Identification of regulatory factors that control nervous system form, function, and regeneration in the planarian Schmidtea mediterranea

Neurons are born from stem cells, migrate to their final location, form synaptic connections, and terminally differentiate by a process known as neurogenesis. Although this phenomenon is observed in adult organisms across metazoans, most animals lack the ability to repair catastrophic damages to the central nervous system (CNS) caused by injury, disease or aging. By contrast, planarians have the amazing ability to regenerate all tissue types (including the CNS) from a population of pluripotent adult stem cells they maintain throughout their life, making these animals a powerful system to research stem cell-based regeneration in vivo. To investigate how adult stem cells are directed to generate new neurons during CNS regeneration, we examined the basic helix-loop-helix (bHLH) transcription factor family in planarians. Many bHLH family members regulate neurogenesis during development and are associated with nervous system diseases, yet their functions in adult stem cells and mature neurons remain unclear. We identified 44 planarian bHLH homologs, determined their tissue-specific expression in the adult animal, and examined their function using RNA interference. These analyses identified nine bHLHs expressed in stem cells and neurons that were required for CNS regeneration, including homologs of Collier/Olfactory- 1/Early B-cell factor (coe), Single-minded (sim), and Hairy enhancer of split (hesl-3). Furthermore, we demonstrated that coe, sim and hesl-3 mRNA were detected in lineage-committed progenitors. Our functional screen revealed that gene silencing of coe results in CNS regeneration defects. COE genes play conserved roles in nervous system development and are associated with CNS diseases; however, the genetic programs downstream of these genes remain largely unknown. By comparing the transcriptome profiles of control and coe-deficient animals, we identified over 900 differentially expressed genes, including 397 downregulated genes enriched for CNS functions. We examined downregulated genes and identified new targets of COE in mature neurons, some of which were required for CNS regeneration. Furthermore, we found novel genes expressed in stem cell progeny that function downstream of COE and were critical for stem cell homeostasis. These findings demonstrate that COE regulates genetic programs essential for CNS homeostasis and regeneration, providing insights into how COE proteins function in the adult nervous syste