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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.


Analysis of the Wnt pathway and other developmental signaling groups. a. Clusters of expression of Wnt pathway genes of the GO group in the oral regeneration response. Three clusters were discerned including genes of the following expression patterns (with representative genes): 1. early upregulated (Nv-Wnt11, Nv-Wnt16, fzd-10 precursor). 2. downregulated and then upregulated (Nv-Wnt6,10). 3.late upregulated (Nv-Wnt1, Nv-WntA). Each gene is plotted (gray) in addition to the mean expression profile for that cluster (blue). A full list of the genes and their cluster can be found in Additional file 8: Table S6. b. A proposed hypothetical schematic of the canonical and PCP Wnt pathways interaction in aboral regeneration. The question marks depict signaling interactions which are less established and are thus more assumptive. The bent arrows represent a possible negative feedback loop between cilia and the early canonical Wnt complex that is highly speculative at this stage
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Fig5: Analysis of the Wnt pathway and other developmental signaling groups. a. Clusters of expression of Wnt pathway genes of the GO group in the oral regeneration response. Three clusters were discerned including genes of the following expression patterns (with representative genes): 1. early upregulated (Nv-Wnt11, Nv-Wnt16, fzd-10 precursor). 2. downregulated and then upregulated (Nv-Wnt6,10). 3.late upregulated (Nv-Wnt1, Nv-WntA). Each gene is plotted (gray) in addition to the mean expression profile for that cluster (blue). A full list of the genes and their cluster can be found in Additional file 8: Table S6. b. A proposed hypothetical schematic of the canonical and PCP Wnt pathways interaction in aboral regeneration. The question marks depict signaling interactions which are less established and are thus more assumptive. The bent arrows represent a possible negative feedback loop between cilia and the early canonical Wnt complex that is highly speculative at this stage

Mentions: Three distinct clusters of Wnt pathway genes could be identified based on clustering of their oral regeneration expression patterns (Fig. 5a). The largest cluster had an expression pattern in which its genes were upregulated at 8 h and therein either remained upregulated thereafter or showed a decrease in expression but always above their initial time 0 levels. We termed this cluster “early upregulated” (Fig. 5a1) and it contained Wnts4, 11 and 16, Frizzled1 and 10, intracellular Wnt pathway members like Tcf/Lef-1, Axin and naked-cuticle homolog1(Nkd1) as well as the Wnt secretion regulator Wntless and the Wnt inhibitors Notum and Dkk (Additional file 8: Table S6, Additional file 9: Figure S4 and Fig. 3d). Another cluster included genes that were initially downregulated and then upregulated in later time points with some returning to the baseline by hour 72 (Fig. 5a2). This cluster contained Wnt6 and 10, Frizzled2, two Wnt co-receptor LRP adapter protein genes and two protocadherin fat4 like genes, which are associated with planar cell polarity (PCP) activity and growth control via the Hippo pathway [70, 71]. The third cluster contained genes that were upregulated at a later stage (Fig. 5a3), beginning at hour 24, and was thus termed “late upregulated”, with only three Wnt factors: Wnts1, 2 and A, which are closely related in a Wnt family cladistics analysis as reported by Hensel et al. [72] but are more distantly related according to Kusserow et al. [73]. This clustering of different pathway components indicates a pattern of co-regulation, elucidation of which may be important for deciphering the different stages of the oral vs. aboral patterning process in regeneration in the future studies.Fig. 5


A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis
Analysis of the Wnt pathway and other developmental signaling groups. a. Clusters of expression of Wnt pathway genes of the GO group in the oral regeneration response. Three clusters were discerned including genes of the following expression patterns (with representative genes): 1. early upregulated (Nv-Wnt11, Nv-Wnt16, fzd-10 precursor). 2. downregulated and then upregulated (Nv-Wnt6,10). 3.late upregulated (Nv-Wnt1, Nv-WntA). Each gene is plotted (gray) in addition to the mean expression profile for that cluster (blue). A full list of the genes and their cluster can be found in Additional file 8: Table S6. b. A proposed hypothetical schematic of the canonical and PCP Wnt pathways interaction in aboral regeneration. The question marks depict signaling interactions which are less established and are thus more assumptive. The bent arrows represent a possible negative feedback loop between cilia and the early canonical Wnt complex that is highly speculative at this stage
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig5: Analysis of the Wnt pathway and other developmental signaling groups. a. Clusters of expression of Wnt pathway genes of the GO group in the oral regeneration response. Three clusters were discerned including genes of the following expression patterns (with representative genes): 1. early upregulated (Nv-Wnt11, Nv-Wnt16, fzd-10 precursor). 2. downregulated and then upregulated (Nv-Wnt6,10). 3.late upregulated (Nv-Wnt1, Nv-WntA). Each gene is plotted (gray) in addition to the mean expression profile for that cluster (blue). A full list of the genes and their cluster can be found in Additional file 8: Table S6. b. A proposed hypothetical schematic of the canonical and PCP Wnt pathways interaction in aboral regeneration. The question marks depict signaling interactions which are less established and are thus more assumptive. The bent arrows represent a possible negative feedback loop between cilia and the early canonical Wnt complex that is highly speculative at this stage
Mentions: Three distinct clusters of Wnt pathway genes could be identified based on clustering of their oral regeneration expression patterns (Fig. 5a). The largest cluster had an expression pattern in which its genes were upregulated at 8 h and therein either remained upregulated thereafter or showed a decrease in expression but always above their initial time 0 levels. We termed this cluster “early upregulated” (Fig. 5a1) and it contained Wnts4, 11 and 16, Frizzled1 and 10, intracellular Wnt pathway members like Tcf/Lef-1, Axin and naked-cuticle homolog1(Nkd1) as well as the Wnt secretion regulator Wntless and the Wnt inhibitors Notum and Dkk (Additional file 8: Table S6, Additional file 9: Figure S4 and Fig. 3d). Another cluster included genes that were initially downregulated and then upregulated in later time points with some returning to the baseline by hour 72 (Fig. 5a2). This cluster contained Wnt6 and 10, Frizzled2, two Wnt co-receptor LRP adapter protein genes and two protocadherin fat4 like genes, which are associated with planar cell polarity (PCP) activity and growth control via the Hippo pathway [70, 71]. The third cluster contained genes that were upregulated at a later stage (Fig. 5a3), beginning at hour 24, and was thus termed “late upregulated”, with only three Wnt factors: Wnts1, 2 and A, which are closely related in a Wnt family cladistics analysis as reported by Hensel et al. [72] but are more distantly related according to Kusserow et al. [73]. This clustering of different pathway components indicates a pattern of co-regulation, elucidation of which may be important for deciphering the different stages of the oral vs. aboral patterning process in regeneration in the future studies.Fig. 5

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.