Mapping of Mitochondrial RNA-Protein Interactions by Digital RNase Footprinting
Ganqiang Liu,
Timothy R. Mercer,
Anne-Marie J. Shearwood,
Stefan J. Siira,
Moira E. Hibbs,
John S. Mattick,
Oliver Rackham,
Aleksandra Filipovska
Affiliations
Ganqiang Liu
Garvan Institute of Medical Research, Sydney NSW 2010, Australia
Timothy R. Mercer
Garvan Institute of Medical Research, Sydney NSW 2010, Australia
Anne-Marie J. Shearwood
Western Australian Institute for Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth WA 6000, Australia
Stefan J. Siira
Western Australian Institute for Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth WA 6000, Australia
Moira E. Hibbs
Western Australian Institute for Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth WA 6000, Australia
John S. Mattick
Garvan Institute of Medical Research, Sydney NSW 2010, Australia
Oliver Rackham
Western Australian Institute for Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth WA 6000, Australia
Aleksandra Filipovska
Western Australian Institute for Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth WA 6000, Australia
Human 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.
