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Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.

Rodríguez-Esteban G, González-Sastre A, Rojo-Laguna JI, Saló E, Abril JF - BMC Genomics (2015)

Bottom Line: These results are accessible via web for the community of researchers.DGE is a valuable tool for gene discovery, quantification and annotation.The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes.

View Article: PubMed Central - PubMed

Affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain. gresteban@scientist.com.

ABSTRACT

Background: The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking.

Results: Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC.

Conclusions: DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes.

No MeSH data available.


Related in: MedlinePlus

Splashplot projection of the X1/X2 versus Xin expression changes. X-axis represents tags fold change of X1 with respect to Xin, while Y-axis corresponds to fold change differences between X2 and Xin. Fold change is here calculated as the log base 2 of absolute value of difference between X1, or X2, and Xin, while the direction of the change will be given by the sign of that subtraction. Each of the figure quadrants provide insights on tags expression considering the three cell fractions simultaneously. Upper right quadrant contain tags being overexpressed in both X1 and X2 with respect to Xin; bottom left quadrant has those tags overexpressed in Xin versus the other two fractions. Points over the X-axis or Y-axis correspond to tags for which expression levels change only in one cell fraction, X1 or X2, with respect to Xin. The shift trend on most points towards the right vertical hyperbola reflects a higher expression level in X1 when compared to X2 or Xin (otherwise points will fit closer to both diagonals).
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Fig5: Splashplot projection of the X1/X2 versus Xin expression changes. X-axis represents tags fold change of X1 with respect to Xin, while Y-axis corresponds to fold change differences between X2 and Xin. Fold change is here calculated as the log base 2 of absolute value of difference between X1, or X2, and Xin, while the direction of the change will be given by the sign of that subtraction. Each of the figure quadrants provide insights on tags expression considering the three cell fractions simultaneously. Upper right quadrant contain tags being overexpressed in both X1 and X2 with respect to Xin; bottom left quadrant has those tags overexpressed in Xin versus the other two fractions. Points over the X-axis or Y-axis correspond to tags for which expression levels change only in one cell fraction, X1 or X2, with respect to Xin. The shift trend on most points towards the right vertical hyperbola reflects a higher expression level in X1 when compared to X2 or Xin (otherwise points will fit closer to both diagonals).

Mentions: The validity of our approach is corroborated by the expression levels detected in 40 already known and well-characterized neoblast genes (Table 2), plus another 29 genes described in the literature with evidence of also being neoblast related (Table 3). As can be observed in Figure 5, both sets of genes show the expected expression pattern along the vertical right hyperbola, indicating a clear X1 specificity, with two exceptions overrepresented in X2: Smed-nlk-1 and Smed-prog-1, which is described to be found in postmitotic cells [53]. Smed-dlx and Smed-sp6-9 are key genes in eye formation [54]; despite their localized activation, DGE was sensitive enough to identify both of them predominantly in the X1 subfraction. Moreover, we could detect expression of genes such as Smed-smg-1—which is described as broadly expressed through all tissues, including neoblasts [55]—in both neoblasts and differentiated cells. Finally, 133 clones from two different studies [6,56] focussing on regeneration, stemness and tissue homeostasis are, indeed, significantly overexpressed in neoblasts (Additional file 7).Table 2


Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.

Rodríguez-Esteban G, González-Sastre A, Rojo-Laguna JI, Saló E, Abril JF - BMC Genomics (2015)

Splashplot projection of the X1/X2 versus Xin expression changes. X-axis represents tags fold change of X1 with respect to Xin, while Y-axis corresponds to fold change differences between X2 and Xin. Fold change is here calculated as the log base 2 of absolute value of difference between X1, or X2, and Xin, while the direction of the change will be given by the sign of that subtraction. Each of the figure quadrants provide insights on tags expression considering the three cell fractions simultaneously. Upper right quadrant contain tags being overexpressed in both X1 and X2 with respect to Xin; bottom left quadrant has those tags overexpressed in Xin versus the other two fractions. Points over the X-axis or Y-axis correspond to tags for which expression levels change only in one cell fraction, X1 or X2, with respect to Xin. The shift trend on most points towards the right vertical hyperbola reflects a higher expression level in X1 when compared to X2 or Xin (otherwise points will fit closer to both diagonals).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4494696&req=5

Fig5: Splashplot projection of the X1/X2 versus Xin expression changes. X-axis represents tags fold change of X1 with respect to Xin, while Y-axis corresponds to fold change differences between X2 and Xin. Fold change is here calculated as the log base 2 of absolute value of difference between X1, or X2, and Xin, while the direction of the change will be given by the sign of that subtraction. Each of the figure quadrants provide insights on tags expression considering the three cell fractions simultaneously. Upper right quadrant contain tags being overexpressed in both X1 and X2 with respect to Xin; bottom left quadrant has those tags overexpressed in Xin versus the other two fractions. Points over the X-axis or Y-axis correspond to tags for which expression levels change only in one cell fraction, X1 or X2, with respect to Xin. The shift trend on most points towards the right vertical hyperbola reflects a higher expression level in X1 when compared to X2 or Xin (otherwise points will fit closer to both diagonals).
Mentions: The validity of our approach is corroborated by the expression levels detected in 40 already known and well-characterized neoblast genes (Table 2), plus another 29 genes described in the literature with evidence of also being neoblast related (Table 3). As can be observed in Figure 5, both sets of genes show the expected expression pattern along the vertical right hyperbola, indicating a clear X1 specificity, with two exceptions overrepresented in X2: Smed-nlk-1 and Smed-prog-1, which is described to be found in postmitotic cells [53]. Smed-dlx and Smed-sp6-9 are key genes in eye formation [54]; despite their localized activation, DGE was sensitive enough to identify both of them predominantly in the X1 subfraction. Moreover, we could detect expression of genes such as Smed-smg-1—which is described as broadly expressed through all tissues, including neoblasts [55]—in both neoblasts and differentiated cells. Finally, 133 clones from two different studies [6,56] focussing on regeneration, stemness and tissue homeostasis are, indeed, significantly overexpressed in neoblasts (Additional file 7).Table 2

Bottom Line: These results are accessible via web for the community of researchers.DGE is a valuable tool for gene discovery, quantification and annotation.The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes.

View Article: PubMed Central - PubMed

Affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain. gresteban@scientist.com.

ABSTRACT

Background: The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking.

Results: Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC.

Conclusions: DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes.

No MeSH data available.


Related in: MedlinePlus