BackgroundUnidirectional regeneration in the basal chordateCiona intestinalisinvolves the proliferation of adult stem cells residing in the branchial sac vasculature and the migration of progenitor cells to the site of distal injury. However, after theCionabody is bisected, regeneration occurs in the proximal but not in the distal fragments, even if the latter include a part of the branchial sac with stem cells. A transcriptome was sequenced and assembled from the isolated branchial sacs of regenerating animals, and the information was used to provide insights into the absence of regeneration in distal body fragments.ResultsWe identified 1149 differentially expressed genes, which were separated into two major modules by weighted gene correlation network analysis, one consisting of mostly upregulated genes correlated with regeneration and the other consisting of only downregulated genes associated with metabolism and homeostatic processes. Thehsp70,dnaJb4, andbag3genes were among the highest upregulated genes and were predicted to interact in an HSP70 chaperone system. The upregulation of HSP70 chaperone genes was verified and their expression confirmed in BS vasculature cells previously identified as stem and progenitor cells. siRNA-mediated gene knockdown showed thathsp70anddnaJb4,but notbag3,are required for progenitor cell targeting and distal regeneration. However, neitherhsp70nordnaJb4were strongly expressed in the branchial sac vasculature of distal fragments, implying the absence of a stress response. Heat shock treatment of distal body fragments activatedhsp70anddnaJb4expression indicative of a stress response, induced cell proliferation in branchial sac vasculature cells, and promoted distal regeneration.ConclusionsThe chaperone system geneshsp70,dnaJb4, andbag3are significantly upregulated in the branchial sac vasculature following distal injury, defining a stress response that is essential for regeneration. The stress response is absent from distal fragments, but can be induced by a heat shock, which activates cell division in the branchial sac vasculature and promotes distal regeneration. This study demonstrates the importance of a stress response for stem cell activation and regeneration in a basal chordate, which may have implications for understanding the limited regenerative activities in other animals, including vertebrates.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12915-023-01633-y.