Effect of intron size on splicing efficiency in retroviral transcripts.

abstract：:Histone H2A ubiquitination plays critical roles in transcriptional repression and deoxyribonucleic acid (DNA) damage response. More attention has been focused on ubiquitin E3 ligases of H2A, however, less is known about the negative regulators of H2A ubiquitination. Here we identified HSCARG as a new negative regulato...

journal_title：Nucleic acids research

authors： Hu B,Li S,Zhang X,Zheng X

更新日期：2014-05-01 00:00:00

abstract：:The DNA unwinding element (DUE) is a sequence rich in adenine and thymine residues present within the origin region of both prokaryotic and eukaryotic replicons. Recently, it has been shown that this is the site where bacterial DnaA proteins, the chromosomal replication initiators, form a specific nucleoprotein filame...

journal_title：Nucleic acids research

authors： Wegrzyn K,Fuentes-Perez ME,Bury K,Rajewska M,Moreno-Herrero F,Konieczny I

更新日期：2014-07-01 00:00:00

abstract：:The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (c...

journal_title：Nucleic acids research

authors： Cullen D,Wilson LJ,Grey GL,Henner DJ,Turner G,Ballance DJ

更新日期：1987-11-25 00:00:00

abstract：:Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5'-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured...

journal_title：Nucleic acids research

authors： Cang X,Šponer J,Cheatham TE 3rd

更新日期：2011-05-01 00:00:00

abstract：:Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (N...

journal_title：Nucleic acids research

authors： Wilson SE,Smith MC

更新日期：1998-05-15 00:00:00

abstract：:Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which ...

journal_title：Nucleic acids research

authors： Dai M,Wang P,Boyd AD,Kostov G,Athey B,Jones EG,Bunney WE,Myers RM,Speed TP,Akil H,Watson SJ,Meng F

更新日期：2005-11-10 00:00:00

abstract：:We have analysed DNA modification in a HapII site (CCGG) present in the major intron of the discontinuous rabbit beta-globin gene. In most somatic tissues, including erythroid and non-erythroid tissues, about 50% of the DNA is resistant to cleavage at this site by HapII, though 100% cleavage is found with the isoschiz...

journal_title：Nucleic acids research

authors： Waalwijk C,Flavell RA

更新日期：1978-12-01 00:00:00

abstract：:pS194 is a naturally occurring Staphylococcus aureus plasmid encoding streptomycin resistance. The plasmid has a copy number of about 25 per cell, and belongs to the inc5 incompatibility group. The nucleotide sequence of pS194 has been determined and consists of 4397 base pairs including four open reading frames poten...

journal_title：Nucleic acids research

authors： Projan SJ,Moghazeh S,Novick RP

更新日期：1988-03-25 00:00:00

abstract：:The thermal denaturation spectra of E. coli 50s and 30s ribosomal sub units and of their isolated RNA's were studied over the wavelength range of 2300-3000 Angstrom. It was possible to fit the experimental denaturation spectra with super positions of the reference spectra for denaturation of A - U and G - C base pairs...

journal_title：Nucleic acids research

authors： Araco A,Belli M,Giorgi C,Onori G

更新日期：1975-03-01 00:00:00

abstract：:As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality fac...

journal_title：Nucleic acids research

authors： Schmalzing D,Belenky A,Novotny MA,Koutny L,Salas-Solano O,El-Difrawy S,Adourian A,Matsudaira P,Ehrlich D

更新日期：2000-05-01 00:00:00

abstract：:Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...

journal_title：Nucleic acids research

authors： Chung CZ,Jaramillo JE,Ellis MJ,Bour DYN,Seidl LE,Jo DHS,Turk MA,Mann MR,Bi Y,Haniford DB,Duennwald ML,Heinemann IU

更新日期：2019-04-08 00:00:00

abstract：:The ever growing number of completely sequenced prokaryotic genomes facilitates cross-species comparisons by genomic annotation algorithms. This paper introduces a new probabilistic framework for comparative genomic analysis and demonstrates its utility in the context of improving the accuracy of prokaryotic gene star...

journal_title：Nucleic acids research

authors： Walker M,Pavlovic V,Kasif S

更新日期：2002-07-15 00:00:00

abstract：:The modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer, is in many cases not due to genetic defects, suggesting dysregulation through alternative mechanisms. The identity of these molecular events remains for the most part unknown. Here, we identified TFII-I as a novel repressor of GL...

journal_title：Nucleic acids research

authors： McCleary-Wheeler AL,Paradise BD,Almada LL,Carlson AJ,Marks DL,Vrabel A,Vera RE,Sigafoos AN,Olson RL,Fernandez-Zapico ME

更新日期：2020-07-27 00:00:00

abstract：:Histone modifications are fundamental to chromatin structure and transcriptional regulation, and are recognized by a limited number of protein folds. Among these folds are PHD fingers, which are present in most chromatin modification complexes. To date, about 15 PHD finger domains have been structurally characterized,...

journal_title：Nucleic acids research

authors： Slama P,Geman D

更新日期：2011-03-01 00:00:00

abstract：:KpnI restriction of DNAs from all anthropoid primates studied releases a conspicuous series of segments representing families of long, interspersed repetitive DNAs termed here the KpnI 1.2, 1.5, 1.8 and 1.9 kb families. Human KpnI 1.2 to 1.9 kb segments representative of these families were isolated and separately clo...

journal_title：Nucleic acids research

authors： Shafit-Zagardo B,Maio JJ,Brown FL

更新日期：1982-05-25 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：:Human somatic cells have essentially no telomerase activity. Telomerase is linked to tumor genesis and is a valuable marker for malignant growth. Extreme paucity of the enzyme neccessitated development of a PCR-based assay, 'telomeric repeat amplification protocol' (TRAP). Unfortunately, this method is not without dif...

journal_title：Nucleic acids research

authors： Krupp G,Kühne K,Tamm S,Klapper W,Heidorn K,Rott A,Parwaresch R

更新日期：1997-02-15 00:00:00

abstract：:APOBEC3G (A3G), a host protein that inhibits HIV-1 reverse transcription and replication in the absence of Vif, displays cytidine deaminase and single-stranded (ss) nucleic acid binding activities. HIV-1 nucleocapsid protein (NC) also binds nucleic acids and has a unique property, nucleic acid chaperone activity, whic...

journal_title：Nucleic acids research

authors： Iwatani Y,Chan DS,Wang F,Stewart-Maynard K,Sugiura W,Gronenborn AM,Rouzina I,Williams MC,Musier-Forsyth K,Levin JG

更新日期：2007-01-01 00:00:00

abstract：:A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called i...

journal_title：Nucleic acids research

authors： Le Rhun A,Lécrivain AL,Reimegård J,Proux-Wéra E,Broglia L,Della Beffa C,Charpentier E

更新日期：2017-03-17 00:00:00

abstract：:The main goal of this review is to provide some guide-lines for choosing a proper method when searching for differentially expressed transcripts. The choice of an approach should depend upon particular features of the experiment and project requirements. We outline some general considerations to help decide between di...

journal_title：Nucleic acids research

authors： Matz MV,Lukyanov SA

更新日期：1998-12-15 00:00:00

abstract：:Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated Cas proteins comprise a prokaryotic RNA-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. The type I-E CRISPR interference complex Cascade from Escherichia coli is composed of...

journal_title：Nucleic acids research

authors： Beloglazova N,Kuznedelov K,Flick R,Datsenko KA,Brown G,Popovic A,Lemak S,Semenova E,Severinov K,Yakunin AF

更新日期：2015-01-01 00:00:00

abstract：:The alcohol dehydrogenase (Adh) gene of D. melanogaster is transcribed from two different promoters during fly development: the distal (adult) and the proximal (embryonic-larval). Certain aspects of Adh gene regulation are represented in Drosophila continuous cell lines. We have used Drosophila tissue culture cells in...

journal_title：Nucleic acids research

authors： Benyajati C,Ayer S,McKeon J,Ewel A,Huang J

更新日期：1987-10-12 00:00:00

abstract：:Metagenomics has been employed to systematically sequence, classify, analyze and manipulate the entire genetic material isolated from environmental samples. Finding genes within metagenomic sequences remains a formidable challenge, and noncoding RNA genes other than those encoding rRNA and tRNA are not well annotated ...

journal_title：Nucleic acids research

authors： Zhu Y,Pulukkunat DK,Li Y

更新日期：2007-01-01 00:00:00

abstract：:Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche on earth. In order to understand the plasticity of TRNs in bacteria, we studied the conservation of currently known TRNs...

journal_title：Nucleic acids research

authors： Lozada-Chávez I,Janga SC,Collado-Vides J

更新日期：2006-07-13 00:00:00

abstract：:MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...

journal_title：Nucleic acids research

authors： Viegas SC,Silva IJ,Saramago M,Domingues S,Arraiano CM

更新日期：2011-04-01 00:00:00

abstract：:Structural Maintenance of Chromosomes (SMC) proteins are vital for a wide range of processes including chromosome structure and dynamics, gene regulation and DNA repair. Eukaryotes have three SMC complexes, consisting of heterodimeric pairs of six different SMC proteins along with several specific regulatory subunits....

journal_title：Nucleic acids research

authors： Griese JJ,Witte G,Hopfner KP

更新日期：2010-06-01 00:00:00

abstract：:Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes and maintains telomeric DNA. Studies of telomeres and telomerase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as Tetrahymena thermophila. To examine the expression of telomerase, we investigated the...

journal_title：Nucleic acids research

authors： Hargrove BW,Bhattacharyya A,Domitrovich AM,Kapler GM,Kirk K,Shippen DE,Kunkel GR

更新日期：1999-11-01 00:00:00

abstract：:A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoa...

journal_title：Nucleic acids research

authors： Lahoud G,Timoshchuk V,Lebedev A,Arar K,Hou YM,Gamper H

更新日期：2008-12-01 00:00:00

abstract：:Human cells are, in general, poor recipients of foreign DNA, which has severely hampered the cloning of genes by direct phenotypic correction of deficient human cell lines after DNA mediated gene transfer. In this communication a methodology is presented which largely circumvents this problems. The method relies on th...

journal_title：Nucleic acids research

authors： Belt PB,Jongmans W,de Wit J,Hoeijmakers JH,van de Putte P,Backendorf C

更新日期：1991-09-25 00:00:00

abstract：:p16INK4a and p21WAF1, two major cyclin-dependent kinase inhibitors, are the products of two tumor suppressor genes that play important roles in various cellular metabolic pathways. p21WAF1 is up-regulated in response to different DNA damaging agents. While the activation of p21WAF1 is p53-dependent following -rays, th...

journal_title：Nucleic acids research

authors： Al-Mohanna MA,Al-Khalaf HH,Al-Yousef N,Aboussekhra A

更新日期：2007-01-01 00:00:00