Novel transcriptional networks regulated by CLOCK in human neurons

The molecular mechanisms underlying human brain evolution are not fully understood; however, previous work suggested that expression of the transcription factor CLOCK in the human cortex might be relevant to human cognition and disease. In this study, we investigated this novel transcriptional role for CLOCK in human neurons by performing chromatin-immunoprecipitation sequencing for endogenous CLOCK in adult neocortex and RNA-sequencing following CLOCK knockdown in differentiated human neurons in vitro. These data suggested that CLOCK regulates expression of genes involved in neuronal migration, and a functional assay showed that CLOCK knockdown increased neuronal migratory distance. Furthermore, dysregulation of CLOCK disrupts co-expressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks are driven by hub genes with human-specific patterns of expression. Thus, these data support a role for CLOCK-regulated transcriptional cascades involved in human brain evolution and function. We carried out RNA-sequencing (RNA-seq) and ATAC-sequencing (ATAC-seq) in differentiated human neural progenitor cells and ChIP-sequencing (ChIP-seq) in both differentiated human neural progenitor cells and BA10 and BA40 of adult human neocortex. For the Chip-seq, five replicates were used for each of the two Brodmann areas (BA10 and BA40) of adult human frozen brain tissue (i.e. the five replicates of BA10 and BA40 came from the same five individuals). For the RNA-seq, three independent replicates of control and CLOCK knockdown samples were used each time point analyzed. For the ATAC-seq, three independent replicates of control and CLOCK knockdown samples were used.