Abstract：
:Interferons (IFN) play a pivotal role in innate immunity, orchestrating a cell-intrinsic anti-pathogenic state and stimulating adaptive immune responses. The complex interplay between the primary response to IFNs and its modulation by positive and negative feedback loops is incompletely understood. Here, we implement the combination of high-resolution gene-expression profiling of nascent RNA with translational inhibition of secondary feedback by cycloheximide. Unexpectedly, this approach revealed a prominent role of negative feedback mechanisms during the immediate (≤60 min) IFNα response. In contrast, a more complex picture involving both negative and positive feedback loops was observed on IFNγ treatment. IFNγ-induced repression of genes associated with regulation of gene expression, cellular development, apoptosis and cell growth resulted from cycloheximide-resistant primary IFNγ signalling. In silico promoter analysis revealed significant overrepresentation of SP1/SP3-binding sites and/or GC-rich stretches. Although signal transducer and activator of transcription 1 (STAT1)-binding sites were not overrepresented, repression was lost in absence of STAT1. Interestingly, basal expression of the majority of these IFNγ-repressed genes was dependent on STAT1 in IFN-naïve fibroblasts. Finally, IFNγ-mediated repression was also found to be evident in primary murine macrophages. IFN-repressed genes include negative regulators of innate and stress response, and their decrease may thus aid the establishment of a signalling perceptive milieu.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Trilling M,Bellora N,Rutkowski AJ,de Graaf M,Dickinson P,Robertson K,Prazeres da Costa O,Ghazal P,Friedel CC,Albà MM,Dölken Ldoi
10.1093/nar/gkt589subject
Has Abstractpub_date
2013-09-01 00:00:00pages
8107-25issue
17eissn
0305-1048issn
1362-4962pii
gkt589journal_volume
41pub_type
杂志文章abstract：:The nucleotide sequence of Drosophila melanogaster methionine tRNAi was determined to be: pA-G-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-U-G-G-A-A-G-C-G-U-m2G-C-U-G-G-G-C-C-C-A-U-t6A-A-C-C-C-A-G-A-G-m7G-D-m5C-C-C-G-A-G-G-A-U-C-G-m1A-A-A-C-C-U-U-G-C-U-C-U-G-C-U-A-C-C-A(OH). It differs from vertebrate initiator tRNAs in only 6 out ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.2.421
更新日期：1979-02-01 00:00:00
abstract：:Here we advocate the use of 2-dimensional data representation in the context of the informational approach of sequence analysis (Claverie & Bougueleret (1986) Nucleic Acids Research 14, 179-196) by applying these methods to the problem of intron/exon discrimination. Two main findings are reported: i) oligonucleotide p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.5.1729
更新日期：1988-03-11 00:00:00
abstract：:Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind o...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/8.1.197-c
更新日期：1980-01-11 00:00:00
abstract：:The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. The Entrez system provides search and re...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkaa892
更新日期：2021-01-08 00:00:00
abstract：:DNA synthesis by phage T4 DNA polymerase is arrested at specific sequences in single-stranded DNA templates. To determine whether or not T4 DNA polymerase accessory proteins 32, 44, 45 and 62 eliminated recognition of these arrest sites, unique primer-templates were constructed in which DNA synthesis began at a DNA pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.8.3343
更新日期：1986-04-25 00:00:00
abstract：:The interaction of the high mobility group proteins, HMG14 and HMG17, with nucleosome core particles has been studied. The results show that two molecules of HMG14/17 can be bound tightly but reversibly to each core particle and that their affinity for core particles is greater than their affinity for histone-free DNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.17.3757
更新日期：1980-09-11 00:00:00
abstract：:Three endonuclease activities have been partially purified from Saccharomyces cerevisiae on the basis of their activity against x-irradiated closed-circular supercoiled bacteriophage PM2 DNA. These endonucleases also nick apurinic DNA and two out of the three activities incise DNA UV-irradiated with high doses. The en...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.9.3347
更新日期：1978-09-01 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
pub_type： 杂志文章
doi：10.1093/nar/gkz757
更新日期：2020-01-08 00:00:00
abstract：:Multicellular organismal development is controlled by a complex network of transcription factors, promoters and enhancers. Although reliable computational and experimental methods exist for enhancer detection, prediction of their target genes remains a major challenge. On the basis of available literature and ChIP-seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1081
更新日期：2011-04-01 00:00:00
abstract：:Our database on large ribosomal subunit RNA contained 334 sequences in July, 1995. All sequences in the database are aligned, taking into account secondary structure. The aligned sequences are provided, together with incorporated secondary structure information, in several computer-readable formats. These data can eas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.1.92
更新日期：1996-01-01 00:00:00
abstract：:A 5',7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa743
更新日期：2020-10-09 00:00:00
abstract：:Acetyl-CoA Carboxylase catalyzes the first committed step in fatty acid synthesis. Escherichia coli acetyl-CoA carboxylase is composed of biotin carboxylase, carboxyltransferase and biotin carboxyl carrier protein functions. The accA and accD genes that code for the alpha- and beta-subunits, respectively, are not in a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1079
更新日期：2010-03-01 00:00:00
abstract：:We have investigated the substrate specificity of the Ogg1 protein of Saccharomyces cerevisiae (yOgg1 protein) for excision of modified DNA bases from oxidatively damaged DNA substrates using gas chromatography/isotope dilution mass spectrometry. Four DNA substrates prepared by treatment with H2O2/Fe(III)-EDTA/ascorbi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.5.1228
更新日期：1998-03-01 00:00:00
abstract：:Giant chromatin-modifying complexes regulate gene transcription in eukaryotes by acting on chromatin substrates and 'setting' the histone code. The histone deacetylase (HDAC)-associated mammalian Sin3 corepressor complex regulates a wide variety of genes involved in all aspects of cellular physiology. The recruitment ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp051
更新日期：2009-04-01 00:00:00
abstract：:The -1 ribosomal frameshifting requires the existence of an in cis RNA slippery sequence and is promoted by a downstream stimulator RNA. An atypical RNA pseudoknot with an extra stem formed by complementary sequences within loop 2 of an H-type pseudoknot is characterized in the severe acute respiratory syndrome corona...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki731
更新日期：2005-07-29 00:00:00
abstract：:The archaeal and eukaryotic evolutionary domains diverged from each other approximately 2 billion years ago, but many of the core components of their transcriptional and translational machineries still display a readily recognizable degree of similarity in their primary structures. The F and P subunits present in arch...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.21.4299
更新日期：2000-11-01 00:00:00
abstract：:The number of known alternative human isoforms has been increasing steadily with the amount of available transcription data. To date, over 100 000 isoforms have been detected in EST libraries, and at least 75% of human genes have at least one alternative isoform. In this paper, we propose that most alternative splicin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp471
更新日期：2009-08-01 00:00:00
abstract：:DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku613
更新日期：2014-01-01 00:00:00
abstract：:Several different computational problems have been solved using DNA as a medium. However, the DNA computations that have so far been carried out have examined a relatively small number of possible sequence solutions in order to find correct sequence solutions. We have encoded a search algorithm in DNA that required th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.22.5203
更新日期：1998-11-15 00:00:00
abstract：:Here, with the aim of obtaining insight into the intriguing selectivity of G-quadruplex (G4) ligands toward cancer compared to normal cells, a genetically controlled system of progressive transformation in human BJ fibroblasts was analyzed. Among the different comparative evaluations, we found a progressive increase o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv006
更新日期：2015-02-18 00:00:00
abstract：:We have located and sequenced the murine homologue of the hst/k-FGF oncogene in genomic DNA clones that extend 3' from int-2 on mouse chromosome 7. The two genes are in the same transcriptional orientation, less than 20 kilobase pairs (kb) apart, and presumably evolved by tandem duplication of a common ancestral gene....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.11.4037
更新日期：1989-06-12 00:00:00
abstract：:Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase acti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki640
更新日期：2005-06-08 00:00:00
abstract：:Functional genomic elements are marked by characteristic DNA and histone modification signatures. How combinatorial chromatin modification states are recognized by epigenetic reader proteins and how this is linked to their biological function is largely unknown. Here we provide a detailed molecular analysis of chromat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw979
更新日期：2017-02-17 00:00:00
abstract：:The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1124
更新日期：2008-03-01 00:00:00
abstract：:Human transcription factor IIIC contains a 55 kDa polypeptide which specifically interacts with the Adenovirus 2 VAI gene promoter and which mimics most of the DNA binding properties of the entire factor. The specificity and affinity of this protein:DNA interaction was demonstrated by: (i) Separation of purified fract...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.16.4743
更新日期：1990-08-25 00:00:00
abstract：:Sequence-specific DNA-binding proteins play a key role in many fundamental biological processes, such as transcription, DNA replication and recombination. Very often, these DNA-binding proteins introduce structural changes to the target DNA-binding sites including DNA bending, twisting or untwisting and wrapping, whic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq078
更新日期：2010-06-01 00:00:00
abstract：:Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over large phylogenetic dist...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh815
更新日期：2004-09-07 00:00:00
abstract：:Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa550
更新日期：2020-09-18 00:00:00
abstract：:The role of thymine dimerization for previously reported U.V. induced conformational changes has been proved using acetophenone as sensitizer for the specific thymine dimerization upon irradiation at 313 nm. CD results demonstrate that formation of pyrimidine dimers cause typical conformational changes of the DNA B he...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.2.179
更新日期：1975-02-01 00:00:00
abstract：:The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary resource for nucleotide sequence information. With the growing volume and diversity of public sequencing data comes the need for increased sophistication in data organisation, presentation and search services so as to maximise its disc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1129
更新日期：2015-01-01 00:00:00
