Abstract:
:It has been postulated that a myriad of long noncoding RNAs (lncRNAs) contribute to gene regulation. In fission yeast, glucose starvation triggers lncRNA transcription across promoter regions of stress-responsive genes including fbp1 (fructose-1,6-bisphosphatase1). At the fbp1 promoter, this transcription promotes chromatin remodeling and fbp1 mRNA expression. Here, we demonstrate that such upstream noncoding transcription facilitates promoter association of the stress-responsive transcriptional activator Atf1 at the sites of transcription, leading to activation of the downstream stress genes. Genome-wide analyses revealed that ∼50 Atf1-binding sites show marked decrease in Atf1 occupancy when cells are treated with a transcription inhibitor. Most of these transcription-enhanced Atf1-binding sites are associated with stress-dependent induction of the adjacent mRNAs or lncRNAs, as observed in fbp1 These Atf1-binding sites exhibit low Atf1 occupancy and high histone density in glucose-rich conditions, and undergo dramatic changes in chromatin status after glucose depletion: enhanced Atf1 binding, histone eviction, and histone H3 acetylation. We also found that upstream transcripts bind to the Groucho-Tup1 type transcriptional corepressors Tup11 and Tup12, and locally antagonize their repressive functions on Atf1 binding. These results reveal a new mechanism in which upstream noncoding transcription locally magnifies the specific activation of stress-inducible genes via counteraction of corepressors.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Takemata N,Oda A,Yamada T,Galipon J,Miyoshi T,Suzuki Y,Sugano S,Hoffman CS,Hirota K,Ohta Kdoi
10.1093/nar/gkw142subject
Has Abstractpub_date
2016-06-20 00:00:00pages
5174-89issue
11eissn
0305-1048issn
1362-4962pii
gkw142journal_volume
44pub_type
杂志文章abstract::Exposure to genotoxic agents, such as ionizing radiation (IR), produces double-strand breaks, repaired predominantly in mammalian cells by non-homologous end-joining (NHEJ). Ku70 was identified as an interacting partner of a proteolytic Cyclin E (CycE) fragment, p18CycE. p18CycE endogenous generation during IR-induced...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt812
更新日期:2013-12-01 00:00:00
abstract::We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh379
更新日期:2004-07-01 00:00:00
abstract::In human cells DNA damage caused by UV light is mainly repaired by the nucleotide excision repair pathway. This mechanism involves dual incisions on both sides of the damage catalyzed by two nucleases. In mammalian cells XPG cleaves 3' of the DNA lesion while the ERCC1-XPF complex makes the 5' incision. The amino acid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.14.2823
更新日期:1997-07-15 00:00:00
abstract::The P0 scaffold protein of the ribosomal stalk is mainly incorporated into pre-ribosomes in the cytoplasm where it replaces the assembly factor Mrt4. In analyzing the role of the P0 carboxyl terminal domain (CTD) during ribosomal stalk assembly, we found that its complete removal yields a protein that is functionally ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt637
更新日期:2013-10-01 00:00:00
abstract::Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new appro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1175
更新日期:2020-12-08 00:00:00
abstract::The signal recognition particle database (SRPDB) is located at the University of Texas Health Science Center at Tyler and includes tabulations of SRP RNA, SRP protein and SRP receptor sequences. The sequences are annotated with links to the primary databases. They are ordered alphabetically or phylogenetically and are...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.169
更新日期:1999-01-01 00:00:00
abstract::In many viruses and transposons, expression of some genes requires alternative reading of the genetic code, also called recoding. Such events depend on specific mRNA sequences and can lead to read through of an in-frame stop codon or to +1 or -1 frameshifting. Here, we addressed the issue of conservation of recoding r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.9.1557
更新日期:1995-05-11 00:00:00
abstract::SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidden Markov models ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn762
更新日期:2009-01-01 00:00:00
abstract::The ability to induce gene expression in a small molecule dependent manner has led to many applications in target discovery, functional elucidation and bio-production. To date these applications have relied on a limited set of protein-based control mechanisms operating at the level of transcription initiation. The dis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv912
更新日期:2016-02-18 00:00:00
abstract::The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of mus...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx786
更新日期:2017-10-13 00:00:00
abstract::The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki108
更新日期:2005-01-01 00:00:00
abstract::Fifteen years elapsed between the discovery of the double helix (1953) and the first DNA sequencing (1968). Modern DNA sequencing began in 1977, with development of the chemical method of Maxam and Gilbert and the dideoxy method of Sanger, Nicklen and Coulson, and with the first complete DNA sequence (phage X174), whi...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章
doi:10.1093/nar/gkm688
更新日期:2007-01-01 00:00:00
abstract::Initially identified as a factor involved in tyrosine kinase receptor signaling, Grb10-interacting GYF protein 2 (GIGYF2) has later been shown to interact with the 5' cap-binding protein 4EHP as part of a translation repression complex, and to mediate post-transcriptional repression of tethered reporter mRNAs. A curre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky198
更新日期:2018-06-20 00:00:00
abstract::The repAC operon of plasmid RSF1010 consists of the genes for proteins E, F, RepA (DNA helicase), and RepC (origin-binding initiator protein) and is transcriptionally initiated by a promoter called P4. We have studied the expression of the repAC operon in vivo by using fusions to the lacZ reporter gene. The results sh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.21.6215
更新日期:1990-11-11 00:00:00
abstract::Nucleotide substitution, insertion and deletion (indel) events are the major driving forces that have shaped genomes. Using the recently identified human ribosomal protein (RP) pseudogene sequences, we have thoroughly studied DNA mutation patterns in the human genome. We analyzed a total of 1726 processed RP pseudogen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg745
更新日期:2003-09-15 00:00:00
abstract::Pax6 transcription is under the control of two main promoters (P0 and P1), and these are autoregulated by Pax6. Additionally, Pax6 expression is under the control of the TGFbeta superfamily, although the precise mechanisms of such regulation are not understood. The effect of TGFbeta on Pax6 expression was studied in t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1105
更新日期:2007-01-01 00:00:00
abstract::Eucaryotic ribosome biogenesis involves many cis-acting sequences and trans-acting factors, including snoRNAS: We have used directed mutagenesis of rDNA plasmids in yeast to identify critical sequence and structural elements within and flanking the ITS2-proximal stem. This base paired structure, present in the mature ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.10.2106
更新日期:2001-05-15 00:00:00
abstract::Translational repression (TR) plays an important role in post-transcriptional regulation of gene expression and embryonic development in metazoans. TR also regulates the expression of a subset of the cytoplasmic mRNA population during development of fertilized female gametes of the unicellular malaria parasite, Plasmo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1142
更新日期:2008-03-01 00:00:00
abstract::From a sarkosyl-insoluble outer membrane fraction prepared from the Helicobacter pylori strain ATCC 43504, 19 proteins could be sequenced N-terminally by Edman degradation. Oligonucleotides were deduced and used for screening of a genomic library. From the isolated genes, five code for different members of a H.pylori ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.16.3325
更新日期:1999-08-15 00:00:00
abstract::Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv563
更新日期:2015-10-15 00:00:00
abstract::We have isolated a pigment cell-specific cDNA clone from a B16 mouse melanoma cDNA library by differential hybridization. The mRNA of isolated cDNA is highly expressed in B16 melanoma cells and in black mouse (C57BL/6) skin, but is not detectable in mouse neuroblastoma cells nor in K1735 mouse amelanotic melanoma cell...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2413
更新日期:1986-03-25 00:00:00
abstract::Procaryotic DNA polymerases contain an associated 3'----5' exonuclease activity which provides a proofreading function and contributes substantially to replication fidelity. DNA polymerases of the eucaryotic herpes-type viruses contain similar associated exonuclease activities. We have investigated the fidelity of pol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.3.1185
更新日期:1987-02-11 00:00:00
abstract::ProtoNet is an automatic hierarchical classification of the protein sequence space. In 2004, the ProtoNet (version 4.0) presents the analysis of over one million proteins merged from SwissProt and TrEMBL databases. In addition to rich visualization and analysis tools to navigate the clustering hierarchy, we incorporat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki007
更新日期:2005-01-01 00:00:00
abstract::The bZip proteins GCN4 and C/EBP differ in their DNA binding specificities: GCN4 binds well to the pseudopalindromic AP1 site 5'-A4T3G2A1C0T1C2'A3'T4'-3' and to the palindromic ATF/CREB sequence 5'-A4T3G2A1-C0*G0'T1'C2'A3'T4'-3'; C/EBP preferentially recognizes the palindromic sequence 5'-A4T3T2G1C0*G0'C1'A2'-A3'T4'-3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.20.4162
更新日期:1995-10-25 00:00:00
abstract::Mouse embryo fibroblasts (MEFs) are convenient sources for biochemical studies when cell number in mouse embryos is limiting. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we performed strand- and allele-specific RNA deep sequencing. We used sequenom allelotyping in embryo and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1042
更新日期:2014-02-01 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::Small inverted repeats (small palindromes) on plasmids have been shown to mediate a recombinational rearrangement event in Escherichia coli leading to the formation of inverted dimers (giant palindromes). This recombinational rearrangement event is efficient and independent of RecA and RecBCD. In this report, we propo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.15.3009
更新日期:1997-08-01 00:00:00
abstract::Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching stru...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt795
更新日期:2013-12-01 00:00:00
abstract::The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh531
更新日期:2004-04-23 00:00:00
abstract::Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa131
更新日期:2020-05-07 00:00:00