Niemelä Elina H, Oghabian Ali, Staals Raymond H J, Greco Dario, Pruijn Ger J M, Frilander Mikko J
Institute of Biotechnology, P.O. Box 56, FI-00014 University of Helsinki, Finland.
Department of Biomolecular Chemistry, Radboud Institute for Molecular Life Sciences and Institute for Molecules and Materials, Radboud University Nijmegen,The Netherlands.
Nucleic Acids Res. 2014 Jun;42(11):7358-69. doi: 10.1093/nar/gku391. Epub 2014 May 21.
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.
U12型内含子是多种真核生物基因组中一类罕见的内含子。在人类基因组中，它们的数量超过700个。与主要的U2型内含子相比，这些内含子中的一部分已被证明剪接速度较慢。这表明小剪接体在处理含有U12型内含子的转录本时具有限速调节功能。然而，剪接速度较慢的普遍性以及部分加工的前体mRNA的后续命运仍然未知。在这里，我们对含有U12型内含子的转录本的核滞留进行了全面分析，并为人类细胞中此类转录本的核降解提供了证据。使用SOLiD RNA测序技术，我们发现，在正常细胞中，U12型内含子的平均滞留率比周围的U2型内含子高2倍。此外，我们发现外切体的RRP41和DIS3亚基的敲低稳定了一组重叠的U12型内含子。RRP41敲低导致U12型内含子的降解动力学变慢，并在整体上上调U12型而非U2型内含子的滞留率。我们的结果表明，U12型内含子的剪接效率较低，并被外切体靶向。这些特征支持了它们在调节细胞mRNA水平中的作用。
