REST-governed gene expression profiling in a neuronal cell model reveals novel direct and indirect processes of repression and up-regulation

Gene expression, governed by low levels of the transcription repressor REST, is critical for neurons also upon their differentiation. In neurons, however, only a fraction of the possible REST-dependent genes has been identified. To expand the identification of specific, REST-dependent genes we have investigated two clones of the PC12 line, a recognized neuronal cell model, spontaneously expressing low and high levels of REST. Previous data had documented that the molecular, structural and functional differences of the two clones depend largely on their differential expression of REST-dependent genes. Comprehensive RNA-Seq analyses of the 13.700 genes expressed, validated by RT-PCR and encoded protein analysis, have identified, in the high-REST clone, two groups of almost 900 repressed and up-regulated genes,. Repression is largely due to direct binding of REST to target genes, up-regulation to indirect effects, mediated by REST repression of repressive transcription factors. Among neuronal functions, some were found to be governed by the REST-repressed genes, others by the upregulated genes. Almost all genes governing functions such as neurosecretion, excitability, and receptor channel signaling in the high REST clone were found to be repressed, however a few were unchanged or up-regulated. The genes of non-channel receptors (G protein-coupled, of growth factors and others), although variably affected, were most often upregulated, together with the genes of intracellular kinases, small G proteins, cytoskeleton, various types of cell adhesion proteins and proteins of the extracellular matrix. The results have revealed the complexity of the REST molecular and functional role, deciphering new aspects of its variable participation in neuronal functions. REST-dependent genes governing functions other than those mentioned here, have also been identified, providing new tools for the interpretation and investigation of physiological and disease processes.