Epigenomics of neural cells: REST-induced down- and up-regulation of gene expression in a two clone PC12 cell model.

Cell epigenomics depends on the marks released by transcription factors operating via the assembly of complexes that induce focal changes of DNA and histone structure. Among these factors is REST, a repressor that, via its strong decrease, governs both neuronal and neural cell differentiation and specificity. REST operation on thousands of possible genes can occur directly or via indirect mechanisms including repression of other factors. In previous studies of gene down- and up-regulation, processes had been only partially investigated in neural cells. PC12 are well known neural cells sharing properties with neurons. In the widely used PC12 populations, low-REST cells coexist with few, spontaneous high-REST PC12 cells. High- and low-REST PC12 clones were employed to investigate the role and the mechanisms of the repressor action. Among 15,500 expressed genes we identified 1,770 target and non-target, RESTdependent genes. Functionally, these genes were found to operate in many pathways, from synaptic function to extracellular matrix. Mechanistically, downregulated genes were predominantly repressed directly by REST; up-regulated genes were mostly governed indirectly. Among other factors, Polycomb complexes cooperated with REST for down-regulation, Smad3 and Myod1 participated in up-regulation. In conclusion, we have highlighted that PC12 clones are a useful model to investigate REST, opening opportunities to development of epigenomic investigation.细胞表观基因组学（Cell Epigenomics）的调控依赖于转录因子介导的表观遗传标记：这类转录因子通过组装复合物，诱导DNA与组蛋白结构发生局域性改变。这类转录因子中的REST（REST）是一种阻遏蛋白，其表达量的显著下调可调控神经元与神经细胞的分化及细胞特异性的建立。REST可通过直接或间接机制调控数以千计的潜在靶基因，其中间接机制包括对其他转录因子的阻遏作用。既往针对基因上调与下调的研究中，神经细胞内的相关调控过程仅得到了部分阐释。PC12细胞是一类经典的神经细胞模型，其生物学特性与神经元高度相似。在广泛应用的PC12细胞群体中，低表达REST的细胞与少量自发形成的高表达REST的PC12细胞共同存在。本研究通过构建并利用高REST表达与低REST表达的PC12细胞克隆，探究该阻遏蛋白的调控功能与作用机制。在15500个检测到表达的基因中，本研究共鉴定出1770个REST依赖性基因，涵盖直接靶基因与间接调控的非靶基因。功能富集分析显示，这些基因广泛参与多条生物学通路，涵盖突触功能与细胞外基质调控等多个领域。从分子机制来看，受REST下调的基因主要通过REST的直接结合实现阻遏；而受上调的基因则大多通过间接通路受到调控。在其他协同调控因子中，多梳复合物（Polycomb Complexes）可与REST协同实现基因下调，而Smad3与Myod1则参与基因上调过程。综上，本研究证实PC12细胞克隆是探究REST调控功能的理想模型，为表观基因组学研究的发展提供了新的契机。