Global analysis of the nuclear processing of transcripts with unspliced U12-type introns by the exosome.
U12-type introns are a rare class of introns in the genomes of diverse eukaryotes. In the human genome, they number over 700. A subset of these introns has been shown to be spliced at a slower rate compared to the major U2-type introns. This suggests a rate-limiting regulatory function for the minor spliceosome in the processing of transcripts containing U12-type introns. However, both the generality of slower splicing and the subsequent fate of partially processed pre-mRNAs remained unknown. Here, we present a global analysis of the nuclear retention of transcripts containing U12-type introns and provide evidence for the nuclear decay of such transcripts in human cells. Using SOLiD RNA sequencing technology, we find that, in normal cells, U12-type introns are on average 2-fold more retained than the surrounding U2-type introns. Furthermore, we find that knockdown of RRP41 and DIS3 subunits of the exosome stabilizes an overlapping set of U12-type introns. RRP41 knockdown leads to slower decay kinetics of U12-type introns and globally upregulates the retention of U12-type, but not U2-type, introns. Our results indicate that U12-type introns are spliced less efficiently and are targeted by the exosome. These characteristics support their role in the regulation of cellular mRNA levels.
Institute of Biotechnology, P.O. Box 56, FI-00014 University of Helsinki, Finland.
Elina H
EH
Niemelä
Institute of Biotechnology, P.O. Box 56, FI-00014 University of Helsinki, Finland.
Ali
A
Oghabian
Department of Biomolecular Chemistry, Radboud Institute for Molecular Life Sciences and Institute for Molecules and Materials, Radboud University Nijmegen,The Netherlands.
Raymond H J
RH
Staals
Unit of Systems Toxicology, Finnish Institute of Occupational Health, Topeliuksenkatu 41 a A, FI-00250 Helsinki, Finland.
Dario
D
Greco
Department of Biomolecular Chemistry, Radboud Institute for Molecular Life Sciences and Institute for Molecules and Materials, Radboud University Nijmegen,The Netherlands.
Ger J M
GJ
Pruijn
Institute of Biotechnology, P.O. Box 56, FI-00014 University of Helsinki, Finland mikko.frilander@helsinki.fi.
Mikko J
MJ
Frilander
D002460:Cell Line; D002467:Cell Nucleus / Q000201:enzymology / Q000378:metabolism*; D063326:Exosome Multienzyme Ribonuclease Complex / Q000037:antagonists & inhibitors / Q000378:metabolism*; D006801:Humans; D007438:Introns; D012322:RNA Precursors / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability; D012333:RNA, Messenger / Q000378:metabolism*; D012342:RNA, Small Nuclear / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000037:antagonists & inhibitors
D012322:RNA Precursors; D012333:RNA, Messenger; D012342:RNA, Small Nuclear; D016601:RNA-Binding Proteins; C096986:U12 small nuclear RNA; C415835:EXOSC4 protein, human; D063326:Exosome Multienzyme Ribonuclease Complex; C551543:DIS3 protein, human