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Gene regulation in developing neurons: factRing in alternative splicing and nonsense-mediated decay


How neurons develop in the brain is a remarkably complex feat, relying on coordinated changes in the expression levels of numerous genes. Many genes involved in neuronal differentiation are controlled in a switch-like manner, assuming, for example, an 'on' state in proliferating stem and progenitor cells and a fully 'off' state in mature neurons. The molecular mechanisms underlying such tight regulation of large groups of genes are not well understood.

Alternative splicing (AS) is an important gene regulation mechanism, well known for its role in expanding the diversity of proteins in the developing brain. Previous studies have additionally shown that AS can control gene expression levels by modulating the ratio between productively spliced messenger RNAs (mRNAs) encoding functional proteins and unproductively spliced RNAs, which are eliminated by the RNA quality control mechanism known as nonsense-mediated decay (NMD). Such scheduled production of AS transcripts vulnerable to NMD (AS-NMD) can occur through alternative exons whose inclusion in mature mRNA either stimulates or represses NMD. However, the extent to which these two regulation strategies, and AS-NMD in general, are used to control gene expression in developing neurons has remained an open question.

A new study by CDN researchers Anna Zhuravskaya (first author) and Karen Yap from Eugene Makeyev’s lab, along with Fursham Hamid, published in Genome Biology, has explored this fascinating problem. The team first developed a computer program, factR2, which annotates custom transcriptomes and shortlists AS-NMD events with strong regulatory potential. The researchers then combined this bioinformatics tool with longitudinal RNA sequencing analyses of developing neurons and acute inhibition of the NMD pathway to systematically identify genes regulated by AS-NMD during neuronal differentiation. A particularly interesting finding reported by Zhuravskaya et al. is that many functionally related genes, which are strongly suppressed in developing neurons, encode NMD-stimulating alternative exons. Importantly, inactivation of these exons using a CRISPR-Cas9 genome editing approach compromises the ability of their 'host' genes to be efficiently switched off in neurons.

Overall, the study by Zhuravskaya et al. provides an accessible workflow to address the challenge of understanding the role of AS-NMD in various biological contexts and suggests that this mechanism has a profound impact on gene expression dynamics in the developing brain.