You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.

Title: Yorkie is required to restrict the injury responses in planarians}
Article:
Abstract:
Regeneration requires the precise integration of cues that initiate proliferation, direct differentiation, and ultimately re-pattern tissues to the proper size and scale. Yet how these processes are integrated with wounding responses remains relatively unknown. The freshwater planarian, Schmidtea mediterranea, is an ideal model to study the stereotyped proliferative and transcriptional responses to injury due to its high capacity for regeneration. Here, we characterize the effector of the Hippo signalling cascade, yorkie, during planarian regeneration and its role in restricting early injury responses. In yki( RNAi) regenerating animals, wound responses are hyper-activated such that both stem cell proliferation and the transcriptional wound response program are heighted and prolonged. Using this observation, we also uncovered novel wound-induced genes by RNAseq that were de-repressed in yki( RNAi) animals compared with controls. Additionally, we show that yki( RNAi) animals have expanded epidermal and muscle cell populations, which we hypothesize are the increased sources of wound-induced genes. Finally, we show that in yki( RNAi) animals, the sensing of the size of an injury by eyes or the pharynx is not appropriate, and the brain, gut, and midline cannot remodel or scale correctly to the size of the regenerating fragment. Taken together, our results suggest that yki functions as a key molecule that can integrate multiple aspects of the injury response including proliferation, apoptosis, injury-induced transcription, and patterning.
Introduction:
Regeneration is a growth-controlled program that is observed across the animal kingdom[1]. Neo-natal mice can regrow missing digit tips, salamanders can replace missing limbs, while other organisms, such as hydrazoans and planarians, can regenerate virtually any tissue[1, 2, 3, 4, 5]. A common path to successful regeneration is a wounding program that first replaces the missing tissue through proliferation( epimorphosis) and subsequently re-patterns and re-scales the pre-existing tissue to match the new proportions of the animal( morphallaxis)[6, 7]. Failure to initiate or cease aspects of either process can result in under- or overgrown tissues, respectively. Yet how proliferation and patterning may be regulated in the correct spatiotemporal manner to determine size and scaling of regenerating tissues remains poorly understood. The asexual planarian, Schmidtea mediterranea, displays a remarkable ability control growth because it can regenerate any missing tissue upon amputation, then rescale the entire animal in proportion to the amount of remaining tissue. Planarian regenerative capacity is derived from its near ubiquitous population of adult stem cells( neoblasts), which are also the only mitotic cells in the animal and at least some of which are pluripotent[8, 9, 10]. In response to tissue removal, a stereotypical bimodal pattern of proliferation occurs, first at 6 hours post amputation( hpa) and then at 48 hpa[11]. Simultaneously, a generic transcriptional injury response program is expressed with distinct temporal and spatial patterns[12, 13]. However, it is unknown how these two processes may be linked and what regulator( s) may determine the onset or decay of responses to injury. As regeneration progresses, the missing tissues are replaced, reintegrated with the prexisiting tissue, and then morphallaxis begins to achieve proper proportions of the regenerated animal[6]. For example, in planarians the WNT polarity gradients must be rescaled to accommodate the new size of the worm[14], and the brain can be dynamically scaled by the combined action of WNT, notum, and the hedgehog pathways[15, 16]. Therefore, the planarian is a unique model to understand the active processes of growth—proliferation, patterning, and scaling—in an adult regenerative context. The Hippo pathway is universal regulator of growth control and is a kinase cascade that impinges on the transcriptional co-activator, Yorkie,( in vertebrates: YAP1/2 and paralog TAZ)[17, 18]. Constitutive activation of Yki or YAP results in overgrown tissues in flies and vertebrates, suggesting a conserved role in promoting cell division[17, 19, 20]. However, YAP can be growth-restrictive in highly proliferative and regenerative tissues, such as the mammalian intestine[21]. Indeed, we have previously demonstrated that planarian yorkie( Smed-yki) is required to restrict stem cell proliferation, yet yki( RNAi) animals also fail to regenerate[22]. This conundrum between increased proliferation with an undergrowth phenotype suggests that growth control, patterning, and/or wound-responses are dysregulated, although this remains to be tested. Here, we examine the role of Yki in the known responses to injury, specifically stem cell proliferation and the early transcriptional wound response. In yki( RNAi) animals, we demonstrate that the proliferative and transcriptional injury responses are both hyper-activated and temporally prolonged. Despite increased proliferation, stem cells showed no block in differentiation, and surprisingly, produced increased numbers of epidermal and muscle cells. Using an RNA-deep sequencing( RNAseq) time course, we determine that yki( RNAi) regenerates have significantly up-regulated known and novel wound-induced genes, many of which have known roles in patterning. We then show that yki( RNAi) animals fail to maintain proper size and scaling of the brain, midline, and gut during morphallaxis and have altered kinetics of homeostatic eye replacement. Altogether, this study demonstrates that Yki is a highly pleiotropic yet critical regulator of multiple early wound response processes.
Discussion:
Our previous work with yki in planarians was primarily on the pleiotropic roles in intact animals. We described additional defects in regeneration, but did not have tools or markers to explore those defects. We had demonstrated that cell division was not blocked, nor was differentiation[22]. Here, we focused on why regeneration was failing in yki( RNAi) fragments. It was not particularly surprising that yki( RNAi) animals displayed hyper-proliferation, accompanying increased differentiation, and increased TUNEL staining, similar to Yki’s role in intact animals. More interesting was the up-regulation of key members of the transcriptional wound response( summarized in Fig 7). In the broad context of phenotypes for mutants in the Hippo pathway, it is well known that this gene cascade controls tissue growth, patterning, proliferation, and cell death. It would be interesting to determine whether specific tissue defects in other systems are caused by dysregulation of wounding programs. For example, mutations in TAZ, the vertebrate paralog of YAP, cause polycystic kidneys[46, 47] and cystic kidneys also have altered Hippo signalling[48], while mutations in the core kinase cassette of the Hippo pathway in adults can cause tissue overgrowths in specific instances of homeostasis or regeneration[49]. In planarian regeneration, we find that both the wound response( Fig 2 and Fig 3), as well as patterning molecules, are dysregulated( Fig 5H). If both responses are under the control of Yki/YAP in other systems, it could explain many of the disparate phenotypes observed in various mutants in the Hippo pathway. A lingering question from this work is whether Yki is a direct repressor of the transcriptional wound response, or whether it is a secondary defect in other tissue types. Although Yorkie/YAP is commonly associated with gene activation, it may also function as a co-repressor by associating with the NuRD complex to repress downstream transcription[50]. Alternatively, it has been well established that both the epidermis and muscle of planarians are the sites of the transcriptional wound response, to a large extent[12, 13], and these very tissues are increased in yki( RNAi) animals( Fig 4 and Fig 5). Because intact yki( RNAi) animals show increased epithelial differentiation and increased muscle cells prior to amputation( S7A and S7B Fig), perhaps an alternative model is that there are simply more cells to transcribe a particular wound-responsive gene or that defects in the epithelium causes induction of wounding, similar to what was observed in[30]. In this case, Yki’s role would indirectly affect the wound response and instead, Yki may function in establishing the appropriate cell size and cell density ratio of a given tissue, such as the epidermis. Although we cannot rule out this explanation due to the pleiotropy of Yki, we believe that Yki’s effects on the wound-response in planarians is direct due to the fact that we detect increased expression of key genes in the wound program in intact animals prior to any injury( S7C and S7D Fig). Although Yki is thought to be a transcriptional co-activator, there are clearly cell non-autonomous effects in yki( RNAi) animals. For example, proliferation is altered in stem cells, yet yki is not expressed appreciably in the stem cell compartment. Because stem cell proliferation in planarians has stereotyped responses to injury and the injury program is increased in yki( RNAi) animals( Fig 2 and Fig 3), we suggest that the simplest explanation of the data is that yki( RNAi) causes de-repression of the wound program, thereby increasing the stem cell response through extrinsic signals. Although the wound-induced signal( s) that directly trigger the bimodal waves of proliferation during regeneration remain elusive in planarians, correlations between the transcriptional and proliferative response may be inferred. For example, the two responses overlap temporally[11, 12, 13] and follistatin( RNAi) regenerating animals fail to express a second wave of wound-induced genes and do not mount a second burst of proliferation[38, 51]. Therefore, the transcriptional injury response, which is regulated by Yki( Fig 2 and Fig 3) may be required to initiate proliferation. Similarly, during Drosophila midgut regeneration, Yki is activated in the non-proliferative enterocytes to secrete cytokines that stimulate intestinal stem cell proliferation in a non-autonomous fashion[52, 53]. Equally possible is that Yki has roles in cell death or cell longevity, which can also explain the defects seen in yki( RNAi) animals. For example, the increased epithelial cells in yki( RNAi) could be due to either increased differentiation, or increased longevity of the epithelial cells themselves. A similar mechanism could be at work for muscle since both the epithelium and muscle express yki( S1D Fig). Finally, we observe consistently increased cell death in yki( RNAi) animals( S1C Fig). In other systems, dying cells often express cytokines to trigger their replacement[54, 55]. Although we have no evidence for this compensatory-proliferation mechanism of signaling in planarians, it could be a conserved mechanism of triggering increased cell divisions, thereby leading to increases of specific cell types. A key reagent to distinguish these possibilities would be an antibody and to determine what cell types and in what contexts Yki becomes activated and goes into the nucleus. Another key feature of the transcriptional injury response is to lay the foundation for axial and tissue re-scaling, yet the biology of tissue scaling in planarians remains nebulous. The 12 hpa time point is the peak temporal expression window for the majority of wound-induced patterning molecules[12, 13], including wnt1, which is crucial in determining axial polarity[35]. Interestingly, many of the dysregulated wound-induced genes in yki( RNAi) have roles in patterning( Fig 3A and Fig 5H). Indeed, wnt1 was significantly increased in yki( RNAi) animals( Fig 5E). Modulating patterning can have consequences in regeneration by affecting pole determination, cell fate decisions, or organ sizing and scaling[15, 16, 33, 56, 57, 58]. We hypothesize that the failures in regeneration in yki( RNAi) may be attributed to the mis-expression of multiple patterning molecules( Fig 5H). In addition, the process of morphallaxis was also altered in yki( RNAi)( Fig 6D and 6E, S6 Fig). Therefore, the dysregulated transcriptional injury response in yki( RNAi) may be responsible for the changes in proliferation and patterning that likely have detrimental effects on scaling and sizing during regeneration( Fig 6F and 6H and Fig 7). What could be causing the upregulation of the transcriptional injury response in yki( RNAi) animals? One possibility may be epithelial integrity which serves as a negative feedback regulator of the transcriptional injury responses. Smed-egr-5( RNAi)( early growth factor 5), a crucial post-mitotic epidermal determinant, causes a loss of epithelial integrity and increased wound-induced gene expression[30]. Similarly, yki( RNAi) animals had increased epidermal density concurrent with increased wound-induced gene expression( Fig 4). In other systems, the roles for YAP in regulating cell density converge upon inputs such as cytoskeletal tension and mechanosensation[59, 60]; yet, how tension may function in planarian biology, or in a regenerative context, remains unknown. Another source of upstream cues may come from the previously characterized pathways that have roles in regulating the planarian injury responses, including TGFβ signalling through the Activin-Follistatin axis, SMG-1, mTOR, and JNK signalling[38, 61, 62]. Yki/YAP also have described roles in interacting with each of these pathways, however, the interactions remain to be biochemically elucidated in planarians[63, 64, 65, 66]. Therefore, multiple wounding cues and signals may converge on Yki to direct the injury responses. Taken together, we have shown that Yki is required to restrict the magnitude and duration of the injury responses, which coordinate proliferation, differentiation, and patterning to ultimately dictate scaling during regeneration.
The planarian displays a remarkable ability to regenerate any tissue from mere fragments of its original size . This high capacity to regenerate is attributed to the abundant population of pluripotent adult stem cells . In response to an injury , such as an amputation , stem cells proliferate and replace the lost tissues de novo ( epimorphosis ) , whereas existing tissue must rescale to the correct proportions in relation to the new fragment size ( morphallaxis ) . Currently , the molecules that control either the responses to injury or the ones that mediate size and scaling are not well understood . For instance , how are the injury responses precisely activated and shut down to ensure regenerating tissues are not under- or overgrown ? Here , we find that Yki , the effector of the Hippo signalling cascade , is a critical molecule that influences several injury processes during regeneration . Loss of Yki function in regenerating animals resulted in increased and temporally dysregulated expression of wound-induced genes , proliferation , and apoptosis . Genes that are injury induced were mis-expressed in yki ( RNAi ) animals , which also showed increases in the epidermal and muscle cell populations . Taken together , our findings suggest that the injury responses must be restricted to ensure proper regenerative outcomes of correct scale , and that Yki is a key regulator in these processes .