CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function

Abstract

RNA–binding proteins have emerged as causal agents of complex neurological diseases. Mice deficient for neuronal RNA–binding protein CELF4 have a complex neurological disorder with epilepsy as a prominent feature. Human CELF4 has recently been associated with clinical features similar to those seen in mutant mice. CELF4 is expressed primarily in excitatory neurons, including large pyramidal cells of the cerebral cortex and hippocampus, and it regulates excitatory but not inhibitory neurotransmission. We examined mechanisms underlying neuronal hyperexcitability in Celf4 mutants by identifying CELF4 target mRNAs and assessing their fate in the absence of CELF4 in view of their known functions. CELF4 binds to at least 15%–20% of the transcriptome, with striking specificity for the mRNA 3′ untranslated region. CELF4 mRNA targets encode a variety of proteins, many of which are well established in neuron development and function. While the overall abundance of these mRNA targets is often dysregulated in Celf4 deficient mice, the actual expression changes are modest at the steady-state level. In contrast, by examining the transcriptome of polysome fractions and the mRNA distribution along the neuronal cell body-neuropil axis, we found that CELF4 is critical for maintaining mRNA stability and availability for translation. Among biological processes associated with CELF4 targets that accumulate in neuropil of mutants, regulation of synaptic plasticity and transmission are the most prominent. Together with a related study of the impact of CELF4 loss on sodium channel Na _v1.6 function, we suggest that CELF4 deficiency leads to abnormal neuronal function by combining a specific effect on neuronal excitation with a general impairment of synaptic transmission. These results also expand our understanding of the vital roles RNA–binding proteins play in regulating and shaping the activity of neural circuits.

Author Summary

Epilepsy is a devastating brain disorder whereby a loss of regulation of electrochemical signals between neurons causes too much excitation and ultimately results in an “electrical storm” known as a seizure. Epilepsy can be heritable, but it is usually genetically complex, resulting from a collaboration of many genes. It is also a frequent feature of other common brain diseases, such as autism spectrum disorder and intellectual disability, likely because these diseases have a similar dysregulation of neuronal communication. To understand more about how the brain regulates electrical activity, we focused on an RNA–binding protein called CELF4, because a) mice that lack CELF4 have a complex form of epilepsy that includes features of other neurological diseases and b) this kind of protein has the potential to be a master regulator. We show that CELF4 binds to a vast array of mRNAs, and without CELF4 these mRNAs accumulate in the wrong places and can produce the wrong amount of protein. Moreover, many of these mRNAs encode key players in electrochemical signaling between neurons. Although the defects in individual mRNAs are modest, like a genetically complex disease, together these alterations collude to cause neurological symptoms including recurrent seizures.