Integrated Expression Profiling and Genome-Wide Analysis of ChREBP Targets Reveals the Dual Role for ChREBP in Glucose-Regulated Gene Expression

The carbohydrate response element binding protein (ChREBP), a basic helix-loop-helix/leucine zipper transcription factor, plays a critical role in the control of lipogenesis in the liver. To identify the direct targets of ChREBP on a genome-wide scale and provide more insight into the mechanism by which ChREBP regulates glucose-responsive gene expression, we performed chromatin immunoprecipitation-sequencing and gene expression analysis. We identified 1153 ChREBP binding sites and 783 target genes using the chromatin from HepG2, a human hepatocellular carcinoma cell line. A motif search revealed a refined consensus sequence (CABGTG-nnCnG-nGnSTG) to better represent critical elements of a functional ChREBP binding sequence. Gene ontology analysis shows that ChREBP target genes are particularly associated with lipid, fatty acid and steroid metabolism. In addition, other functional gene clusters related to transport, development and cell motility are significantly enriched. Gene set enrichment analysis reveals that ChREBP target genes are highly correlated with genes regulated by high glucose, providing a functional relevance to the genome-wide binding study. Furthermore, we have demonstrated that ChREBP may function as a transcriptional repressor as well as an activator.碳水化合物反应元件结合蛋白（carbohydrate response element binding protein，ChREBP）是一种碱性螺旋-环-螺旋/亮氨酸拉链转录因子，在肝脏脂质生成的调控过程中发挥关键作用。为在全基因组范围内鉴定ChREBP的直接靶标，并深入解析其调控葡萄糖应答基因表达的分子机制，本研究开展了染色质免疫共沉淀测序（chromatin immunoprecipitation-sequencing）与基因表达分析。研究以人肝癌细胞系HepG2的染色质为实验材料，共鉴定得到1153个ChREBP结合位点与783个靶基因。通过基序搜索，我们获得了一条优化的保守序列（CABGTG-nnCnG-nGnSTG），该序列可更精准地反映功能性ChREBP结合序列的核心元件。基因本体（gene ontology，GO）分析结果显示，ChREBP靶基因显著富集于脂质、脂肪酸及类固醇代谢通路。此外，与物质转运、发育及细胞运动相关的其他功能基因簇也呈现显著富集。基因集富集分析（gene set enrichment analysis，GSEA）结果表明，ChREBP靶基因与高葡萄糖调控的基因具有高度相关性，为全基因组结合位点研究提供了功能层面的佐证。进一步研究证实，ChREBP既可作为转录激活因子，也可作为转录抑制因子发挥功能。