Intron-specific patterns of divergence of lin-11 regulatory function in the C. elegans nervous system

Abstract

The diversity of neurons in the nervous system is specified by many genes, including those that encode transcription factors (TFs) and play crucial roles in coordinating gene transcription. To understand how the spatiotemporal expression of TF genes is regulated to generate neuronal diversity, we used one member of the LIM-Hox family, lin-11, as a model that is necessary for the differentiation of amphid neurons in the nematode C. elegans and a related species C. briggsae. We characterized transcriptional regulation of lin-11 and uncovered regulatory roles of two of the largest introns, intron 3 and intron 7. These introns promote lin-11 expression in non-overlapping sets of neurons. Phenotypic rescue experiments in C. elegans revealed that intron 3 is capable of restoring lin-11 function based on gene expression patterns and behavioral assays. Interestingly, intron 3-driven reporter expression showed differences in neuronal cell types between C. briggsae and C. elegans, indicating evolutionary changes in lin-11 regulation between the two species. Reciprocal transformation experiments provided further evidence consistent with functional changes in both cis and trans regulation of lin-11. To further investigate transcriptional regulation of lin-11, we dissected the intronic regions in C. elegans and identified cell-specific enhancers. These enhancers possess multiple sequence blocks that are conserved among Caenorhabditis species and possess TF binding sites. We tested the role of a subset of predicted TFs and discovered that while three of them (SKN-1, CEH-6, and CRH-1) act via the intron 3 enhancer to negatively regulate lin-11 expression in neurons, another TF (CES-1) acts positively via the intron 7 enhancer. Overall, our findings demonstrate that neuronal expression of lin-11 involves multiple TF regulators and regulatory modules some of which have diverged in Caenorhabditis nematodes.

Neuronal regulated ire-1-dependent mRNA decay controls germline differentiation in Caenorhabditis elegans

“…We observed high levels of ectopic nuclei in the gonads of ASE(-) che-1 mutants compared to wild-type animals in the absence of ER stress, similar to those observed in flp-6(- ) mutants ( Figure 2E ). In contrast, two lin-11 mutants, which lack a critical transcription factor involved in ASG fate specification and are thus ASG defective ( Amon and Gupta, 2017 ), exhibited low levels of ectopic nuclei in their gonads, similar to wild-type animals ( Figure 2E ). These observations suggest that the ASE sensory neuron actively prevents GED in gld-1(RNAi); ced-3(RNAi ) animals.…”

“…2E). In contrast, two lin-11 mutants, which lack a critical transcription factor involved in ASG fate specification and are thus ASG defective [37], exhibited low GED levels similar to wild-type animals (Fig. 2E).…”

Neuronal specification in C. elegans: combining lineage inheritance with intercellular signaling

“…If the regulatory mechanisms are conserved, the expression pattern would stay the same; if changes happened in cis-regulatory elements or in trans factors, the expression patterns driven by the reporters would vary. For example, in C. elegans, the transcription factor CEH-6 regulates lin-11 expression in the interneuron RIC by binding to an intronic enhancer; in C. briggsae, the endogenous lin-11 enhancer fails to drive expression in RIC, while reciprocal promoter swaps do drive expression in RIC (Amon and Gupta, 2017). Interestingly, an independent comparative RNAi screen found evidence for functional divergence of the CEH-6 transcription factor between C. elegans and C. briggsae (Verster, Ramani, McKay, & Fraser, 2014).…”