Detection of PIWI and piRNAs in the mitochondria of mammalian cancer cells

Biochemical and Biophysical Research Communications

Volumn 446, Issue 1, 2014, Pages 218-223

  Kwon, Changhyuk ^a   Tak, Hyosun ^b   Rho, Mina ^c   Chang, Hae Ryung ^a   Kim, Yon Hui ^a   Kim, Kyung Tae ^a   Balch, Curt ^d   Lee, Eun Kyung ^b   Nam, Seungyoon ^a  

^a National Cancer Center   (South Korea)

^b The Catholic University of Korea   (South Korea)

^c Hanyang University   (South Korea)

^d Indiana University School of Medicine   (United States)

Author keywords

Bioinformatics; Genomics; Mitochondria; Non coding RNAs; piRNA; Piwi; Sequence analysis; Small RNA Seq

Indexed keywords

MITOCHONDRIAL DNA; PIWI INTERACTING RNA; PIWI PROTEIN; RNA; SMALL UNTRANSLATED RNA;

ANIMAL CELL; ARTICLE; CANCER CELL; CELL FRACTIONATION; CELLULAR DISTRIBUTION; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; MAMMAL CELL; MITOCHONDRIAL GENOME; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ALIGNMENT; WESTERN BLOTTING;

EUKARYOTA; MAMMALIA;

BIOINFORMATICS; GENOMICS; MITOCHONDRIA; NON-CODING RNAS; PIRNA; PIWI; SEQUENCE ANALYSIS; SMALL RNA-SEQ;

ARGONAUTE PROTEINS; CELL LINE, TUMOR; DNA, MITOCHONDRIAL; EXPRESSED SEQUENCE TAGS; GENOME, MITOCHONDRIAL; HEK293 CELLS; HELA CELLS; HUMANS; MITOCHONDRIAL PROTEINS; NEOPLASM PROTEINS; NEOPLASMS; RNA; RNA, NEOPLASM; RNA, SMALL INTERFERING;

EID: 84898010472     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2014.02.112     Document Type: Article

References (31)

1. M.C. Siomi, K. Sato, and D. Pezic et al. PIWI-interacting small RNAs: the vanguard of genome defence Nat. Rev. Mol. Cell Biol. 12 2011 246 258
2. A. Le Thomas, K.F. Toth, and A.A. Aravin To be or not to be a piRNA: genomic origin and processing of piRNAs Genome Biol. 15 2014 204
3. N.V. Rozhkov, M. Hammell, and G.J. Hannon Multiple roles for Piwi in silencing Drosophila transposons Genes Dev. 27 2013 400 412
4. A. Le Thomas, A.K. Rogers, and A. Webster et al. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state Genes Dev. 27 2013 390 399
5. H. Ishizu, H. Siomi, and M.C. Siomi Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines Genes Dev. 26 2012 2361 2373
6. S. Bamezai, V.P. Rawat, and C. Buske Concise review: the Piwi-piRNA axis: pivotal beyond transposon silencing Stem Cells 30 2012 2603 2611
7. H. Heyn, H.J. Ferreira, and L. Bassas et al. Epigenetic disruption of the PIWI pathway in human spermatogenic disorders PLoS ONE 7 2012 e47892
8. S. Siddiqi, and I. Matushansky Piwis and piwi-interacting RNAs in the epigenetics of cancer J. Cell. Biochem. 113 2012 373 380
9. R. Suzuki, S. Honda, and Y. Kirino PIWI expression and function in cancer Front. Genet. 3 2012 204
10. L. Sripada, D. Tomar, and P. Prajapati et al. Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA PLoS ONE 7 2012 e44873
11. T. Watanabe, S. Chuma, and Y. Yamamoto et al. MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline Dev. Cell 20 2011 364 375
12. T.R. Mercer, S. Neph, and M.E. Dinger et al. The human mitochondrial transcriptome Cell 146 2011 645 658
13. A. Girard, R. Sachidanandam, and G.J. Hannon et al. A germline-specific class of small RNAs binds mammalian Piwi proteins Nature 442 2006 199 202
14. J. Goecks, A. Nekrutenko, and J. Taylor Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol. 11 2010 R86
15. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
16. H. Li, B. Handsaker, and A. Wysoker et al. The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
17. A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
18. P.M. Krzyzanowski, F.D. Price, and E.M. Muro et al. Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery PLoS ONE 6 2011 e20561
19. L.R. Meyer, A.S. Zweig, and A.S. Hinrichs et al. The UCSC Genome Browser database: extensions and updates 2013 Nucleic Acids Res. 41 2013 D64 D69
20. S.W. Yu, H. Wang, and M.F. Poitras et al. Mediation of poly(ADP-ribose) polymerase-1-dependent cell death by apoptosis-inducing factor Science 297 2002 259 263
21. C.R. Galiveti, T.S. Rozhdestvensky, and J. Brosius et al. Application of housekeeping npcRNAs for quantitative expression analysis of human transcriptome by real-time PCR RNA 16 2010 450 461
22. M.I. Sanchez, T.R. Mercer, and S.M. Davies et al. RNA processing in human mitochondria Cell Cycle 10 2011 2904 2916
23. A. Furia, M. Moscato, and G. Cali et al. The ribonuclease/angiogenin inhibitor is also present in mitochondria and nuclei FEBS Lett. 585 2011 613 617
24. J.T. Robinson, H. Thorvaldsdottir, and W. Winckler et al. Integrative genomics viewer Nat. Biotechnol. 29 2011 24 26
25. J. Cheng, J.M. Guo, and B.X. Xiao et al. PiRNA, the new non-coding RNA, is aberrantly expressed in human cancer cells Clin. Chim. Acta 412 2011 1621 1625
26. M.G. Claros, and P. Vincens Computational method to predict mitochondrially imported proteins and their targeting sequences Eur. J. Biochem. 241 1996 779 786
27. D.M. Thompson, and R. Parker Stressing out over tRNA cleavage Cell 138 2009 215 219
28. P.K. Padmanabhan, C. Dumas, and M. Samant et al. Novel features of a PIWI-like protein homolog in the parasitic protozoan Leishmania PLoS ONE 7 2012 e52612
29. A.H. Schapira Mitochondrial diseases Lancet 379 2012 1825 1834
30. M.B. Sporn, and K.T. Liby NRF2 and cancer: the good, the bad and the importance of context Nat. Rev. Cancer 12 2012 564 571
31. A. Janic, L. Mendizabal, and S. Llamazares et al. Ectopic expression of germline genes drives malignant brain tumor growth in Drosophila Science 330 2010 1824 1827