Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis

Abstract

SummaryNon-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 has been assigned as a key player of neuronal differentiation via its complex but little understood regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human induced pluripotent stem cells. Upon neuronal induction, miR-124-deleted cells underwent neurogenesis and became functional neurons, albeit with altered morphology and neurotransmitter specification. Using RNA-induced-silencing-complex precipitation, we identified 98 high-confidence miR-124 targets, of which some directly led to decreased viability. By performing advanced transcription-factor-network analysis, we identified indirect miR-124 effects on apoptosis, neuronal subtype differentiation, and the regulation of previously uncharacterized zinc finger transcription factors. Our data emphasize the need for combined experimental- and system-level analyses to comprehensively disentangle and reveal miRNA functions, including their involvement in the neurogenesis of diverse neuronal cell types found in the human brain.

Transcriptome stability profiling using 5’-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells

“…RIP-seq following AGO pull-down showed that 100 transcripts were enriched upon miR-155 induction and, of those, only 67 were predicted targets and only nine of those predicted targets showed regulation by decay. Similarly, Kutsche et al [73] also found that out of 127 differentially AGO2enriched and upregulated genes upon miR-124 deletion, only 98 were predicted targets. Taken together, these studies and out data suggest that miRNA-dependent regulation of targets without predicted binding sites could either be a by-product of miRNA overexpression that overloads AGO2 RISC with the candidate miRNA or could be a genuine interaction via currently unknown mechanisms.…”

MiR-124 and small molecules synergistically regulate the direct generation of neuronal cells from rat cortical reactive astrocytes

“…Studies have revealed the functional signi cance of miRs in regulating CNS development [42]. MiR-124, one of the most highly expressed miRs in the mammalian brain, is closely associated with the regulation of neurogenesis and neuronal differentiation [43]. Given that both astrocytes and neurons are derived from NSCs and that miR-124 is a neuronal fate determinant during neurodevelopment [44], we hypothesised that differential miR-124 expression might affect their distinct cell fates.…”

Integrative Transcriptomics Reveals Sexually Dimorphic Control of the Cholinergic/Neurokine Interface in Schizophrenia and Bipolar Disorder

“…For example, miR-124 is DE between LA-N-2 and LA-N-5 cells after neurokine induction. A recent analysis of complete miR-124 knockout in human induced pluripotent stem cells (iPSCs) (Kutsche et al, 2018) found extensive subsequent transcriptional perturbations, in STAT5B among others, and a shift from glutamate to ACh in the resulting functional neurons. Although the authors did not address this cholinergic aspect, their data and ours co-indicate an influence of miR-124 on the neuronal cholinergic phenotype.…”