The synthesis of fatty acids and cholesterol is regulated by three membrane-bound transcription factors: sterol regulatory element-binding proteins (SREBP)-1a, -1c, and -2. Their function in liver has been characterized in transgenic mice that overexpress each SREBP isoform and in mice that lack all three nuclear SREBPs because of gene knockout of SREBP cleavage-activating protein (SCAP) required for nuclear localization of SREBPs. Here, we use oligonucleotide arrays hybridized with RNA from livers of three lines of mice (transgenic for SREBP-1a, transgenic for SREBP-2, and knockout for SCAP) to identify genes that are likely to be direct targets of SREBPs in liver. Application of stringent combinatorial criteria to the transgenic/knockout approach allows identification of genes whose activities are likely controlled directly by the SREBPs. Overall design: Transgenic mice that overexpress transcriptionally active nuclear forms of human SREBP-1a (TgSREBP-1a) or SREBP-2 (TgSREBP-2) and mice that lack SCAP (Scap–/–) in liver were used. Studies included five 12- to 16-wk-old male TgSREBP-1a and TgSREBP-2 mice and five male littermate wild-type controls. Mice were fed a high protein/low carbohydrate diet for 2 weeks before liver removal to elicit high-level expression of the nSREBPs. Studies using liver-specific Scap–/– mice included five 10- to 12-wk-old male Scap–/–;MX1-Cre and corresponding wild-type mice that received four i.p. injections of polyinosinic-polycytidylic acid to induce the Cre recombinase. Mice were fed Teklad chow and livers removed 14 days after the last injection. Liver RNA was prepared using RNA STAT-60 (Tel-Test, Friendswood, TX). Equal aliquots of total RNA from each of five mice per group were pooled (total, 20 μg) and used for biotin labeling as described in the Affymetrix technical bulletin. Hybridization, washing, scanning, and analysis of the Affymetrix GeneChip Murine Genome MU74A, -B, and -C version 2 arrays (Affymetrix, Santa Clara, CA) were carried out. Duplicate hybridizations were performed with each RNA sample and data processed with MICROARRAY SUITE 5.0 (Affymetrix) software.