Abstract:
:Sae2 cooperates with the Mre11-Rad50-Xrs2 (MRX) complex to initiate resection of DNA double-strand breaks (DSBs) and to maintain the DSB ends in close proximity to allow their repair. How these diverse MRX-Sae2 functions contribute to DNA damage resistance is not known. Here, we describe mre11 alleles that suppress the hypersensitivity of sae2Δ cells to genotoxic agents. By assessing the impact of these mutations at the cellular and structural levels, we found that all the mre11 alleles that restore sae2Δ resistance to both camptothecin and phleomycin affect the Mre11 N-terminus and suppress the resection defect of sae2Δ cells by lowering MRX and Tel1 association to DSBs. As a consequence, the diminished Tel1 persistence potentiates Sgs1-Dna2 resection activity by decreasing Rad9 association to DSBs. By contrast, the mre11 mutations restoring sae2Δ resistance only to phleomycin are located in Mre11 C-terminus and bypass Sae2 function in end-tethering but not in DSB resection, possibly by destabilizing the Mre11-Rad50 open conformation. These findings unmask the existence of structurally distinct Mre11 domains that support resistance to genotoxic agents by mediating different processes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Cassani C,Gobbini E,Vertemara J,Wang W,Marsella A,Sung P,Tisi R,Zampella G,Longhese MPdoi
10.1093/nar/gky086subject
Has Abstractpub_date
2018-04-06 00:00:00pages
2990-3008issue
6eissn
0305-1048issn
1362-4962pii
4840239journal_volume
46pub_type
杂志文章abstract::Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.3.695
更新日期:2000-02-01 00:00:00
abstract::The bHLH transcription factor MyoD, the prototypical master regulator of differentiation, directs a complex program of gene expression during skeletal myogenesis. The up-regulation of the cdk inhibitor p57kip2 plays a critical role in coordinating differentiation and growth arrest during muscle development, as well as...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks619
更新日期:2012-09-01 00:00:00
abstract::The log kobs vs. pH profiles were determined in the intermediate acidity region for the glycosyl hydrolysis of guanosine and its 8-amino, 8-monomethylamino, 8-dimethylamino and 8-bromo derivatives. The decreased rate of the 8-amino and enhanced rate of the 8-bromo compound compared to guanosine support an A type mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.3.697
更新日期:1977-03-01 00:00:00
abstract::The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outco...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg096
更新日期:2003-01-01 00:00:00
abstract::We examined the 3'-flanking regions required for accurate 3'-end formation of wheat histone H3 mRNA using gene expression in transformed sunflower cells. The introduction of mutations into the conserved sequence AATGGAAATG in the 3'-flanking region of plant histone genes, located 22 bp upstream from the polyadenylatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.6.1052
更新日期:1994-03-25 00:00:00
abstract::The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1020
更新日期:2018-01-04 00:00:00
abstract::Alternative splicing (AS) is a post-transcriptional process considered to be responsible for the huge diversity of proteins in higher eukaryotes. AS events are regulated by different splicing factors (SFs) that bind to sequence elements on the RNA. SFmap is a web server for predicting putative SF binding sites in geno...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq444
更新日期:2010-07-01 00:00:00
abstract::The dissection of RNA editing mechanisms in PHYSARUM: mitochondria has been hindered by the absence of a soluble in vitro system. Based on our studies in isolated mitochondria, insertion of non-encoded nucleotides into PHYSARUM: mitochondrial RNAs is closely linked to transcription. Here we have fractionated mitochond...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.19.3695
更新日期:2000-10-01 00:00:00
abstract::Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiRe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx610
更新日期:2017-09-06 00:00:00
abstract::Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1055
更新日期:2020-01-08 00:00:00
abstract::The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main nove...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw300
更新日期:2016-07-08 00:00:00
abstract::Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of hig...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq808
更新日期:2011-02-01 00:00:00
abstract::Insertion of the four major nucleotides at the 5'-side of the anticodon triplet of E. coli tRNAMetf was performed by joining of the half molecules obtained by limited digestion with RNase A and the chemically synthesized tetranucleotide pN-C-A-U using RNA ligase. Insertion of U-U at the 5'-side or A and A-A at the 3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.10.3685
更新日期:1985-05-24 00:00:00
abstract::The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki317
更新日期:2005-03-23 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::Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG(5)T, in ammonium acetate. The intermediates and products were separated according to their mass (number of strands and inner cations) and quantified. The study of the temporal ev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq208
更新日期:2010-08-01 00:00:00
abstract::Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa898
更新日期:2021-01-08 00:00:00
abstract::DNA cytosine-5 methyltransferases (C5-MTases) are valuable models to study sequence-specific modification of DNA and are becoming increasingly important tools for biotechnology. Here we describe a structure-guided rational protein design combined with random mutagenesis and selection to change the specificity of the H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp772
更新日期:2009-11-01 00:00:00
abstract::Extreme overloading of HPLC columns with sample can create a condition of binding site saturation causing competition and displacement among solutes during column elution. This has been termed solute-displacement chromatography (SD-HPLC). We present an example of this phenomenon for the preparative fractionation and p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.12.2913
更新日期:1993-06-25 00:00:00
abstract::The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.2.555
更新日期:1988-01-25 00:00:00
abstract::In mammalian cells, DNA damage induces robust changes in gene expression and these changes contribute to the proper execution of cellular responses to DNA damage, including DNA repair, cell cycle arrest and apoptosis. The transcription factor E2F-1 has been suggested to play a key role in the regulation of cell cycle-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.491
更新日期:1999-01-15 00:00:00
abstract::The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm908
更新日期:2008-01-01 00:00:00
abstract::Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt177
更新日期:2013-05-01 00:00:00
abstract::The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg047
更新日期:2003-01-01 00:00:00
abstract::This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.9.2951
更新日期:1982-05-11 00:00:00
abstract::In apurinic acid, a single-stranded polydeoxyribonucleotide easily obtained upon depurination of DNA, the proton resonances arising from thymine and cytosine are readily observable in aqueous solution of 25 degrees C. Two methyl thymine resonances, centered at 1.88 ppm and separated by 0.045 ppm, are observed. We attr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.8.999
更新日期:1974-08-01 00:00:00
abstract::DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw447
更新日期:2016-08-19 00:00:00
abstract::PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.22.10669
更新日期:1988-11-25 00:00:00
abstract::Heat shock genes are activated by the binding of the heat shock transcription factor (HSF) to heat shock elements (HSEs), consisting of arrays of the 5-bp unit NGAAN arranged as inverted repeats. Here, we have investigated the interaction of the 5-bp unit with HSFs of Drosophila and Saccharomyces. Mutations within the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.2.167
更新日期:1994-01-25 00:00:00
abstract::In the last decade polycistronic vectors have become essential tools for both basic science and gene therapy applications. In order to co-express heterologous polypeptides, different systems have been developed from Internal Ribosome Entry Site (IRES) based vectors to the use of the 2A peptide. Unfortunately, these me...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp716
更新日期:2009-11-01 00:00:00