Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes -- Data Supplement - HTML Page - 4923SuppTable6Legend.htslp -- Proceedings of the National Academy of Sciences

Supporting Table 6 Table 6.
Affymetrix microarrays were hybridized to RNA samples as described in the legend to Table 5. "Strict Criteria" denotes the number of genes whose expression was either increased (↑) an average of ≥2.5-fold or decreased (↓) an average of at least 40%. "Affymetrix Criteria" denotes the number of genes whose expression was significantly increased or decreased according to affymetrix microarray suite 5.0. Genes represented multiple times were counted only once.
Profiles
a-i represent 9 of 27 possible combinatorial patterns of gene expression that most likely reflect genes that are regulated either directly or indirectly by SREBPs. Profile a denotes genes increased in both TgSREBP-1a and -2 livers and decreased in Scap^-/-livers. When Affymetrix criteria were used, 42 additional genes not listed in Table 6 were identified. Two of the 42 genes encoded proteins that have obvious connections to lipid metabolism. One of those, 3b-hydroxysteroid-D8,D 7-isomerase, is a cholesterol biosynthetic enzyme that was increased 2.8-fold in TgSREBP-2 liver, 1.5-fold in TgSREBP-1a liver, and reduced by 38% in Scap^-/- liver. The other, tricarboxylate transport protein, transports citrate out of the mitochondria into the cytosol where ATP citrate lyase can convert it to acetyl-CoA for use in cholesterol and fatty acid biosynthesis. Profile
b denotes genes increased in TgSREBP-1a and decreased in Scap^-/-livers. When Affymetrix criteria were used, 34 additional genes were identified, 5 of which (epidermal fatty acid binding protein-5, acyl-CoA binding protein, Elovl5, acetyl-CoA acyltransferase-1, and glucokinase) are involved in lipid metabolism. Epidermal fatty acid binding protein-5 and acyl-CoA binding protein are intracellular proteins that bind medium and long chain fatty acyl-CoAs with high affinity . In TgSREBP-1a mice, these proteins are presumably induced to accommodate the increase in fatty acid production. The acyl-CoA binding protein has been previously identified as a sterol regulatory element-binding protein (SREBP)-1a target gene . Elovl5 carries out the initial reaction in the elongation of very-long-chain unsaturated fatty acids . Acetyl-CoA acyltransferase-1 (also called peroxisomal 3-ketoacyl-CoA thiolase) is involved in b-oxidation of very-long-chain fatty acids . Glucokinase is required for glucose utilization; an increase in its mRNA by SREBP-1 overexpression was previously reported in primary hepatocytes .
Profile
c denotes genes that may be regulated preferentially by SREBP-2. Reducing the inclusion criteria from "Strict" to "Affymetrix" identified an additional 12 genes not listed in Table 3, one of which, CTP:phosphoethanolamine cytidylyltransferase, has a clear connection to lipid metabolism. It catalyzes the synthesis of CDP-ethanolamine from phosphoethanolamine and is a regulatory enzyme in the pathway of phosphatidyl ethanolamine synthesis . Profiles
d─f denote genes whose expression is increased in transgenic SREBP liver but not decreased in Scap^-/- liver, suggesting that their basal level of expression is not dependent on nSREBPs. These three profiles contain 937 genes, the functions of which encompass a wide variety of biologic processes. Of note are 11 genes that relate to lipid metabolism, including lipoprotein lipase; glucose-6-phosphate dehydrogenase-2; glucose-6-phosphate dehydrogenase, X-linked; adiponutrin; phosphatidylcholine transfer protein; lipins-1, -2, and -3; insulin-like growth factor binding protein-1; and Niemann Pick, type C2.
Profiles g
─i denote genes potentially repressed by SREBPs. Few of these genes had any direct connection to lipid metabolism with the exception of carnitine palmitoyltransferase-1 (CPT-1), which regulates b-oxidation of fatty acids.

1. Gossett, R. E., Edmondson, R. D., Jolly, C. A., Cho, T.-H., Russell, D. H., Knudsen, J., Kier, A. B. & Schroeder, F. (1998) Arch. Biochem. Biophys. 350, 201─213.

2. Swinnen, J. V., Alen, P., Heyns, W. & Verhoeven, G. (1998) J. Biol. Chem. 273, 19938─19944.

3. Leonard, A. E., Bobik, E. G., Dorado, J., Kroeger, P. E., Chuang, L.-T., Thurmond, J. M., Parker-Barnes, J. M., Das, T., Huang, Y.-S. & Mukerji, P. (2000) Biochem. J. 350, 765─770.

4. Cook, W. S., Jain, S., Jia, Y., Cao, W.-Q., Yeldandi, A. V., Reddy, J. K. & Rao, M. S. (2001) Exp. Cell Res. 268, 70─76.

5. Foretz, M., Guichard, C., Ferre, P. & Foufelle, F. (1999) Proc. Natl. Acad. Sci. USA 96, 12737─12742.

6. Bladergroen, B. A., Houweling, M., Geelen, M. J. H. & Van Golde, L. M. G. (1999) Biochem. J. 343, 107─114.