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A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis

View Article: PubMed Central - PubMed

ABSTRACT

Background: The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies greatly in different animals with the sea anemone Nematostella vectensis, a basal cnidarian model animal, displaying remarkable whole-body regeneration competence.

Results: In order to study this process in Nematostella we performed an RNA-Seq screen wherein we analyzed and compared the transcriptional response to bisection in the wound-proximal body parts undergoing oral (head) or aboral (tail) regeneration at several time points up to the initial restoration of the basic body shape. The transcriptional profiles of regeneration responsive genes were analyzed so as to define the temporal pattern of differential gene expression associated with the tissue-specific oral and aboral regeneration. The identified genes were characterized according to their GO (gene ontology) assignations revealing groups that were enriched in the regeneration process with particular attention to their affiliation to the major developmental signaling pathways. While some of the genes and gene groups thus analyzed were previously known to be active in regeneration, we have also revealed novel and surprising candidate genes such as cilia-associated genes that likely participate in this important developmental program.

Conclusions: This work highlighted the main groups of genes which showed polarization upon regeneration, notably the proteinases, multiple transcription factors and the Wnt pathway genes that were highly represented, all displaying an intricate temporal balance between the two sides. In addition, the evolutionary comparison performed between regeneration in different animal model systems may reveal the basic mechanisms playing a role in this fascinating process.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-016-3027-1) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Comparison of “head” vs. “tail” gene expression in the regeneration of Nematostella and Planaria. A cartoon of the two animals is presented with the oral (head) part of Nematostella aligned with the posterior (tail) part of Planaria according to the comparison in which these ends express an assembly of Wnts and other universal bilaterian posterior markers, while the aboral part resembles the Planarian anterior (head) part in the expression of universal anterior markers such as Six3/6 and Wnt inhibitors like sFRPs [51]. Some of the markers specific for the main axis ends are depicted with Wnts and Wnt pathway genes in red and orange, FGF pathway members in brown, homeobox factors in light blue, forkhead (Fox) factors in purple, and other TFs in green. An anterior Planaria regeneration marker and protease, proprotein convertase 2 (PC2) and its ortholog in Nematostella, the late aboral Pep8 gene are marked in grey. Highlighted in light green are bona fide orthologs that are expressed as expected according to this comparison, while yellow marks polarized genes that are expressed in an ‘inverted’ position, which can indicate evolutionary change in the regeneration program. aThe FoxD1 gene is induced at the oral regenerating region in Nematostella however it is aboral in embryonic/larval development and becomes orally expressed upon metamorphosis and tentacle budding [95]. bDickkopf (DKK) is expressed higher orally at 8 h after the induction of regeneration and higher in the aboral part later than 24 h. cRunt-1 is induced in anterior sites upon eye and neural brain regeneration in Planaria but is also expressed in posterior wound sites [35, 37] and https://radiant.wi.mit.edu/app/
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Fig7: Comparison of “head” vs. “tail” gene expression in the regeneration of Nematostella and Planaria. A cartoon of the two animals is presented with the oral (head) part of Nematostella aligned with the posterior (tail) part of Planaria according to the comparison in which these ends express an assembly of Wnts and other universal bilaterian posterior markers, while the aboral part resembles the Planarian anterior (head) part in the expression of universal anterior markers such as Six3/6 and Wnt inhibitors like sFRPs [51]. Some of the markers specific for the main axis ends are depicted with Wnts and Wnt pathway genes in red and orange, FGF pathway members in brown, homeobox factors in light blue, forkhead (Fox) factors in purple, and other TFs in green. An anterior Planaria regeneration marker and protease, proprotein convertase 2 (PC2) and its ortholog in Nematostella, the late aboral Pep8 gene are marked in grey. Highlighted in light green are bona fide orthologs that are expressed as expected according to this comparison, while yellow marks polarized genes that are expressed in an ‘inverted’ position, which can indicate evolutionary change in the regeneration program. aThe FoxD1 gene is induced at the oral regenerating region in Nematostella however it is aboral in embryonic/larval development and becomes orally expressed upon metamorphosis and tentacle budding [95]. bDickkopf (DKK) is expressed higher orally at 8 h after the induction of regeneration and higher in the aboral part later than 24 h. cRunt-1 is induced in anterior sites upon eye and neural brain regeneration in Planaria but is also expressed in posterior wound sites [35, 37] and https://radiant.wi.mit.edu/app/

Mentions: Finally, we compared the expression patterns of the key genes we identified in our screening to those reported in the well-studied regeneration plan of the Planaria, where the head vs. tail regeneration program has been studied in depth [24, 27, 28, 38, 92]. To this end, we identified the Nematostella orthologs of the known Planaria anterior and posterior marker genes which are also induced during regeneration in a polarized fashion. When no bona fide orthologs could be found we added the closest homologous genes that also show polarized expression to complete the picture (Additional file 13: Table S9 and Fig. 7). Many of our oral-induced genes corresponded to the tail/posterior genes/markers of the Planaria and inversely, the aboral genes matched those of the head/anterior Planarian genes (Fig. 7). This relationship between the cnidarian oral/aboral axis and the anterior/posterior axis of bilaterians has been reported recently [51], where the aboral part of Nematostella shows a molecular resemblance to the anterior part of bilaterians, and inversely, the oral region has similarity to the posterior bilaterian side. Thus, the aforementioned master aboral territory gene Six3/6 [51] and the OtxC gene that are highly expressed in aboral regeneration (Fig. 3d) have orthologs in Planaria that are anteriorly expressed (Fig. 7). We also detected a higher aboral expression of FGF1a [93] (Fgf20 in [57]) and FGF-R1- like with a corresponding head expression of the FGF-receptor like ndk, ndl-3 and ndl-4 Planaria genes. Interestingly, we also found several oral enriched Nematostella FGF factors induced in regeneration (Fig. 7), however, the identity of their receptors as well as of the aboral FGF factors and their effect in each side awaits further studies. Interestingly, we found that the forkhead factors FoxA2 and FoxB in Nematostella, which were reported to be expressed in the pharynx during larval development and in young adults [94, 95], have a late high oral expression pattern. Accordingly, they most likely correspond to their Planarian counterpart FoxA, which was shown to be a pharynx marker [96] and a factor that is essential for the formation of this organ in Planaria and perhaps in all eumetazoans that contain pharynx/foregut [97].Fig. 7


A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis
Comparison of “head” vs. “tail” gene expression in the regeneration of Nematostella and Planaria. A cartoon of the two animals is presented with the oral (head) part of Nematostella aligned with the posterior (tail) part of Planaria according to the comparison in which these ends express an assembly of Wnts and other universal bilaterian posterior markers, while the aboral part resembles the Planarian anterior (head) part in the expression of universal anterior markers such as Six3/6 and Wnt inhibitors like sFRPs [51]. Some of the markers specific for the main axis ends are depicted with Wnts and Wnt pathway genes in red and orange, FGF pathway members in brown, homeobox factors in light blue, forkhead (Fox) factors in purple, and other TFs in green. An anterior Planaria regeneration marker and protease, proprotein convertase 2 (PC2) and its ortholog in Nematostella, the late aboral Pep8 gene are marked in grey. Highlighted in light green are bona fide orthologs that are expressed as expected according to this comparison, while yellow marks polarized genes that are expressed in an ‘inverted’ position, which can indicate evolutionary change in the regeneration program. aThe FoxD1 gene is induced at the oral regenerating region in Nematostella however it is aboral in embryonic/larval development and becomes orally expressed upon metamorphosis and tentacle budding [95]. bDickkopf (DKK) is expressed higher orally at 8 h after the induction of regeneration and higher in the aboral part later than 24 h. cRunt-1 is induced in anterior sites upon eye and neural brain regeneration in Planaria but is also expressed in posterior wound sites [35, 37] and https://radiant.wi.mit.edu/app/
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Fig7: Comparison of “head” vs. “tail” gene expression in the regeneration of Nematostella and Planaria. A cartoon of the two animals is presented with the oral (head) part of Nematostella aligned with the posterior (tail) part of Planaria according to the comparison in which these ends express an assembly of Wnts and other universal bilaterian posterior markers, while the aboral part resembles the Planarian anterior (head) part in the expression of universal anterior markers such as Six3/6 and Wnt inhibitors like sFRPs [51]. Some of the markers specific for the main axis ends are depicted with Wnts and Wnt pathway genes in red and orange, FGF pathway members in brown, homeobox factors in light blue, forkhead (Fox) factors in purple, and other TFs in green. An anterior Planaria regeneration marker and protease, proprotein convertase 2 (PC2) and its ortholog in Nematostella, the late aboral Pep8 gene are marked in grey. Highlighted in light green are bona fide orthologs that are expressed as expected according to this comparison, while yellow marks polarized genes that are expressed in an ‘inverted’ position, which can indicate evolutionary change in the regeneration program. aThe FoxD1 gene is induced at the oral regenerating region in Nematostella however it is aboral in embryonic/larval development and becomes orally expressed upon metamorphosis and tentacle budding [95]. bDickkopf (DKK) is expressed higher orally at 8 h after the induction of regeneration and higher in the aboral part later than 24 h. cRunt-1 is induced in anterior sites upon eye and neural brain regeneration in Planaria but is also expressed in posterior wound sites [35, 37] and https://radiant.wi.mit.edu/app/
Mentions: Finally, we compared the expression patterns of the key genes we identified in our screening to those reported in the well-studied regeneration plan of the Planaria, where the head vs. tail regeneration program has been studied in depth [24, 27, 28, 38, 92]. To this end, we identified the Nematostella orthologs of the known Planaria anterior and posterior marker genes which are also induced during regeneration in a polarized fashion. When no bona fide orthologs could be found we added the closest homologous genes that also show polarized expression to complete the picture (Additional file 13: Table S9 and Fig. 7). Many of our oral-induced genes corresponded to the tail/posterior genes/markers of the Planaria and inversely, the aboral genes matched those of the head/anterior Planarian genes (Fig. 7). This relationship between the cnidarian oral/aboral axis and the anterior/posterior axis of bilaterians has been reported recently [51], where the aboral part of Nematostella shows a molecular resemblance to the anterior part of bilaterians, and inversely, the oral region has similarity to the posterior bilaterian side. Thus, the aforementioned master aboral territory gene Six3/6 [51] and the OtxC gene that are highly expressed in aboral regeneration (Fig. 3d) have orthologs in Planaria that are anteriorly expressed (Fig. 7). We also detected a higher aboral expression of FGF1a [93] (Fgf20 in [57]) and FGF-R1- like with a corresponding head expression of the FGF-receptor like ndk, ndl-3 and ndl-4 Planaria genes. Interestingly, we also found several oral enriched Nematostella FGF factors induced in regeneration (Fig. 7), however, the identity of their receptors as well as of the aboral FGF factors and their effect in each side awaits further studies. Interestingly, we found that the forkhead factors FoxA2 and FoxB in Nematostella, which were reported to be expressed in the pharynx during larval development and in young adults [94, 95], have a late high oral expression pattern. Accordingly, they most likely correspond to their Planarian counterpart FoxA, which was shown to be a pharynx marker [96] and a factor that is essential for the formation of this organ in Planaria and perhaps in all eumetazoans that contain pharynx/foregut [97].Fig. 7

View Article: PubMed Central - PubMed

ABSTRACT

Background: The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies greatly in different animals with the sea anemone Nematostella vectensis, a basal cnidarian model animal, displaying remarkable whole-body regeneration competence.

Results: In order to study this process in Nematostella we performed an RNA-Seq screen wherein we analyzed and compared the transcriptional response to bisection in the wound-proximal body parts undergoing oral (head) or aboral (tail) regeneration at several time points up to the initial restoration of the basic body shape. The transcriptional profiles of regeneration responsive genes were analyzed so as to define the temporal pattern of differential gene expression associated with the tissue-specific oral and aboral regeneration. The identified genes were characterized according to their GO (gene ontology) assignations revealing groups that were enriched in the regeneration process with particular attention to their affiliation to the major developmental signaling pathways. While some of the genes and gene groups thus analyzed were previously known to be active in regeneration, we have also revealed novel and surprising candidate genes such as cilia-associated genes that likely participate in this important developmental program.

Conclusions: This work highlighted the main groups of genes which showed polarization upon regeneration, notably the proteinases, multiple transcription factors and the Wnt pathway genes that were highly represented, all displaying an intricate temporal balance between the two sides. In addition, the evolutionary comparison performed between regeneration in different animal model systems may reveal the basic mechanisms playing a role in this fascinating process.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-016-3027-1) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus