Abstract:
:Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination factor of Archaea, the ribonuclease aCPSF1, and elucidated its 3'-end cleavage triggered termination mechanism. The depletion of Mmp-aCPSF1 in Methanococcus maripaludis caused a genome-wide transcription termination defect and disordered transcriptome. Transcript-3'end-sequencing revealed that transcriptions primarily terminate downstream of a uridine-rich motif where Mmp-aCPSF1 performed an endoribonucleolytic cleavage, and the endoribonuclease activity was determined to be essential to the in vivo transcription termination. Co-immunoprecipitation and chromatin-immunoprecipitation detected interactions of Mmp-aCPSF1 with RNA polymerase and chromosome. Phylogenetic analysis revealed that the aCPSF1 orthologs are ubiquitously distributed among the archaeal phyla, and two aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to terminate transcription of M. maripaludis. Therefore, the aCPSF1 dependent termination mechanism could be widely employed in Archaea, including Lokiarchaeota belonging to Asgard Archaea, the postulated archaeal ancestor of Eukaryotes. Strikingly, aCPSF1-dependent archaeal transcription termination reported here exposes a similar 3'-cleavage mode as the eukaryotic RNA polymerase II termination, thus would shed lights on understanding the evolutionary linking between archaeal and eukaryotic termination machineries.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yue L,Li J,Zhang B,Qi L,Li Z,Zhao F,Li L,Zheng X,Dong Xdoi
10.1093/nar/gkaa702subject
Has Abstractpub_date
2020-09-25 00:00:00pages
9589-9605issue
17eissn
0305-1048issn
1362-4962pii
5898609journal_volume
48pub_type
杂志文章abstract::Sets of genes expressed in the same tissue are believed to be under the regulation of a similar set of transcription factors, and can thus be assumed to contain similar structural patterns in their regulatory regions. Here we present a study of the structural patterns in promoters of genes expressed specifically in 26...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp866
更新日期:2010-01-01 00:00:00
abstract::A dinucleoside monophosphate, 6,2'-anhydro-6-oxy-1-beta-D-arabinofuranosyluracil-phosphoryl- (3'-5')-6,2'-anhydro-6-oxy-1-beta-D-arabinofuranosyluracil (I) was synthesized by the condensation reaction using DCC from 5'-monomethoxytrityl derivative(VII) and 3'-acetyl-5'-phosphate(X) of the monomer units. Yield was ca. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.3.479
更新日期:1974-03-01 00:00:00
abstract::During DNA replication replicative polymerases move in discrete mechanical steps along the DNA template. To address how the chemical cycle is coupled to mechanical motion of the enzyme, here we use optical tweezers to study the translocation mechanism of individual bacteriophage Phi29 DNA polymerases during processive...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv204
更新日期:2015-04-20 00:00:00
abstract::We have adapted a method for making libraries of mutations in any specific gene for use in the fission yeast Schizosaccharomyces pombe . This elegant and simple method consists of PCR amplification of the gene of interest, followed by co-transformation of fission yeast with the PCR fragment and a linearized plasmid ve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.20.4783
更新日期:1998-10-15 00:00:00
abstract::Naturally occurring hammerhead ribozymes are produced by rolling circle replication followed by self-cleavage. This results in monomer-length catalytic RNAs which have self-complementary sequences that can occupy their trans -binding domains and potentially block their ability to cleave other RNA strands. Here we show...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.3.776
更新日期:2000-02-01 00:00:00
abstract::Five peaks of DNA glycosylase activity showing a preference for MNNG alkylated DNA have been identified from extracts of adapted M. luteus. They are numerically designated as GI to GV in order of their decreasing molecular weights. The first two of these peaks have been highly purified. GI, is a constitutive heat labi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.16.6607
更新日期:1987-08-25 00:00:00
abstract::The antigene strategy based on site-specific recognition of duplex DNA by triplex DNA formation has been exploited in a wide range of biological activities. However, specific triplex formation is mostly restricted to homo-purine strands within the target duplex DNA, due to the destabilizing effect of CG and TA inversi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky704
更新日期:2018-09-28 00:00:00
abstract::We have previously characterized an extracellular nuclease from Pseudomonas BAL 31 which, in addition to other activities, displays a double-strand exonuclease activity which progressively shortens both strands of linear duplex DNA molecules from both termini. This degradation is accomplished without the introduction ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.5.1445
更新日期:1978-05-01 00:00:00
abstract::Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current versi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr201
更新日期:2011-07-01 00:00:00
abstract::Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein, which binds both single-stranded (ss) and double-stranded (ds) DNA and facilitates the formation of higher order protein-DNA complexes in vitro. LrpC binds at different sites within the same DNA molecule promoting intramolecular liga...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj418
更新日期:2006-01-10 00:00:00
abstract::Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction data...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl783
更新日期:2007-01-01 00:00:00
abstract::The ARF tumour suppressor stabilizes p53 by negatively regulating the E3 ubiquitin ligase MDM2 to promote cell cycle arrest and cell death. However, ARF is also able to arrest cell proliferation by inhibiting ribosome biogenesis. In greater part this is achieved by targeting the transcription termination factor I (TTF...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks198
更新日期:2012-07-01 00:00:00
abstract::We have generated a codon usage table for Pseudomonas aeruginosa. Codon usage in P. aeruginosa is extremely biased. In contrast to E. coli and yeast, P. aeruginosa preferentially uses those codons within a synonymous codon group with the strongest predicted codon-anticodon interaction. We were unable to correlate a pa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.19.9323
更新日期:1988-10-11 00:00:00
abstract::Southern blot analyses using reduced stringency hybridization conditions have been employed to search for sequence homologies between rodent VL30 genes and murine leukemia virus (MuLV) proviruses. These constitute two classes of transposon-like elements previously believed to be genetically unrelated. Our results demo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.2.305
更新日期:1983-01-25 00:00:00
abstract::DNA methylation is the best-studied epigenetic modification and describes the conversion of cytosine to 5-methylcytosine. The importance of this phenomenon is that aberrant promoter hypermethylation is a common occurrence in cancer and is frequently associated with gene silencing. Various techniques are currently avai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnj017
更新日期:2006-02-07 00:00:00
abstract::Recently, we reported a multicopy mammalian plasmid with a structure related to polyoma. The plasmid, named L factor, was found at a high copy number (5,000 or more per cell) in a subclone derived from mouse L cells. We attempted to utilize L factor as a plasmid vector for mammalian cells. A series of composite DNA co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.21.8815
更新日期:1987-11-11 00:00:00
abstract::Specific binding of HIV-1 viral protein NCp7 to a unique 35-base RNA stem-loop SL1 is critical for formation and packaging of the genomic RNA dimer found within HIV-1 virions. NCp7 binding stimulates refolding of SL1 from a metastable kissing dimer (KD) into thermodynamically stable linear dimer (LD). Using UV melting...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm097
更新日期:2007-01-01 00:00:00
abstract::The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq834
更新日期:2011-01-01 00:00:00
abstract::Small nucleolar RNAs (snoRNAs) are among the first discovered and most extensively studied group of small non-coding RNA. However, most studies focused on a small subset of snoRNAs that guide the modification of ribosomal RNA. In this study, we annotated the expression pattern of all box C/D snoRNAs in normal and canc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku664
更新日期:2014-09-01 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 for published life science journals. The Entrez system provides search and re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1095
更新日期:2018-01-04 00:00:00
abstract::Telomeric regions of the genome are inherently difficult-to-replicate due to their propensity to generate DNA secondary structures and form nucleoprotein complexes that can impede DNA replication fork progression. Precisely how cells respond to DNA replication stalling within a telomere remains poorly characterized, l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz158
更新日期:2019-05-21 00:00:00
abstract::TAP/hNXF1 is a key factor that mediates general cellular mRNA export from the nucleus, and its orthologs are structurally and functionally conserved from yeast to humans. Metazoans encode additional proteins that share homology and domain organization with TAP/hNXF1, suggesting their participation in mRNA metabolism; ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki706
更新日期:2005-07-13 00:00:00
abstract::The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr248
更新日期:2011-07-01 00:00:00
abstract::We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3722
更新日期:1996-10-01 00:00:00
abstract::The cloned 18 S ribosomal RNA gene from Saccharomyces cerevisiae have been sequenced, using the Maxam-Gilbert procedure. From this data the complete sequence of 1789 nucleotides of the 18 S RNA was deduced. Extensive homology with many eucaryotic as well as E. coli ribosomal small subunit rRNA (S-rRNA) has been observ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.23.5779
更新日期:1980-12-11 00:00:00
abstract::RNA molecules play different roles in coding, decoding and gene expression regulation. Such roles are often associated to the RNA secondary or tertiary structures. The folding dynamics lead to multiple secondary structures of long RNA molecules, since an RNA molecule might fold into multiple distinct native states. De...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1249
更新日期:2014-12-16 00:00:00
abstract::We present the complete sequence of an mRNA which is induced by estrogen in the human breast cancer cell line MCF-7 [pS2 mRNA, Masiakowski et al., Nucleic Acids Res. 10, 7895-7903 (1982)]. Primer extension and cloning of double-stranded cDNA (ds-cDNA) into a vector designed to make full-length cDNA were used to determ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.6.2861
更新日期:1984-03-26 00:00:00
abstract::The nucleotide sequence of a region located on the adenovirus type 5 genome between coordinates 59.9 and 62.5 has been determined. This region comprises the 3'-termini of mRNAs coding for the hexon and the DNA binding protein. The sequence reveals the presence of an open reading frame in r-strand transcripts downstrea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.24.6033
更新日期:1980-12-20 00:00:00
abstract::Unlike short interfering RNAs (siRNAs), which are commonly designed to repress a single messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RNAs that have evolved to concurrently repress multiple mRNA targets through imperfect complementarity. MicroRNA target recognition i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku171
更新日期:2014-05-01 00:00:00
abstract::The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although sing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt345
更新日期:2013-07-01 00:00:00