Abstract:
:Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC directly competes with Pol III for chromatin occupancy as demonstrated by inversely correlated tDNA binding. The association of TFIIIC with tDNA was stronger under unfavorable respiratory conditions and in the presence of Maf1. Induction of tDNA transcription by glucose-activated protein kinase A (PKA) was correlated with the down-regulation of TFIIIC occupancy on tDNA. The conditions that activate the PKA signaling pathway promoted the binding of TFIIIB subunits, Brf1 and Bdp1, with tDNA, but decreased their interaction with TFIIIC. Association of Brf1 and Bdp1 with TFIIIC was much stronger under repressive conditions, potentially restricting TFIIIB recruitment to tDNA and preventing Pol III recruitment. Altogether, we propose a model in which, depending on growth conditions, TFIIIC promotes activation or repression of tDNA transcription.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Ciesla M,Skowronek E,Boguta Mdoi
10.1093/nar/gky656subject
Has Abstractpub_date
2018-10-12 00:00:00pages
9444-9455issue
18eissn
0305-1048issn
1362-4962pii
5058965journal_volume
46pub_type
杂志文章abstract::Accumulating evidence has demonstrated that transcriptional regulation is affected by DNA methylation. Understanding the perturbation of DNA methylation-mediated regulation between transcriptional factors (TFs) and targets is crucial for human diseases. However, the global landscape of DNA methylation-mediated transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa041
更新日期:2020-03-18 00:00:00
abstract::New transcripts generated by RNA polymerase II (RNAPII) are generally processed in order to form mature mRNAs. Two key processing steps include a precise cleavage within the 3' end of the pre-mRNA, and the subsequent polymerization of adenosines to produce the poly(A) tail. In yeast, these two functions are performed ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx674
更新日期:2017-09-29 00:00:00
abstract::The cnjC gene from the protozoan Tetrahymena thermophila was completely sequenced. The deduced gene product was found to have significant sequence similarity to the yeast and prokaryotic RNA polymerase subunits involved with subunit assembly. Since cnjC is active only during the sexual stage (conjugation) of Tetrahyme...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.10.2953
更新日期:1990-05-25 00:00:00
abstract::Mixed-lineage leukemia (MLL) maintains the expression of cellular memory genes during development, while leukemic MLL fusion proteins aberrantly maintain expression of hematopoietic stem cell program genes such as HOXA9 to cause leukemia. However, the molecular mechanism of gene activation is unclear. Here we show tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1394
更新日期:2014-04-01 00:00:00
abstract::Plant mitochondrial genomes show much more evolutionary plasticity than those of animals. We analysed the first mitochondrial DNA (mtDNA) of a lycophyte, the quillwort Isoetes engelmannii, which is separated from seed plants by more than 350 million years of evolution. The Isoetes mtDNA is particularly rich in recombi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp532
更新日期:2009-08-01 00:00:00
abstract::Antisense oligodeoxynucleotides targeted to Ha-ras mRNA have been designed to discriminate between the codon 12-mutated oncogene and the normal proto-oncogene. An in vitro assay using two different sources of RNase H (rabbit reticulocyte lysates and nuclear extract from HeLa cells) was used to characterize oligonucleo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3411
更新日期:1995-09-11 00:00:00
abstract::The gene-external part of the human 7S L promoter was analyzed by transcription in vitro and in vivo. Compared to the wild type promoter (-178), a -66 5'deletion mutant revealed full activity in vitro but was inefficiently transcribed in vivo. Further deletion to -37 reduced template activity to 50% in vitro and to ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.6779
更新日期:1990-12-11 00:00:00
abstract::Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly challenging problem. We report here a computer program, RDC-PROSPECT, for protein structure prediction based on a struct...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh204
更新日期:2004-01-26 00:00:00
abstract::Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a large number of economically-significant crops. Traditional 'dot-blot hybridization' or PCR-based assays for identifyin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.7.e23
更新日期:2000-04-01 00:00:00
abstract::The mode of action of regulated promoters is largely determined by kinetic parameters which govern the interaction between promoters and proteins involved in induction and repression of transcription. To gain insight into the interplay between positively and negatively acting transcriptional regulators, in this case A...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.18.3873
更新日期:2001-09-15 00:00:00
abstract::The codon UGA located 5' adjacent to an mRNA hairpin within fdhF mRNA promotes the incorporation of the amino acid selenocysteine into formate dehydrogenase H of Escherichia coli. The loop region of this mRNA hairpin has been shown to bind to the special elongation factor SELB, which also forms a complex with selenocy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.20.3903
更新日期:1996-10-15 00:00:00
abstract::In Saccharomyces cerevisiae, the DNA damage response (DDR) is activated by the spatio-temporal colocalization of Mec1-Ddc2 kinase and the 9-1-1 clamp. In the absence of direct means to monitor Mec1 kinase activation in vivo, activation of the checkpoint kinase Rad53 has been taken as a proxy for DDR activation. Here, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1222
更新日期:2010-04-01 00:00:00
abstract::Understanding the cellular uptake and intracellular trafficking of dendrimer-DNA complexes is an important prerequisite for improving the transfection efficiency of non-viral vector-mediated gene delivery. Dendrimers are synthetic polymers used for gene transfer. Although these cationic molecules show promise as versa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh595
更新日期:2004-05-17 00:00:00
abstract::The mutation patterns at Cas9 targeted sites contain unique information regarding the nuclease activity and repair mechanisms in mammalian cells. However, analytical framework for extracting such information are lacking. Here, we present a novel computational platform called Rational InDel Meta-Analysis (RIMA) that en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky653
更新日期:2018-09-19 00:00:00
abstract::RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep Reg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1077
更新日期:2019-01-08 00:00:00
abstract::The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3'-5' exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv260
更新日期:2015-04-30 00:00:00
abstract::LNA oligonucleotides constitute a class of bicyclic RNA analogues having an exceptionally high affinity for their complementary DNA and RNA target molecules. We here report a novel method for highly efficient isolation of intact poly(A)+ RNA using an LNA-substituted oligo(dT) affinity ligand, based on the increased af...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh056
更新日期:2004-04-19 00:00:00
abstract::Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG isla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa556
更新日期:2020-09-04 00:00:00
abstract::DNA polymerase delta (Pol δ) is responsible for the elongation and maturation of Okazaki fragments in eukaryotic cells. Proliferating cell nuclear antigen (PCNA) recruits Pol δ to the DNA and serves as a processivity factor. Here, we show that PCNA also stimulates the catalytic rate of Saccharomyces cerevisiae Pol δ b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1321
更新日期:2019-02-28 00:00:00
abstract::Kinetically monitored, reverse transcriptase-initiated PCR (kinetic RT-PCR, kRT-PCR) is a novel application of kinetic PCR for high throughput transcript quantitation in total cellular RNA. The assay offers the simplicity and flexibility of an enzyme assay with distinct advantages over DNA microarray hybridization and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.2.e2
更新日期:2000-01-15 00:00:00
abstract::Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specifi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.10.2199
更新日期:2001-05-15 00:00:00
abstract::The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9861
更新日期:1987-12-10 00:00:00
abstract::Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt915
更新日期:2014-01-01 00:00:00
abstract::Chromatin modulation at various cis-acting elements is critical for V(D)J recombination during T and B cell development. MARbeta, a matrix-associated region (MAR) located upstream of the T cell receptor beta (TCRbeta) enhancer (Ebeta), serves a crucial role in silencing Ebeta-mediated TCR activation. By DNaseI hyperse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh807
更新日期:2004-09-15 00:00:00
abstract::SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm407
更新日期:2007-07-01 00:00:00
abstract::The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less conservation with the corresponding region in RAD54. The biochemical roles of this region of RAD54B are not known, alth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn516
更新日期:2008-10-01 00:00:00
abstract::It is known that DNA curvature plays a certain role in gene regulation. The distribution of curved DNA in promoter regions is evolutionarily preserved, and it is mainly determined by temperature of habitat. However, very little is known on the distribution of DNA curvature in termination sites. Our main objective was ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl230
更新日期:2006-05-05 00:00:00
abstract::Knowledge of subcellular localizations (SCLs) of plant proteins relates to their functions and aids in understanding the regulation of biological processes at the cellular level. We present PlantLoc, a highly accurate and fast webserver for predicting the multi-label SCLs of plant proteins. The PlantLoc server has two...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt428
更新日期:2013-07-01 00:00:00
abstract::Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 ca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm485
更新日期:2007-01-01 00:00:00
abstract::p73, the p53 homologue, exists as a transactivation-domain-proficient TAp73 or deficient deltaN(DN)p73 form. Expectedly, the oncogenic DNp73 that is capable of inactivating both TAp73 and p53 function, is over-expressed in cancers. However, the role of TAp73, which exhibits tumour-suppressive properties in gain or los...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn414
更新日期:2008-08-01 00:00:00