Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression

Background: Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF ( REI silencing transcription factor) and CREB ( cAMP response element-binding protein), and microRNAs ( miRNAs). How these two classes of regulators act together to mediate neuronal gene expression is unclear. Results: Using comparative sequence analysis, here we report the identification of 895 sites ( NRSE) as the putative targets of REST. A set of the identified NRSE sites is present in the vicinity of the miRNA genes that are specifically expressed in brain-related tissues, suggesting the transcriptional regulation of these miRNAs by REST. We have further identified target genes of these miRNAs, and discovered that REST and its cofactor complex are targets of multiple brain-related miRNAs including miR-124a, miR-9 and miR-132. Given the role of both REST and miRNA as repressors, these findings point to a double-negative feedback loop between REST and the miRNAs in stabilizing and maintaining neuronal gene expression. Additionally, we find that the brain-related miRNA genes are highly enriched with evolutionarily conserved cAMP response elements ( CRE) in their regulatory regions, implicating the role of CREB in the positive regulation of these miRNAs. Conclusion: The expression of neuronal genes and neuronal identity are controlled by multiple factors, including transcriptional regulation through REST and post-transcriptional modification by several brain-related miRNAs. We demonstrate that these different levels of regulation are coordinated through extensive feedbacks, and propose a network among REST, CREB proteins and the brain-related miRNAs as a robust program for mediating neuronal gene expression.