The human mitochondrial transcriptome

Cell

Volumn 146, Issue 4, 2011, Pages 645-658

  Mercer, Tim R ^a   Neph, Shane ^b   Dinger, Marcel E ^a   Crawford, Joanna ^a   Smith, Martin A ^a   Shearwood, Anne Marie J ^c   Haugen, Eric ^b   Bracken, Cameron P ^d   Rackham, Oliver ^c   Stamatoyannopoulos, John A ^b   Filipovska, Aleksandra ^c   Mattick, John S ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^d CENTRE FOR CANCER BIOLOGY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; MESSENGER RNA; RIBOSOME RNA; RNA; TRANSCRIPTOME; TRANSFER RNA;

ARTICLE; CELL LINE; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; MITOCHONDRION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 80052007901     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2011.06.051     Document Type: Article

References (77)

1. S. Anderson, A.T. Bankier, B.G. Barrell, M.H. de Bruijn, A.R. Coulson, J. Drouin, I.C. Eperon, D.P. Nierlich, B.A. Roe, and F. Sanger Sequence and organization of the human mitochondrial genome Nature 290 1981 457 465 (Pubitemid 11159074)
2. A. Bhat, A. Koul, S. Sharma, E. Rai, S.I. Bukhari, M.K. Dhar, and R.N. Bamezai The possible role of 10398A and 16189C mtDNA variants in providing susceptibility to T2DM in two North Indian populations: a replicative study Hum. Genet. 120 2007 821 826 (Pubitemid 46128837)
3. G. Cannino, C.M. Di Liegro, and A.M. Rinaldi Nuclear-mitochondrial interaction Mitochondrion 7 2007 359 366 (Pubitemid 350082356)
4. M. Crimi, R. Del Bo, S. Galbiati, M. Sciacco, A. Bordoni, N. Bresolin, and G.P. Comi Mitochondrial A12308G polymorphism affects clinical features in patients with single mtDNA macrodeletion Eur. J. Hum. Genet. 11 2003 896 898 (Pubitemid 37406996)
5. G.E. Crooks, G. Hon, J.-M. Chandonia, and S.E. Brenner WebLogo: a sequence logo generator Genome Res. 14 2004 1188 1190 (Pubitemid 38811555)
6. N.S. Entelis, S. Kieffer, O.A. Kolesnikova, R.P. Martin, and I.A. Tarassov Structural requirements of tRNALys for its import into yeast mitochondria Proc. Natl. Acad. Sci. USA 95 1998 2838 2843
7. N.S. Entelis, O.A. Kolesnikova, R.P. Martin, and I.A. Tarassov RNA delivery into mitochondria Adv. Drug Deliv. Rev. 49 2001 199 215 (Pubitemid 32493809)
8. R.P. Fisher, J.N. Topper, and D.A. Clayton Promoter selection in human mitochondria involves binding of a transcription factor to orientation- independent upstream regulatory elements Cell 50 1987 247 258
9. R.P. Fisher, T. Lisowsky, M.A. Parisi, and D.A. Clayton DNA wrapping and bending by a mitochondrial high mobility group-like transcriptional activator protein J. Biol. Chem. 267 1992 3358 3367
10. J.M. Fusté, S. Wanrooij, E. Jemt, C.E. Granycome, T.J. Cluett, Y. Shi, N. Atanassova, I.J. Holt, C.M. Gustafsson, and M. Falkenberg Mitochondrial RNA polymerase is needed for activation of the origin of light-strand DNA replication Mol. Cell 37 2010 67 78
11. M.A. German, M. Pillay, D.H. Jeong, A. Hetawal, S. Luo, P. Janardhanan, V. Kannan, L.A. Rymarquis, K. Nobuta, and R. German Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends Nat. Biotechnol. 26 2008 941 946
12. T. Gesell, and S. Washietl Dinucleotide controlled null models for comparative RNA gene prediction BMC Bioinformatics 9 2008 248
13. S.C. Ghivizzani, C.S. Madsen, M.R. Nelen, C.V. Ammini, and W.W. Hauswirth In organello footprint analysis of human mitochondrial DNA: human mitochondrial transcription factor A interactions at the origin of replication Mol. Cell. Biol. 14 1994 7717 7730 (Pubitemid 24373523)
14. M.X. Guan, J.A. Enriquez, N. Fischel-Ghodsian, R.S. Puranam, C.P. Lin, M.A. Maw, and G. Attardi The deafness-associated mitochondrial DNA mutation at position 7445, which affects tRNASer(UCN) precursor processing, has long-range effects on NADH dehydrogenase subunit ND6 gene expression Mol. Cell. Biol. 18 1998 5868 5879 (Pubitemid 28450538)
15. K. Hancock, A.J. LeBlanc, D. Donze, and S.L. Hajduk Identification of nuclear encoded precursor tRNAs within the mitochondrion of Trypanosoma brucei J. Biol. Chem. 267 1992 23963 23971 (Pubitemid 23088211)
16. D. Haussecker, Y. Huang, A. Lau, P. Parameswaran, A.Z. Fire, and M.A. Kay Human tRNA-derived small RNAs in the global regulation of RNA silencing RNA 16 2010 673 695
17. W.W. Hauswirth, and D.A. Clayton Length heterogeneity of a conserved displacement-loop sequence in human mitochondrial DNA Nucleic Acids Res. 13 1985 8093 8104
18. J.R. Hesselberth, X. Chen, Z. Zhang, P.J. Sabo, R. Sandstrom, A.P. Reynolds, R.E. Thurman, S. Neph, M.S. Kuehn, and W.S. Noble Global mapping of protein-DNA interactions in vivo by digital genomic footprinting Nat. Methods 6 2009 283 289
19. I.J. Holt, J. He, C.C. Mao, J.D. Boyd-Kirkup, P. Martinsson, H. Sembongi, A. Reyes, and J.N. Spelbrink Mammalian mitochondrial nucleoids: organizing an independently minded genome Mitochondrion 7 2007 311 321 (Pubitemid 47304014)
20. A. Jacquier The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs Nat. Rev. Genet. 10 2009 833 844
21. F.V. Karginov, S. Cheloufi, M.M. Chong, A. Stark, A.D. Smith, and G.J. Hannon Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases Mol. Cell 38 2010 781 788
22. S.S. Khogali, B.M. Mayosi, J.M. Beattie, W.J. McKenna, H. Watkins, and J. Poulton A common mitochondrial DNA variant associated with susceptibility to dilated cardiomyopathy in two different populations Lancet 357 2001 1265 1267 (Pubitemid 32539059)
23. M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne, D. Horsman, S.J. Jones, and M.A. Marra Circos: an information aesthetic for comparative genomics Genome Res. 19 2009 1639 1645
24. N. Lane, and W. Martin The energetics of genome complexity Nature 467 2010 929 934
25. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
26. Y.S. Lee, Y. Shibata, A. Malhotra, and A. Dutta A novel class of small RNAs: tRNA-derived RNA fragments (tRFs) Genes Dev. 23 2009 2639 2649
27. H. Lin, Z. Zhang, M.Q. Zhang, B. Ma, and M. Li ZOOM! Zillions of oligos mapped Bioinformatics 24 2008 2431 2437
28. J. Lu, Y. Qian, Z. Li, A. Yang, Y. Zhu, R. Li, L. Yang, X. Tang, B. Chen, and Y. Ding Mitochondrial haplotypes may modulate the phenotypic manifestation of the deafness-associated 12S rRNA 1555A>G mutation Mitochondrion 10 2010 69 81
29. C. Mayr, and D.P. Bartel Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells Cell 138 2009 673 684
30. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, and M. Daly The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Genome Res. 20 2010 1297 1303
31. R. Morin, M. Bainbridge, A. Fejes, M. Hirst, M. Krzywinski, T. Pugh, H. McDonald, R. Varhol, S. Jones, and M. Marra Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing Biotechniques 45 2008 81 94
32. R.M. Myers, J. Stamatoyannopoulos, M. Snyder, I. Dunham, R.C. Hardison, B.E. Bernstein, T.R. Gingeras, W.J. Kent, E. Birney, B. Wold, G.E. Crawford ENCODE Project Consortium A user's guide to the encyclopedia of DNA elements (ENCODE) PLoS Biol. 9 2011 e1001046
33. T. Nagaike, T. Suzuki, T. Katoh, and T. Ueda Human mitochondrial mRNAs are stabilized with polyadenylation regulated by mitochondria-specific poly(A) polymerase and polynucleotide phosphorylase J. Biol. Chem. 280 2005 19721 19727 (Pubitemid 41379497)
34. M. Noll Internal structure of the chromatin subunit Nucleic Acids Res. 1 1974 1573 1578
35. D. Ojala, J. Montoya, and G. Attardi tRNA punctuation model of RNA processing in human mitochondria Nature 290 1981 470 474 (Pubitemid 11159076)
36. D.J. Pagliarini, S.E. Calvo, B. Chang, S.A. Sheth, S.B. Vafai, S.E. Ong, G.A. Walford, C. Sugiana, A. Boneh, and W.K. Chen A mitochondrial protein compendium elucidates complex I disease biology Cell 134 2008 112 123 (Pubitemid 351916708)
37. J.S. Pedersen, G. Bejerano, A. Siepel, K. Rosenbloom, K. Lindblad-Toh, E.S. Lander, J. Kent, W. Miller, and D. Haussler Identification and classification of conserved RNA secondary structures in the human genome PLoS Comput. Biol. 2 2006 e33
38. D.B. Percival, and T.W. Walden Spectral Analysis for Physical Applications: Multitaper and Conventional Univariate Techniques 1993 Cambridge University Press Cambridge
39. J. Piechota, R. Tomecki, K. Gewartowski, R. Szczesny, A. Dmochowska, M. Kudła, L. Dybczyńska, P.P. Stepien, and E. Bartnik Differential stability of mitochondrial mRNA in HeLa cells Acta Biochim. Pol. 53 2006 157 168
40. W. Rossmanith, and J. Holzmann Processing mitochondrial (t)RNAs: new enzyme, old job Cell Cycle 8 2009 1650 1653
41. M.A. Rubio, J.J. Rinehart, B. Krett, S. Duvezin-Caubet, A.S. Reichert, D. Söll, and J.D. Alfonzo Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import Proc. Natl. Acad. Sci. USA 105 2008 9186 9191
42. P.J. Sabo, M.S. Kuehn, R. Thurman, B.E. Johnson, E.M. Johnson, H. Cao, M. Yu, E. Rosenzweig, J. Goldy, and A. Haydock Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays Nat. Methods 3 2006 511 518 (Pubitemid 43941768)
43. E. Sbis, A. Tullo, M. Nardelli, F. Tanzariello, and C. Saccone Transcription mapping of the Ori L region reveals novel precursors of mature RNA species and antisense RNAs in rat mitochondrial genome FEBS Lett. 296 1992 311 316
44. R.C. Scarpulla Transcriptional paradigms in mammalian mitochondrial biogenesis and function Physiol. Rev. 88 2008 611 638 (Pubitemid 351520089)
45. C. Shin, J.W. Nam, K.K. Farh, H.R. Chiang, A. Shkumatava, and D.P. Bartel Expanding the microRNA targeting code: functional sites with centered pairing Mol. Cell 38 2010 789 802
46. S. Slomovic, D. Laufer, D. Geiger, and G. Schuster Polyadenylation and degradation of human mitochondrial RNA: the prokaryotic past leaves its mark Mol. Cell. Biol. 25 2005 6427 6435 (Pubitemid 41023219)
47. S. Suissa, Z. Wang, J. Poole, S. Wittkopp, J. Feder, T.E. Shutt, D.C. Wallace, G.S. Shadel, and D. Mishmar Ancient mtDNA genetic variants modulate mtDNA transcription and replication PLoS Genet. 5 2009 e1000474
48. J. Sylvestre, S. Vialette, M. Corral Debrinski, and C. Jacq Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria Genome Biol. 4 2003 R44
49. R.J. Szczesny, L.S. Borowski, L.K. Brzezniak, A. Dmochowska, K. Gewartowski, E. Bartnik, and P.P. Stepien Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance Nucleic Acids Res. 38 2010 279 298
50. R.W. Taylor, and D.M. Turnbull Mitochondrial DNA mutations in human disease Nat. Rev. Genet. 6 2005 389 402 (Pubitemid 40577182)
51. R. Temperley, R. Richter, S. Dennerlein, R.N. Lightowlers, and Z.M. Chrzanowska-Lightowlers Hungry codons promote frameshifting in human mitochondrial ribosomes Science 327 2010 301
52. R.J. Temperley, S.H. Seneca, K. Tonska, E. Bartnik, L.A. Bindoff, R.N. Lightowlers, and Z.M. Chrzanowska-Lightowlers Investigation of a pathogenic mtDNA microdeletion reveals a translation-dependent deadenylation decay pathway in human mitochondria Hum. Mol. Genet. 12 2003 2341 2348 (Pubitemid 37160878)
53. R.J. Temperley, M. Wydro, R.N. Lightowlers, and Z.M. Chrzanowska- Lightowlers Human mitochondrial mRNAs - like members of all families, similar but different Biochim. Biophys. Acta 1797 2010 1081 1085
54. C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat. Biotechnol. 28 2010 511 515
55. G. Wang, H.W. Chen, Y. Oktay, J. Zhang, E.L. Allen, G.M. Smith, K.C. Fan, J.S. Hong, S.W. French, and J.M. McCaffery PNPASE regulates RNA import into mitochondria Cell 142 2010 456 467
56. S. Washietl, I.L. Hofacker, M. Lukasser, A. Hüttenhofer, and P.F. Stadler Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome Nat. Biotechnol. 23 2005 1383 1390 (Pubitemid 41679390)
57. E. Yakubovskaya, E. Mejia, J. Byrnes, E. Hambardjieva, and M. Garcia-Diaz Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription Cell 141 2010 982 993
58. C. Zhang Novel functions for small RNA molecules Curr. Opin. Mol. Ther. 11 2009 641 651
59. Czech, B.; Zhou, R.; Erlich, Y.; Brennecke, J.; Binari, R.; Villalta, C.; Gordon, A.; Perrimon, N.; and Hannon, G.J. (2009). Hierarchical rules for Argonaute loading in Drosophila. Mol. Cell 36, 445-456.
60. de Hoon, M.J.; Imoto, S.; Nolan, J.; and Miyano, S. (2004). Open source clustering software. Bioinformatics 20, 1453-1454. (Pubitemid 38931415)
61. German, M.A.; Pillay, M.; Jeong, D.H.; Hetawal, A.; Luo, S.; Janardhanan, P.; Kannan, V.; Rymarquis, L.A.; Nobuta, K.; German, R.; et al. (2008). Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol. 26, 941-946.
62. Gesell, T.; and Washietl, S. (2008). Dinucleotide controlled null models for comparative RNA gene prediction. BMC Bioinformatics 9, 248.
63. Haussecker, D.; Huang, Y.; Lau, A.; Parameswaran, P.; Fire, A.Z.; and Kay, M.A. (2010). Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16, 673-695.
64. Hesselberth, J.R.; Chen, X.; Zhang, Z.; Sabo, P.J.; Sandstrom, R.; Reynolds, A.P.; Thurman, R.E.; Neph, S.; Kuehn, M.S.; Noble, W.S.; et al. (2009). Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods 6, 283-289.
65. John, S.; Sabo, P.J.; Thurman, R.E.; Sung, M.H.; Biddie, S.C.; Johnson, T.A.; Hager, G.L.; and Stamatoyannopoulos, J.A. (2011). Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43, 264-268.
66. Langmead, B.; Trapnell, C.; Pop, M.; and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.
67. Lin, H.; Zhang, Z.; Zhang, M.Q.; Ma, B.; and Li, M. (2008). ZOOM! Zillions of oligos mapped. Bioinformatics 24, 2431-2437.
68. Mayr, C.; and Bartel, D.P. (2009). Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673-684.
69. McKenna, A.; Hanna, M.; Banks, E.; Sivachenko, A.; Cibulskis, K.; Kernytsky, A.; Garimella, K.; Altshuler, D.; Gabriel, S.; Daly, M.; et al. (2010). The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303.
70. Medina, I.; Carbonell, J.; Pulido, L.; Madeira, S.C.; Goetz, S.; Conesa, A.; Tárraga, J.; Pascual-Montano, A.; Nogales-Cadenas, R.; Santoyo, J.; et al. (2010). Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res. 38 (Web Server issue), W210-W213.
71. Pagliarini, D.J.; Calvo, S.E.; Chang, B.; Sheth, S.A.; Vafai, S.B.; Ong, S.E.; Walford, G.A.; Sugiana, C.; Boneh, A.; Chen, W.K.; et al. (2008). A mitochondrial protein compendium elucidates complex I disease biology. Cell 134, 112-123. (Pubitemid 351916708)
72. Percival, D.B.; and Walden, T.W. (1993). Spectral Analysis for Physical Applications: Multitaper and Conventional Univariate Techniques. (Cambridge: Cambridge University Press).
73. Sabo, P.J.; Kuehn, M.S.; Thurman, R.; Johnson, B.E.; Johnson, E.M.; Cao, H.; Yu, M.; Rosenzweig, E.; Goldy, J.; Haydock, A.; et al. (2006). Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat. Methods 3, 511-518. (Pubitemid 43941768)
74. Saldanha, A.J. (2004). Java Treeview - extensible visualization of microarray data. Bioinformatics 20, 3246-3248. (Pubitemid 39619217)
75. Sekimata, M.; Pérez-Melgosa, M.; Miller, S.A.; Weinmann, A.S.; Sabo, P.J.; Sandstrom, R.; Dorschner, M.O.; Stamatoyannopoulos, J.A.; and Wilson, C.B. (2009). CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity 31, 551-564.
76. Trapnell, C.; Williams, B.A.; Pertea, G.; Mortazavi, A.; Kwan, G.; van Baren, M.J.; Salzberg, S.L.; Wold, B.J.; and Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515.
77. Yakubovskaya, E.; Mejia, E.; Byrnes, J.; Hambardjieva, E.; and Garcia-Diaz, M. (2010). Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription. Cell 141, 982-993.