Ribosome profiling reveals features of normal and disease-associated mitochondrial translation

Nature Communications

Volumn 4, Issue , 2013, Pages

  Rooijers, Koos ^a   Loayza Puch, Fabricio ^a   Nijtmans, Leo G ^b   Agami, Reuven ^a,c  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c ROTTERDAM UNIVERSITY OF APPLIED SCIENCES   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSFER RNA; TRYPTOPHAN;

DISEASE INCIDENCE; GENE EXPRESSION; MITOCHONDRION; MUTATION; SIZE DISTRIBUTION;

ARTICLE; CELLULAR DISTRIBUTION; CODON; CONTROLLED STUDY; CYBRID; ENZYME ACTIVITY; GENE EXPRESSION PROFILING; GENETIC CORRELATION; HUMAN; HUMAN CELL; MITOCHONDRIAL GENE; MITOCHONDRIAL TRANSLATION; MITOCHONDRIAL VOLUME; MITOCHONDRION; MUTATION; NUCLEOTIDE SEQUENCE; QUALITY CONTROL; REPRODUCIBILITY; RIBOSOME; RIBOSOME PROTECTED FRAGMENT; RNA TRANSLATION; WILD TYPE;

CELL LINE; DISEASE; HUMANS; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, TRANSFER, TRP; TRANSCRIPTOME;

EID: 84890231951     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3886     Document Type: Article

References (19)

1. Smits, P., Smeitink, J. & van den Heuvel, L. Mitochondrial translation and beyond: processes implicated in combined oxidative phosphorylation deficiencies. J. Biomed. Biotechnol. 2010, 1-24 (2010).
2. Koc, E. C. & Koc, H. Regulation of mammalian mitochondrial translation by post-translational modifications. Biochim. Biophys. Acta 1819, 1055-1066 (2012).
3. Suen, D.-F., Norris, K. L. & Youle, R. J. Mitochondrial dynamics and apoptosis. Genes Dev. 22, 1577-1590 (2008). (Pubitemid 351846838)
4. Sharma, M. R. et al. Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins. Cell 115, 97-108 (2003). (Pubitemid 37255321)
5. Navarro, A. & Boveris, A. The mitochondrial energy transduction system and the aging process. Am. J. Physiol. Cell Physiol. 292, C670-C686 (2007).
6. Lin, M. T. & Beal, M. F. Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. Nature 443, 787-795 (2006). (Pubitemid 44622683)
7. Scharfe, C. et al. Mapping gene associations in human mitochondria using clinical disease phenotypes. PLoS Comput. Biol. 5, e1000374 (2009).
8. Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223 (2009).
9. Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534-1550 (2012).
10. Liu, B., Han, Y. & Qian, S.-B. Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol. Cell 49, 453-463 (2013).
11. Shalgi, R. et al. Widespread regulation of translation by elongation pausing in heat shock. Mol. Cell 49, 439-452 (2013).
12. Smits, P. et al. Functional consequences of mitochondrial tRNATrp and tRNAArg mutations causing combined OXPHOS defects. Eur. J. Hum. Genet. 18, 324-329 (2010).
13. O'Connor, P. B. F., Li, G.-W., Weissman, J. S., Atkins, J. F. & Baranov, P. V. rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. Bioinformatics 29, 1488-1491 (2013).
14. Chan, P. P. & Lowe, T. M. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37, D93-D97 (2009).
15. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
16. Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
17. Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46-53 (2012).
18. Robinson, M. D., McCarthy, D. J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
19. Loayza-Puch, F. et al. p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol. 14, R32 (2013).