Cholinergic neuron circadian clock mediates RNA-binding protein function and contributes to ALS disease phenotypes

Circadian clocks are encoded by a transcription-translation feedback loop that aligns physiological processes with the solar cycle. Previous work linking the circadian clock to the regulation of RNA-binding proteins (RBPs) and alternative splicing provides a foundation for the vital examination of their mechanistic connections in the context of amyotrophic lateral sclerosis (ALS)—a fatal neurodegenerative disease characterized by disrupted RBP function. Here, we reveal enrichment of genes associated with ALS and other neurodegenerative diseases in the spinal cord cholinergic neuron rhythmic transcriptome. We demonstrate that there is circadian regulation of ALS-linked RBPs and rhythmic alternative splicing of genes involved in intracellular transport ( Aftph and Mvb12a ), microtubule cytoskeleton organization ( Limch1 and Drc3 ), and synaptic function ( Sipa1l2 ) in this neuronal sub-type. Further, we show that the cholinergic neuron clock regulates sporadic ALS-associated changes in cytoskeleton and neuromuscular junction synapse gene expression. Finally, we report that cell-type-specific Bmal1 -deletion (i) increases sciatic nerve axon degeneration, (ii) drives alternative splicing of genes encoding ALS-linked RBPs ( Matr3 and Srsf7 ), and (iii) drives alternative splicing of genes associated with microtubule transport and postsynaptic organization. Our results establish a role for the cholinergic neuron clock in RBP function and ALS disease phenotypes.