Publication Date:
2014-09-06
Description:
Post-transcriptional modification of RNA nucleosides occurs in all living organisms. Pseudouridine, the most abundant modified nucleoside in non-coding RNAs, enhances the function of transfer RNA and ribosomal RNA by stabilizing the RNA structure. Messenger RNAs were not known to contain pseudouridine, but artificial pseudouridylation dramatically affects mRNA function--it changes the genetic code by facilitating non-canonical base pairing in the ribosome decoding centre. However, without evidence of naturally occurring mRNA pseudouridylation, its physiological relevance was unclear. Here we present a comprehensive analysis of pseudouridylation in Saccharomyces cerevisiae and human RNAs using Pseudo-seq, a genome-wide, single-nucleotide-resolution method for pseudouridine identification. Pseudo-seq accurately identifies known modification sites as well as many novel sites in non-coding RNAs, and reveals hundreds of pseudouridylated sites in mRNAs. Genetic analysis allowed us to assign most of the new modification sites to one of seven conserved pseudouridine synthases, Pus1-4, 6, 7 and 9. Notably, the majority of pseudouridines in mRNA are regulated in response to environmental signals, such as nutrient deprivation in yeast and serum starvation in human cells. These results suggest a mechanism for the rapid and regulated rewiring of the genetic code through inducible mRNA modifications. Our findings reveal unanticipated roles for pseudouridylation and provide a resource for identifying the targets of pseudouridine synthases implicated in human disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224642/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224642/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carlile, Thomas M -- Rojas-Duran, Maria F -- Zinshteyn, Boris -- Shin, Hakyung -- Bartoli, Kristen M -- Gilbert, Wendy V -- GM081399/GM/NIGMS NIH HHS/ -- GM094303/GM/NIGMS NIH HHS/ -- R00 GM081399/GM/NIGMS NIH HHS/ -- R01 GM094303/GM/NIGMS NIH HHS/ -- R01 GM101316/GM/NIGMS NIH HHS/ -- T32 GM007287/GM/NIGMS NIH HHS/ -- T32GM007287/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Nov 6;515(7525):143-6. doi: 10.1038/nature13802. Epub 2014 Sep 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25192136" target="_blank"〉PubMed〈/a〉
Keywords:
Base Composition
;
Food Deprivation
;
Genetic Code
;
Genome/genetics
;
Humans
;
Intramolecular Transferases/metabolism
;
Pseudouridine/*analysis/chemistry/genetics
;
RNA, Messenger/*chemistry/metabolism
;
RNA, Untranslated/chemistry
;
Saccharomyces cerevisiae/cytology/*genetics
;
Sequence Analysis, RNA
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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