Regulatory mechanisms of planarian regeneration

Thesis

Regeneration of missing tissues requires regulatory mechanisms that ensure the coordinated behaviour of cells in both spatial and temporal dimensions. Planarians are highly regenerative flatworms capable of regenerating any missing body part, providing a suitable model system to understand these regulatory mechanisms. Planarian whole-body regeneration is enabled by a population of adult somatic pluripotent stem cells and a dynamic positional information system that instructs cell differentiation following injury. Although planarian regeneration and its molecular underpinnings have been studied for decades, the mechanisms of gene regulation during regeneration remain poorly understood. In this thesis, we investigate system-wide gene regulatory networks of planarian stem cells, while focusing on the role of TALE homeobox genes in planarian regenerative patterning. To understand the gene regulatory networks of planarian neoblasts, we comprehensively reannotate the genome of the planarian model species Schmidtea mediterranea, compile a list of its transcription factors, and discover enhancer-like regions active in stem cells by combining epigenomic evidence from histone modifications and chromatin accessibility. By integrating footprints of transcription factors in these enhancer-like regions, we construct emergent gene regulatory networks that provide testable hypotheses for how transcription factors maintain stemness and drive cell lineage differentiation in planarian stem cells. As our compilation of transcription factors identified multiple uncharacterised TALE homeobox genes within the genome of S. mediterranea, we continued to study the phylogeny of the TALE gene repertoire. Our analysis revealed that S. mediterranea possesses both evolutionarily conserved and recently evolved lineage-specific TALE genes, including both spiralian- and platyhelminth-specific genes. Among the conserved TALE genes, pbx-1 and prep had been previously implicated in axial regeneration, and we discovered that an additional TALE factor of the Meis family, meis-2, is required for posterior regeneration. To infer the targets regulated by these TALE factors, we performed transcriptomic and epigenomic profiling following knockdowns. Our analysis of sequencing data, in combination with preliminary functional experiments and existing planarian literature, suggests that pbx-1 and meis-2 regulate as a dimer the posterior pole marker wnt1 and other genes of the posterior specification program, while prep and pbx-1 regulate pole markers and FGFRL family members in the anterior blastema. In conclusion, these findings provide one of the first insights into the gene regulatory networks of planarian regenerative abilities, offering perspectives for understanding the evolution of animal stem cells and body axis patterning, and potential implications for regenerative medicine.

Authors: Neiro, J

• DOI: 10.5287/ora-avovxm4bg
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: stem cells; developmental biology; genomics; regeneration
• Subjects: Stem cells; Evolutionary developmental biology