Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy

Cell Metabolism

Volumn 13, Issue 4, 2011, Pages 367-375

  Seo, Young Kyo ^a   Jeon, Tae Il ^d   Chong, Hansook Kim ^a,b   Biesinger, Jacob ^b,c   Xie, Xiaohui ^b,c   Osborne, Timothy F ^a,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Irvine   (United States)

^d BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHOLESTEROL; FAT DROPLET; STEROL REGULATORY ELEMENT BINDING PROTEIN 2;

ANIMAL CELL; ANIMAL TISSUE; ANTIBODY SPECIFICITY; ARTICLE; AUTOPHAGY; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; GENE; GENETIC ANALYSIS; LIPID METABOLISM; LIVER METABOLISM; MALE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEPLETION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN TARGETING;

ANIMALS; AUTOPHAGY; CELL LINE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION; GENOME; HUMANS; LIVER; MALE; MICE; MICE, INBRED C57BL; MICROTUBULE-ASSOCIATED PROTEINS; MOLECULAR SEQUENCE DATA; RNA INTERFERENCE; RNA, SMALL INTERFERING; STEROL REGULATORY ELEMENT BINDING PROTEIN 2;

MAMMALIA; MUS;

EID: 79953756678     PISSN: 15504131     EISSN: 19327420     Source Type: Journal    
DOI: 10.1016/j.cmet.2011.03.005     Document Type: Article

References (36)

1. Bailey, T.L. (2002). Discovering novel sequence motifs with MEME. Curr. Protoc. Bioinformatics, Chapter 2:Unit 2.4.
2. Bennett, M.K., Seo, Y.-K., Datta, S., Shin, D.-J., and Osborne, T.F. (2008). Selective binding of sterol regulatory element-binding protein isoforms and co-regulatory proteins to promoters for lipid metabolic genes in liver. J. Biol. Chem. 283, 15628-15637.
3. Bolte, S., and CordelièP. (2006). A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213-232.
4. Brown, M.S., and Goldstein, J.L. (1980). Multivalent feedback regulation of HMG CoA reductase, a control mechanism coordinating isoprenoid synthesis and cell growth. J. Lipid Res. 21, 505-517. (Pubitemid 11194847)
5. Cheng, J., Ohsaki, Y., Tauchi-Sato, K., Fujita, A., and Fujimoto, T. (2006). Cholesterol depletion induces autophagy. Biochem. Biophys. Res. Commun. 351, 246-252.
6. Chong, H.K., Infante, A.M., Seo, Y.-K., Jeon, T.-I., Zhang, Y., Edwards, P.A., Xie, X., and Osborne, T.F. (2010). Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1. Nucleic Acids Res. 38, 6007-6017.
7. Dennis, G., Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C., and Lempicki, R.A. (2003). DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, 3.
8. Di Paolo, G., and De Camilli, P. (2006). Phosphoinositides in cell regulation and membrane dynamics. Nature 443, 651-657.
9. He, C., and Klionsky, D.J. (2009). Regulation mechanisms and signaling pathways of autophagy. Annu. Rev. Genet. 43, 67-93.
10. Horton, J.D., Goldstein, J.L., and Brown, M.S. (2002). SREBPs: activators of the complete program of cholesterol and fatty acid synthesis in the liver. J. Clin. Invest. 109, 1125-1131.
11. Horton, J.D., Shah, N.A., Warrington, J.A., Anderson, N.N., Park, S.W., Brown, M.S., and Goldstein, J.L. (2003). Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes. Proc. Natl. Acad. Sci. USA 100, 12027-12032.
12. Jeon, T.I., Zhu, B., Larson, J.L., and Osborne, T.F. (2008). SREBP-2 regulates gut peptide secretion through intestinal bitter taste receptor signaling in mice. J. Clin. Invest. 118, 3693-3700.
13. Johnson, D.S., Mortazavi, A., Myers, R.M., and Wold, B. (2007). Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502. (Pubitemid 46906620)
14. Kim, J.B., Spotts, G.D., Halvorsen, Y.-D., Shih, H.-M., Ellenberger, T., Towle, H.C., and Spiegelman, B.M. (1995). Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain. Mol. Cell. Biol. 15, 2582-2588.
15. Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276, 19937-19944.
16. Mammucari, C., Milan, G., Romanello, V., Masiero, E., Rudolf, R., Del Piccolo, P., Burden, S.J., Di Lisi, R., Sandri, C., Zhao, J., et al. (2007). FoxO3 controls autophagy in skeletal muscle in vivo. Cell Metab. 6, 458-471. (Pubitemid 350163055)
17. Manders, E.M., Stap, J., Brakenhoff, G.J., van Driel, R., and Aten, J.A. (1992). Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy. J. Cell Sci. 103, 857-862. (Pubitemid 23023255)
18. Mann, R.K., and Beachy, P.A. (2004). Novel lipid modifications of secreted protein signals. Annu. Rev. Biochem. 73, 891-923.
19. Mizushima, N., and Klionsky, D.J. (2007). Protein turnover via autophagy: implications for metabolism. Annu. Rev. Nutr. 27, 19-40.
20. Mizushima, N., and Levine, B. (2010). Autophagy in mammalian development and differentiation. Nat. Cell Biol. 12, 823-830.
21. Mizushima, N., Yoshimori, T., and Levine, B. (2010). Methods in mammalian autophagy research. Cell 140, 313-326.
22. Murre, C., Bain, G., van Dijk, M.A., Engel, I., Furnari, B.A., Massari, M.E., Matthews, J.R., Quong, M.W., Rivera, R.R., and Stuiver, M.H. (1994). Structure and function of helix-loop-helix proteins. Biochim. Biophys. Acta 1218, 129-135.
23. Ohsaki, Y., Shinohara, Y., Suzuki, M., and Fujimoto, T.A. (2010). A pitfall in using BODIPY dyes to label lipid droplets for fluorescence microscopy. Histochem. Cell Biol. 133, 477-480.
24. Osborne, T.F. (1995). Transcriptional control mechanisms in the regulation of cholesterol balance. Crit. Rev. Eukaryot. Gene Expr. 5, 317-335.
25. Osborne, T.F., and Espenshade, P.J. (2009). Evolutionary conservation and adaptation in the mechanism that regulates SREBP action: what a long, strange tRIP it's been. Genes Dev. 23, 2578-2591.
26. Sanchez, H.B., Yieh, L., and Osborne, T.F. (1995). Cooperation by sterol regulatory element-binding protein and Sp1 in sterol regulation of low density lipoprotein receptor gene. J. Biol. Chem. 270, 1161-1169.
27. Seo, Y.K., Chong, H.K., Infante, A.M., Im, S.S., Xie, X., and Osborne, T.F. (2009). Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. Proc. Natl. Acad. Sci. USA 106, 13765-13769.
28. Shibata, M., Yoshimura, K., Tamura, H., Ueno, T., Nishimura, T., Inoue, T., Sasaki, M., Koike, M., Arai, H., Kominami, E., and Uchiyama, Y. (2010). LC3, a microtubule-associated protein1A/B light chain3, is involved in cytoplasmic lipid droplet formation. Biochem. Biophys. Res. Commun. 393, 274-279.
29. Singh, R., Kaushik, S., Wang, Y., Xiang, Y., Novak, I., Komatsu, M., Tanaka, K., Cuervo, A.M., and Czaja, M.J. (2009). Autophagy regulates lipid metabolism. Nature 458, 1131-1135.
30. Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., and Mesirov, J.P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.
31. Sumpter, R., Jr., and Levine, B. (2010). Autophagy and innate immunity: triggering, targeting and tuning. Semin. Cell Dev. Biol. 21, 699-711.
32. Toker, A., and Cantley, L.C. (1997). Signalling through the lipid products of phosphoinositide-3-OH kinase. Nature 387, 673-676. (Pubitemid 27270600)
33. Tuteja, G., White, P., Schug, J., and Kaestner, K.H. (2009). Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res. 37, e113.
34. Vallett, S.M., Sanchez, H.B., Rosenfeld, J.M., and Osborne, T.F. (1996). A direct role for sterol regulatory element binding protein in activation of 3-hydroxy-3-methylglutaryl coenzyme A reductase gene. J. Biol. Chem. 271, 12247-12253.
35. van Meer, G., Voelker, D.R., and Feigenson, G.W. (2008). Membrane lipids: where they are and how they behave. Nat. Rev. Mol. Cell Biol. 9, 112-124.
36. Wang, X., Zelenski, N.G., Yang, J., Sakai, J., Brown, M.S., and Goldstein, J.L. (1996). Cleavage of sterol regulatory element binding proteins (SREBPs) by CPP32 during apoptosis. EMBO J. 15, 1012-1020. (Pubitemid 26077829)