of bacteriophage lambda, is lethal to M13-derived vectors when the promoter directs transcription (using the '+' strand as template) toward the M13 origin of replication (ori). Lethality can be relieved by mutation of PR, repression of the promoter by the la...

journal_title：Nucleic acids research

authors： Brown S,Ferm J,Woody S,Gussin G

更新日期：1990-10-25 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：:We have partially purified replicating simian virus 40 (SV40) chromosomes in a form which allows continued DNA synthesis in vitro. We first prepare a soluble DNA-synthesizing system from SV40-infected monkey cells and then sediment the components through a neutral sucrose gradient of extremely low ionic strength. Repl...

journal_title：Nucleic acids research

authors： Edenberg HJ,Waqar MA,Huberman JA

更新日期：1977-09-01 00:00:00

abstract：:The nucleotide sequences of the 5S rRNAs of the oomycete water molds Saprolegnia ferax and Pythium hydnosporum and of the chytrid water molds Blastocladiella simplex and Phlyctochytrium irregulare were determined by chemical and enzymatic partial degradation of 3' and 5' end-labelled molecules, followed by gel sequenc...

journal_title：Nucleic acids research

authors： Walker WF,Doolittle WF

更新日期：1982-09-25 00:00:00

abstract：:MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online...

journal_title：Nucleic acids research

authors： Chen Y,Wang X

更新日期：2020-01-08 00:00:00

abstract：:DNA assembly allows individual DNA constructs or libraries to be assembled quickly and reliably. Most methods are either: (i) Modular, easily scalable and suitable for combinatorial assembly, but leave undesirable 'scar' sequences; or (ii) bespoke (non-modular), scarless but less suitable for construction of combinato...

journal_title：Nucleic acids research

authors： Taylor GM,Mordaka PM,Heap JT

更新日期：2019-02-20 00:00:00

abstract：:We report here the discovery of HMBP, a protein in nuclei of human T-helper lymphocytes and other human cell types, which binds with enhanced affinity to a promoter element in the HIV-1 long terminal repeat when that element is methylated at CpGs, the target site of the human DNA methyltransferase. This promoter eleme...

journal_title：Nucleic acids research

authors： Joel P,Shao W,Pratt K

更新日期：1993-12-11 00:00:00

abstract：:The yeast retrotransposon Ty encodes proteins that assemble into virus-like particles (Ty-VLPs) which can be readily purified. We have recently shown that expression of the pl protein encoded by the TYA gene of Ty is sufficient for particle formation. In this paper we show that when a heterologous coding sequence, hum...

journal_title：Nucleic acids research

authors： Malim MH,Adams SE,Gull K,Kingsman AJ,Kingsman SM

更新日期：1987-09-25 00:00:00

abstract：:Multiple myeloma, the second most frequent hematologic tumor after lymphomas, is an incurable cancer. Recent sequencing efforts have identified the ribonuclease DIS3 as one of the most frequently mutated genes in this disease. DIS3 represents the catalytic subunit of the exosome, a macromolecular complex central to th...

journal_title：Nucleic acids research

authors： Segalla S,Pivetti S,Todoerti K,Chudzik MA,Giuliani EC,Lazzaro F,Volta V,Lazarevic D,Musco G,Muzi-Falconi M,Neri A,Biffo S,Tonon G

更新日期：2015-05-26 00:00:00

abstract：:Tetrahymena thermophila mitochondrial DNA is a linear molecule with two tRNAs, large subunit beta (LSU beta) rRNA (21S rRNA) and LSU alpha rRNA (5.8S-like RNA) encoded near each terminus. The DNA sequence of approximately 550 bp of this region was determined in six species of Tetrahymena. In three species the LSU beta...

journal_title：Nucleic acids research

authors： Morin GB,Cech TR

更新日期：1988-01-11 00:00:00

abstract：:The vitamin D receptor mediates the signal of 1 alpha, 25-dihydroxyvitamin D3 by binding to vitamin D responsive elements in DNA as a homodimer or as a heterodimer composed of one vitamin D receptor subunit and one retinoid X receptor subunit. We have mapped the dimerization interfaces of the vitamin D receptor that i...

journal_title：Nucleic acids research

authors： Nishikawa J,Kitaura M,Imagawa M,Nishihara T

更新日期：1995-02-25 00:00:00

abstract：:In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adap...

journal_title：Nucleic acids research

authors： Hardigan AA,Roberts BS,Moore DE,Ramaker RC,Jones AL,Myers RM

更新日期：2019-08-22 00:00:00

abstract：:Contrary to the expectation, the Merrifield polystyrene resin, 2% cross-linked by divinylbenzene, is as efficient as the polyacrylmorpholide resin for the synthesis of polydeoxyribonucleotides using a phosphotriester method. On the Merrifield resin, the tetradecamer, dTpCpGpTpCpApApCpTpGpGpCpTpT, and the hexadecamer, ...

journal_title：Nucleic acids research

authors： Miyoshi K,Arentzen R,Huang T,Itakura K

更新日期：1980-11-25 00:00:00

abstract：:The phenotypic adjustments of Mycobacterium tuberculosis are commonly inferred from the analysis of transcript abundance. While mechanisms of transcriptional regulation have been extensively analysed in mycobacteria, little is known about mechanisms that shape the transcriptome by regulating RNA decay rates. The aim o...

journal_title：Nucleic acids research

authors： Płociński P,Macios M,Houghton J,Niemiec E,Płocińska R,Brzostek A,Słomka M,Dziadek J,Young D,Dziembowski A

更新日期：2019-06-20 00:00:00

abstract：:Budding yeast telomerase is mainly activated by Tel1/Mec1 (yeast ATM/ATR) on Cdc13 from late S to G2 phase of the cell cycle. Here, we demonstrated that the telomerase-recruitment domain of Cdc13 is also phosphorylated by Cdk1 at the same cell cycle stage as the Tel1/Mec1-dependent regulation. Phosphor-specific gel an...

journal_title：Nucleic acids research

authors： Tseng SF,Shen ZJ,Tsai HJ,Lin YH,Teng SC

更新日期：2009-06-01 00:00:00

abstract：:We constructed several deletion mutants of Escherichia coli single-stranded DNA binding protein (EcoSSB) lacking different parts of the C-terminal region. This region of EcoSSB is composed of two parts: a glycine and proline-rich sequence of approximately 60 amino acids followed by an acidic region of the last 10 amin...

journal_title：Nucleic acids research

authors： Curth U,Genschel J,Urbanke C,Greipel J

更新日期：1996-07-15 00:00:00

abstract：:Heterotrimeric eukaryotic/archaeal translation initiation factor 2 (e/aIF2) binds initiator methionyl-tRNA and plays a key role in the selection of the start codon on messenger RNA. tRNA binding was extensively studied in the archaeal system. The γ subunit is able to bind tRNA, but the α subunit is required to reach h...

journal_title：Nucleic acids research

authors： Naveau M,Lazennec-Schurdevin C,Panvert M,Dubiez E,Mechulam Y,Schmitt E

更新日期：2013-01-01 00:00:00