Abstract
RNase mitochondrial RNA processing (MRP) is an essential, evolutionarily conserved endoribonuclease composed of 10 different protein subunits and a single RNA. RNase MRP has established roles in multiple pathways including ribosome biogenesis, cell cycle regulation, and mitochondrial DNA replication. Although each of these functions is important to cell growth, additional functions may exist given the essential nature of the complex. To identify novel RNase MRP substrates, we utilized RNA immunoprecipitation and microarray chip analysis to identify RNA that physically associates with RNase MRP. We identified several new potential substrates for RNase MRP including a cell cycle-regulated transcript, CTS1; the yeast homolog of the mammalian p27(Kip1), SIC1; and the U2 RNA component of the spliceosome. In addition, we found RNase MRP to be involved in the regulation of the Ty1 transposon RNA. These results reinforce and broaden the role of RNase MRP in cell cycle regulation and help to identify new roles of this endoribonuclease.
Highlights
A global RNase mitochondrial RNA processing (MRP) substrate hunt has never been performed
The identification of RNase MRP-associated TAM bodies and these newly identified substrates suggest that RNase MRP serves a specific role in the regulation of key transcripts, which may be asymmetrically distributed within the cell, to ensure proper cell division and continued cell viability [8]
RNase MRP has been found in TAM bodies, cytoplasmic bodies that localize to the daughter cell prior to cytokinesis [8]
Summary
A global RNase MRP substrate hunt has never been performed. Results: We identified new potential substrates for RNase MRP. RNase mitochondrial RNA processing (MRP) is a highly conserved and essential endoribonuclease enzyme complex present in all eukaryotes with known functions in mitochondrial DNA replication, ribosomal biosynthesis, and cell cycle regulation. We identified the captured RNAs using oligonucleotide microarrays for Saccharomyces cerevisiae We have modified this approach by subjecting the cells to ultraviolet light prior to lysis to covalently bind substrate RNA to the RNase MRP complex and increase the RNA substrate yield [14, 15]. We have called this procedure RNA immunoprecipitation and microarray chip analysis (RIP-chip) [15]. This methodology enabled us to identify several new RNase MRP substrates including CTS1, SIC1, LSR1 and to identify a role for RNase MRP in the Ty1 retrotransposon cycle
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