Genome-wide analyses in neuronal cells reveal that upstream transcription factors regulate lysosomal gene expression.
Genome-wide analyses in neuronal cells reveal that upstream transcription factors regulate lysosomal gene expression.
复制标题
神经元细胞的全基因组分析揭示上游转录因子调节溶酶体基因表达。
作者：
Yamanaka T;Tosaki A;Kurosawa M;Shimogori T;Hattori N;Nukina N
上游转录因子（USF）USF 1和USF 2是普遍表达的转录因子，其特征在于保守的碱性螺旋-环-螺旋/亮氨酸拉链DNA结合结构域。它们形成同源或异源二聚体，并识别E盒基序以调节基因表达。已知它们调节多种细胞功能，包括细胞周期、免疫反应和葡萄糖/脂质代谢，但它们在神经元细胞中的作用仍有待澄清。在这里，我们进行了染色质免疫沉淀的USF 1从小鼠大脑皮层。随后的启动子阵列分析（ChIP芯片）表明USF 1仅与近端启动子区域的CACGTG E-box基序结合。重要的是，USF 1结合靶点的功能注释揭示了与溶酶体功能相关的基因的富集。随后使用神经元细胞系进行的基因表达阵列分析显示，USF的敲低使溶酶体基因表达失调。通过定量RT-PCR验证了改变的表达，支持USF调节溶酶体基因表达的结论。此外，USF敲除略微增加LysoTracker Red染色，这意味着USF在调节溶酶体稳态中的作用。总之，我们全面的基因组规模分析确定了溶酶体基因是神经元细胞中USF的靶基因，这表明了溶酶体调节的潜在额外途径。数据库基因表达阵列和ChIP芯片的数据已分别提交给基因表达综合数据库（GEO），登录号分别为GSE 76615和GSE 76616。
The upstream transcription factors (USFs) USF1 and USF2 are ubiquitously expressed transcription factors that are characterized by a conserved basic helix‐loop‐helix/leucine zipper DNA‐binding domain. They form homo‐ or heterodimers, and recognize E‐box motifs to modulate gene expression. They are known to regulate diverse cellular functions, including the cell cycle, immune responses and glucose/lipid metabolism, but their roles in neuronal cells remain to be clarified. Here, we performed chromatin immunoprecipitation of USF1 from mouse brain cortex. Subsequent promoter array analysis (ChIP‐chip) indicated that USF1 exclusively bound to the CACGTG E‐box motifs in the proximal promoter regions. Importantly, functional annotation of the USF1‐binding targets revealed an enrichment of genes related to lysosomal functions. Gene expression array analysis using a neuronal cell line subsequently revealed that knockdown of USFs de‐regulated lysosomal gene expression. Altered expression was validated by quantitative RT‐PCR, supporting the conclusion that USFs regulate lysosomal gene expression. Furthermore, USF knockdown slightly increased LysoTracker Red staining, implying a role for USFs in modulating lysosomal homeostasis. Together, our comprehensive genome‐scale analyses identified lysosomal genes as targets of USFs in neuronal cells, suggesting a potential additional pathway of lysosomal regulation.DatabaseThe data for the gene expression array and ChIP‐chip have been submitted to the Gene Expression Omnibus (GEO) under accession numbers GSE76615 and GSE76616, respectively.