Mapping of Mitochondrial RNA-Protein Interactions by Digital RNase Footprinting

•Mapping of mitochondrial RNA-protein interactions at a single-nucleotide level•Gene-specific knockdown identifies new and specific RNA binding sites of proteins•Identification of mitochondrial ribosomal footprints on RNAs•Detailed identification of mitochondrial RNA secondary structure in vivo

SummaryHuman mitochondrial DNA is transcribed as long polycistronic transcripts that encompass each strand of the genome and are processed subsequently into mature mRNAs, tRNAs, and rRNAs, necessitating widespread posttranscriptional regulation. Here, we establish methods for massively parallel sequencing and analyses of RNase-accessible regions of human mitochondrial RNA and thereby identify specific regions within mitochondrial transcripts that are bound by proteins. This approach provides a range of insights into the contribution of RNA-binding proteins to the regulation of mitochondrial gene expression.

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