Fogarty Elizabeth A, Kitzman Jacob O, Antonellis Anthony
Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA.
Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
BMC Genomics. 2020 Aug 8;21(1):549. doi: 10.1186/s12864-020-06963-7.
Multicellular organisms adopt various strategies to tailor gene expression to cellular contexts including the employment of multiple promoters (and the associated transcription start sites (TSSs)) at a single locus that encodes distinct gene isoforms. Schwann cells-the myelinating cells of the peripheral nervous system (PNS)-exhibit a specialized gene expression profile directed by the transcription factor SOX10, which is essential for PNS myelination. SOX10 regulates promoter elements associated with unique TSSs and gene isoforms at several target loci, implicating SOX10-mediated, isoform-specific gene expression in Schwann cell function. Here, we report on genome-wide efforts to identify SOX10-regulated promoters and TSSs in Schwann cells to prioritize genes and isoforms for further study.
We performed global TSS analyses and mined previously reported ChIP-seq datasets to assess the activity of SOX10-bound promoters in three models: (i) an adult mammalian nerve; (ii) differentiating primary Schwann cells, and (iii) cultured Schwann cells with ablated SOX10 function. We explored specific characteristics of SOX10-dependent TSSs, which provides confidence in defining them as SOX10 targets. Finally, we performed functional studies to validate our findings at four previously unreported SOX10 target loci: ARPC1A, CHN2, DDR1, and GAS7. These findings suggest roles for the associated SOX10-regulated gene products in PNS myelination.
In sum, we provide comprehensive computational and functional assessments of SOX10-regulated TSS use in Schwann cells. The data presented in this study will stimulate functional studies on the specific mRNA and protein isoforms that SOX10 regulates, which will improve our understanding of myelination in the peripheral nerve.
多细胞生物采用多种策略来根据细胞环境调整基因表达，包括在单个编码不同基因异构体的基因座上使用多个启动子（以及相关的转录起始位点（TSS））。雪旺细胞——外周神经系统（PNS）的髓鞘形成细胞——表现出由转录因子SOX10指导的特殊基因表达谱，这对于PNS髓鞘形成至关重要。SOX10在几个靶基因座上调节与独特TSS和基因异构体相关的启动子元件，这表明SOX10介导的异构体特异性基因表达在雪旺细胞功能中起作用。在此我们报告在全基因组范围内鉴定雪旺细胞中SOX10调节的启动子和TSS的工作成果，以便为进一步研究确定优先研究的基因和异构体。
我们进行了全基因组TSS分析，并挖掘先前报道的ChIP-seq数据集，以评估SOX10结合启动子在三种模型中的活性：（i）成年哺乳动物神经；（ii）分化中的原代雪旺细胞，以及（iii）SOX10功能缺失的培养雪旺细胞。我们探索了SOX10依赖性TSS的特定特征，这为将它们定义为SOX10靶标提供了信心。最后，我们进行了功能研究，以验证我们在四个先前未报道的SOX10靶基因座（ARPC1A、CHN2、DDR1和GAS7）上的发现。这些发现表明相关SOX10调节的基因产物在PNS髓鞘形成中的作用。
总之，我们提供了对雪旺细胞中SOX10调节的TSS使用情况的全面计算和功能评估。本研究中呈现的数据将激发对SOX10调节的特定mRNA和蛋白质异构体的功能研究，这将增进我们对周围神经髓鞘形成的理解。
