Abstract：
:The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions and for base covariation revealed that in most eukaryotes the secondary structure of the area consists of 11 helices and includes two pseudoknots. In one of the pseudoknots, exchange of base pairs between the two stems seems to occur, and covariation analysis points to the presence of a base triple. The area also contains three potential insertion points where additional hairpins or branched structures are present in a number of taxa scattered throughout the eukaryotic domain.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wuyts J,De Rijk P,Van de Peer Y,Pison G,Rousseeuw P,De Wachter Rdoi
10.1093/nar/28.23.4698keywords:
subject
Has Abstractpub_date
2000-12-01 00:00:00pages
4698-708issue
23eissn
0305-1048issn
1362-4962journal_volume
28pub_type
杂志文章abstract：T:Activator protein 1 (AP-1) is a transcription factor that recognizes two versions of a 7-base pair response element, either 5΄- GAG CA-3΄ or 5΄- GAG CA-3΄ (where M = 5-methylcytosine). These two elements share the feature that 5-methylcytosine and thymine both have a methyl group in the same position, 5-carbon of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx057
更新日期：2017-03-17 00:00:00
abstract：:Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1195
更新日期：2021-01-11 00:00:00
abstract：:Kaposi's sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even though vIRF-1 shows sequence homology to the N-terminal DNA-binding domain (DBD) of human IRFs, a specific role for this domain in vIRF-1's function has remaine...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt082
更新日期：2013-04-01 00:00:00
abstract：:Unwanted side effects of drugs are a burden on patients and a severe impediment in the development of new drugs. At the same time, adverse drug reactions (ADRs) recorded during clinical trials are an important source of human phenotypic data. It is therefore essential to combine data on drugs, targets and side effects...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1075
更新日期：2016-01-04 00:00:00
abstract：:Mitotic chromosome structure is pivotal to cell division but difficult to observe in fine detail using conventional methods. DNA catenation has been implicated in both sister chromatid cohesion and chromosome condensation, but has never been observed directly. We have used a lab-on-a-chip microfluidic device and fluor...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks931
更新日期：2012-12-01 00:00:00
abstract：:Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alterna...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1271
更新日期：2013-02-01 00:00:00
abstract：:Ribonucleotides are misincorporated into replicating DNA due to the similarity of deoxyribonucleotides and ribonucleotides, the high concentration of ribonucleotides in the nucleus and the imperfect accuracy of replicative DNA polymerases in choosing the base with the correct sugar. Embedded ribonucleotides change cer...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gku773
更新日期：2014-01-01 00:00:00
abstract：:HT1080 cells stably expressing green fluorescent protein (GFP) linked to a 3' terminal AU-rich element (ARE) proved to be a convenient system to study the dynamics of mRNA stability, as changes in mRNA levels are reflected in increased or decreased fluorescence intensity. This study examined whether mRNA stability can...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh282
更新日期：2004-02-19 00:00:00
abstract：:Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the repl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz090
更新日期：2019-05-07 00:00:00
abstract：:High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku370
更新日期：2014-07-01 00:00:00
abstract：:KU is a heterodimer, consisting of approximately 70 and approximately 80 kDa subunits (KU70 and KU80, respectively), which is involved in a variety of nuclear functions. We generated tbKU80-deficient trypanosomes to explore the potential role of the tbKU complex in telomere maintenance and transcriptional regulation o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh991
更新日期：2004-12-15 00:00:00
abstract：:The disappearance of defined restriction fragments of the beta 1-globin, an albumin and the A1 vitellogenin gene was quantitated after DNase I digestion and expressed by a sensitivity factor defined by a mathematical model. Analysis of naked DNA showed that the gene fragments have similar but not identical sensitivity...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.11.2455
更新日期：1981-06-11 00:00:00
abstract：:Control of RNA processing plays a major role in HIV-1 gene expression. To explore the role of several hnRNP proteins in this process, we carried out a siRNA screen to examine the effect of depletion of hnRNPs A1, A2, D, H, I and K on HIV-1 gene expression. While loss of hnRNPs H, I or K had little effect, depletion of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1238
更新日期：2012-04-01 00:00:00
abstract：:Sequential chromatin immunoprecipitation (SeqChIP) is a procedure in which formaldehyde-crosslinked, protein-DNA complexes from living cells are subjected to two sequential immunoprecipitations with antibodies of different specificity. SeqChIP has been used to address, in a qualitative manner, whether two proteins can...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh148
更新日期：2004-11-01 00:00:00
abstract：:It is believed that depending on the thermodynamic stability of the 5'-strand and the 3'-strand in the stem-loop structure of a precursor microRNA (pre-miRNA), cells preferentially select the less stable one (called the miRNA or guide strand) and destroy the other one (called the miRNA* or passenger strand). However, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm641
更新日期：2007-01-01 00:00:00
abstract：:The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end gu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1170
更新日期：2020-02-20 00:00:00
abstract：:We describe here the cloning, characterization and expression in E. coli of the gene coding for a DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI). This enzyme methylates completely and exclusively CpG sequences. The Spiroplasma gene was transcribed in E. coli using its own promoter. Translation of the entire me...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.5.1145
更新日期：1990-03-11 00:00:00
abstract：:MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression bas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx588
更新日期：2017-09-06 00:00:00
abstract：:As more and more high-throughput data has been produced by next-generation sequencing, it is still a challenge to classify RNA transcripts into protein-coding or non-coding, especially for poorly annotated species. We upgraded our original coding potential calculator, CNCI (Coding-Non-Coding Index), to CNIT (Coding-No...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz400
更新日期：2019-07-02 00:00:00
abstract：:We have reported previously (1) two unexpected consequences of the microinjection into fertilized mouse eggs of a recombinant plasmid designated p12B1, carrying a 343 bp insert of non-repetitive mouse DNA. Injected at very low concentrations, this plasmid could be established as an extrachromosomal genetic element. Wh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.25.7243
更新日期：1991-12-01 00:00:00
abstract：:We describe a novel 3'-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2'-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1293
更新日期：2011-03-01 00:00:00
abstract：:A C-->U mutation (rdn5) in the conserved sarcin/ricin domain of yeast 25S rRNA has been shown to cause translational suppression and paromomycin resistance. It also separates the killing from the misreading effect of this antibiotic. We confirm these findings and provide in vitro evidence that rdn5 causes a 3-fold inc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh860
更新日期：2004-10-11 00:00:00
abstract：:MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku458
更新日期：2014-07-01 00:00:00
abstract：:SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of SIRT6-mediated transcriptional activation is unknown. Here, we employed SIRT6 sepa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz528
更新日期：2019-09-05 00:00:00
abstract：:The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodies...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz574
更新日期：2019-08-22 00:00:00
abstract：:A strategy for DNA computing on surfaces using linked sets of 'DNA words' that are short oligonucleotides (16mers) is proposed. The 16mer words have the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in 8 variable ('v') base locations, and the remaining fixed ('F') base locations are used as a word...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.23.4748
更新日期：1997-12-01 00:00:00
abstract：:Bacillus subtilis plasmid pGR71 is a promoter-probe shuttle vector derived from pUB110. The expression of the cat gene on pGR71 in B. subtilis requires the insertion of a Bacillus promoter and a ribosomal binding site (RBS) into the HindIII cloning site immediately upstream from the cat gene. A recombinant plasmid of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.4.739
更新日期：1990-02-25 00:00:00
abstract：:The main goal of this review is to provide some guide-lines for choosing a proper method when searching for differentially expressed transcripts. The choice of an approach should depend upon particular features of the experiment and project requirements. We outline some general considerations to help decide between di...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/26.24.5537
更新日期：1998-12-15 00:00:00
abstract：:Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interact...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1260
更新日期：2021-01-25 00:00:00
abstract：:Serine integrases are emerging as core tools in synthetic biology and have applications in biotechnology and genome engineering. We have designed a split-intein serine integrase-based system with potential for regulation of site-specific recombination events at the protein level in vivo. The ϕC31 integrase was split i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz936
更新日期：2019-12-02 00:00:00
