Regulation of lipid metabolism by dicer revealed through SILAC mice

Journal of Proteome Research

Volumn 11, Issue 4, 2012, Pages 2193-2205

  Huang, Tai Chung ^a   Sahasrabuddhe, Nandini A ^c,d   Kim, Min Sik ^a   Getnet, Derese ^a   Yang, Yi ^a   Peterson, Jonathan M ^b   Ghosh, Bidyut ^a   Chaerkady, Raghothama ^a   Leach, Steven D ^a   Marchionni, Luigi ^a   Wong, G William ^b   Pandey, Akhilesh ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c Institute of Bioinformatics   (India)

^d MANIPAL UNIVERSITY   (India)

Author keywords

Dicer; lipid; metabolic labeling; microRNA; multiple reaction monitoring; proteomics; ribosome; SILAC; small intestine; triglyceride

Indexed keywords

DICER; FATTY ACID BINDING PROTEIN; LONG CHAIN FATTY ACID COENZYME A LIGASE; MESSENGER RNA; MICROSOMAL TRIGLYCERIDE TRANSFER PROTEIN; TAMOXIFEN;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FEMALE; GENE EXPRESSION PROFILING; IN VIVO STUDY; LIPID METABOLISM; LIPID STORAGE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN TARGETING; PROTEOMICS; REGULATORY MECHANISM; SMALL INTESTINE;

ANIMALS; DEAD-BOX RNA HELICASES; GENE EXPRESSION REGULATION; GENE KNOCKOUT TECHNIQUES; GENETIC ENGINEERING; HISTOCYTOCHEMISTRY; INTESTINE, SMALL; LIPID METABOLISM; MASS SPECTROMETRY; MICE; MICE, INBRED C57BL; MICE, KNOCKOUT; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; RIBONUCLEASE III;

MUS;

EID: 84859562759     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr2009884     Document Type: Article

References (27)

1. Bernstein, E.; Caudy, A. A.; Hammond, S. M.; Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference Nature 2001, 409, 363-366
2. Knight, S. W.; Bass, B. L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans Science 2001, 293, 2269-2271
3. Macrae, I. J.; Zhou, K.; Li, F.; Repic, A.; Brooks, A. N.; Cande, W. Z.; Adams, P. D.; Doudna, J. A. Structural basis for double-stranded RNA processing by Dicer Science 2006, 311, 195-198
4. Li, Q.; Tainsky, M. A. Higher miRNA tolerance in immortal Li-Fraumeni fibroblasts with abrogated interferon signaling pathway Cancer Res. 2011, 71, 255-265
5. Bernstein, E.; Kim, S. Y.; Carmell, M. A.; Murchison, E. P.; Alcorn, H.; Li, M. Z.; Mills, A. A.; Elledge, S. J.; Anderson, K. V.; Hannon, G. J. Dicer is essential for mouse development Nat. Genet. 2003, 35, 215-217
6. Wienholds, E.; Koudijs, M. J.; van Eeden, F. J.; Cuppen, E.; Plasterk, R. H. The microRNA-producing enzyme Dicer1 is essential for zebrafish development Nat. Genet. 2003, 35, 217-218
7. Hebert, S. S.; Papadopoulou, A. S.; Smith, P.; Galas, M. C.; Planel, E.; Silahtaroglu, A. N.; Sergeant, N.; Buee, L.; De Strooper, B. Genetic ablation of Dicer in adult forebrain neurons results in abnormal tau hyperphosphorylation and neurodegeneration Hum. Mol. Genet. 2010, 19, 3959-3969
8. Ho, J.; Ng, K. H.; Rosen, S.; Dostal, A.; Gregory, R. I.; Kreidberg, J. A. Podocytespecific loss of functional microRNAs leads to rapid glomerular and tubular injury J. Am. Soc. Nephrol. 2008, 19, 2069-2075
9. Zhou, L.; Seo, K. H.; He, H. Z.; Pacholczyk, R.; Meng, D. M.; Li, C. G.; Xu, J.; She, J. X.; Dong, Z.; Mi, Q. S. Tie2cre-induced inactivation of the miRNA-processing enzymeDicer disrupts invariant NKT cell development Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 10266-10271
10. ORourke, J. R.; Georges, S. A.; Seay, H. R.; Tapscott, S. J.; McManus, M. T.; Goldhamer, D. J.; Swanson, M. S.; Harfe, B. D. Essential role for Dicer during skeletal muscle development Dev. Biol. 2007, 311, 359-368
11. Sekine, S.; Ogawa, R.; Ito, R.; Hiraoka, N.; McManus, M. T.; Kanai, Y.; Hebrok, M. Disruption of Dicer1 induces dysregulated fetal gene expression and promotes hepatocarcinogenesis Gastroenterology 2009, 136, 2304-2315
12. Koralov, S. B.; Muljo, S. A.; Galler, G. R.; Krek, A.; Chakraborty, T.; Kanellopoulou, C.; Jensen, K.; Cobb, B. S.; Merkenschlager, M.; Rajewsky, N.; Rajewsky, K. Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage Cell 2008, 132, 860-874
13. Muljo, S. A.; Ansel, K. M.; Kanellopoulou, C.; Livingston, D. M.; Rao, A.; Rajewsky, K. Aberrant T cell differentiation in the absence of Dicer J. Exp. Med. 2005, 202, 261-269
14. Kanellopoulou, C.; Muljo, S. A.; Kung, A. L.; Ganesan, S.; Drapkin, R.; Jenuwein, T.; Livingston, D. M.; Rajewsky, K. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing Genes Dev. 2005, 19, 489-501
15. Nakagawa, A.; Shi, Y.; Kage-Nakadai, E.; Mitani, S.; Xue, D. Caspase-dependent conversion of Dicer ribonuclease into a death-promoting deoxyribonuclease Science 2010, 328, 327-334
16. Chaerkady, R.; Pandey, A. Quantitative proteomics for identification of cancer biomarkers Proteomics Clin. Appl. 2007, 1, 1080-1089
17. Manes, N. P.; Dong, L.; Zhou, W.; Du, X.; Reghu, N.; Kool, A. C.; Choi, D.; Bailey, C. L.; Petricoin, E. F. r.; Liotta, L. A.; Popov, S. G. Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry Mol. Cell. Proteomics 2011, 10.1074/mcp.M110.000927
18. Xu, X.; Othman, E.-D.; Issaq, H. J.; Hornung, D.; Al-Hendy, A.; Veenstra, T. D. Multiplexed quantitation of endogenous estrogens and estrogen metabolites in human peritoneal fluid Electrophoresis 2008, 29, 2706-2713
19. Bondarenko, P. V.; Chelius, D.; Shaler, T. A. Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry Anal. Chem. 2002, 74, 4741-4749
20. Liu, H.; Sadygov, R. G.; Yates, J. R. r. A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76, 4193-4201
21. Old, W. M.; Meyer-Arendt, K.; Aveline-Wolf, L.; Pierce, K. G.; Mendoza, A.; Sevinsky, J. R.; Resing, K. A.; Ahn, N. G. Comparison of label-free methods for quantifying human proteins by shotgun proteomics Mol. Cell. Proteomics. 2005, 4, 1487-1502
22. Ross, P. L.; Huang, Y. N.; Marchese, J. N.; Williamson, B.; Parker, K.; Hattan, S.; Khainovski, N.; Pillai, S.; Dey, S.; Daniels, S.; Purkayastha, S.; Juhasz, P.; Martin, S.; Bartlet-Jones, M.; He, F.; Jacobson, A.; Pappin, D. J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol. Cell. Proteomics. 2004, 3, 1154-1169
23. Kruger, M.; Moser, M.; Ussar, S.; Thievessen, I.; Luber, C. A.; Forner, F.; Schmidt, S.; Zanivan, S.; Fassler, R.; Mann, M. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function Cell 2008, 134, 353-364
24. Kim, M. S.; Kandasamy, K.; Chaerkady, R.; Pandey, A. Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer J. Am. Soc. Mass Spectrom. 2010, 21, 1606-1611
25. Woolcock, K. J.; Gaidatzis, D.; Punga, T.; Buhler, M. Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe Nat. Struct. Mol. Biol. 2011, 18, 94-99
26. Giles, K. E.; Ghirlando, R.; Felsenfeld, G. Maintenance of a constitutive heterochromatin domain in vertebrates by a Dicer-dependent mechanism Nat. Cell Biol. 2010, 12, 94-9
27. Murchison, E. P.; Stein, P.; Xuan, Z.; Pan, H.; Zhang, M. Q.; Schultz, R. M.; Hannon, G. J. Critical roles for Dicer in the female germline Genes Dev. 2007, 21, 682-693