Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Methods Enzymol
2015 Jan 01;560:187-217. doi: 10.1016/bs.mie.2015.03.009.
Show Gene links
Show Anatomy links
Pseudouridine in mRNA: Incorporation, Detection, and Recoding.
Wu G
,
Huang C
,
Yu YT
.
???displayArticle.abstract???
It has long been known that pseudouridine (Ψ) is the most abundant modified nucleotide in stable RNAs, including tRNA, rRNA, and snRNA. Recent studies using massive parallel sequencing have uncovered the presence of hundreds of Ψs in mRNAs as well. In eukaryotes and archaea, RNA pseudouridylation is introduced predominantly by box H/ACA RNPs, RNA-protein complexes each consisting of a single RNA moiety and four core proteins. It has been well established that Ψ plays an essential role in regulating the structure and function of stable RNAs in several model organisms, including yeast, Xenopus laevis, and humans. However, the functional role of Ψ in mRNA remains to be elucidated. One possibility (and true for stop/termination codons) is that Ψ influences decoding during translation. It is imperative, therefore, to establish a system, in which one can site-specifically introduce pseudouridylation into target mRNA and biochemically test the impact of mRNA pseudouridylation on protein translation. Here, we present a method for (1) site-specific conversion of uridine into Ψ in mRNA by designer box H/ACA RNP, (2) detection of Ψ in target mRNA using site-specific labeling followed by nuclease digestion and thin layer chromatography, and (3) analysis of recoding of pseudouridylated premature termination codon in mRNA during translation.
Adachi,
Purification of radiolabeled RNA products using denaturing gel electrophoresis.
2014, Pubmed
Adachi,
Purification of radiolabeled RNA products using denaturing gel electrophoresis.
2014,
Pubmed
Bilbille,
The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs.
2009,
Pubmed
Carlile,
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells.
2014,
Pubmed
Chernyakov,
Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.
2008,
Pubmed
Davis,
Stabilization of RNA stacking by pseudouridine.
1995,
Pubmed
DAVIS,
Ribonucleic acids from yeast which contain a fifth nucleotide.
1957,
Pubmed
Durant,
Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine.
1999,
Pubmed
Fernández,
Unusual base pairing during the decoding of a stop codon by the ribosome.
2013,
Pubmed
Ge,
RNA pseudouridylation: new insights into an old modification.
2013,
Pubmed
Huang,
Synthesis and labeling of RNA in vitro.
2013,
Pubmed
Huang,
Inducing nonsense suppression by targeted pseudouridylation.
2012,
Pubmed
Huang,
Post-transcriptional modification of RNAs by artificial Box H/ACA and Box C/D RNPs.
2011,
Pubmed
Karijolich,
Converting nonsense codons into sense codons by targeted pseudouridylation.
2011,
Pubmed
Karijolich,
Insight into the Protein Components of the Box H/ACA RNP.
2008,
Pubmed
King,
Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center.
2003,
Pubmed
Lecointe,
Lack of pseudouridine 38/39 in the anticodon arm of yeast cytoplasmic tRNA decreases in vivo recoding efficiency.
2002,
Pubmed
Lee,
Conformation studies of 13 trinucleoside diphosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and H1' protons.
1980,
Pubmed
Liang,
rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity.
2007,
Pubmed
Lovejoy,
Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae.
2014,
Pubmed
Ma,
Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism.
2005,
Pubmed
Schwartz,
Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.
2014,
Pubmed
Wu,
Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation.
2011,
Pubmed
,
Xenbase
Yu,
Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing.
1998,
Pubmed
,
Xenbase
Yu,
Construction of 4-thiouridine site-specifically substituted RNAs for cross-linking studies.
1999,
Pubmed
