Limits...
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

Predicted functional domains for several of the selected transcript candidates. Functional domains annotation based on Pfam hidden Markov models. Legend box shows a classification of the domain hits based on its match to complete domain model; the boxes height is proportional to the E-value score provided for each match. Significant matches were considered for HMMER [117] E-value < 0.001; however, low-significance matches are also shown, as well as hits to Pfam-B models produced by automated alignment protocols. Further annotation over Smed454 transcripts is already available at the GBrowse2 URL planarian.bio.ub.edu/gbrowse/smed454_transcriptome; an example can also be found on Figure 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Predicted functional domains for several of the selected transcript candidates. Functional domains annotation based on Pfam hidden Markov models. Legend box shows a classification of the domain hits based on its match to complete domain model; the boxes height is proportional to the E-value score provided for each match. Significant matches were considered for HMMER [117] E-value < 0.001; however, low-significance matches are also shown, as well as hits to Pfam-B models produced by automated alignment protocols. Further annotation over Smed454 transcripts is already available at the GBrowse2 URL planarian.bio.ub.edu/gbrowse/smed454_transcriptome; an example can also be found on Figure 4.

Mentions: 8,903 contigs from Smed454_90e—Smed454 from now on—[10] showing significant expression changes (p < 0.001) were selected and, from those, 7,735 contigs presented a hit to a Pfam domain model (Figure 3). For those sequences having a significant hit to a known domain/protein, gene ontology (GO) analysis was performed in order to summarize changes on the biological processes and molecular functions due to the observed expression patterns of the enriched sets of transcripts. Those transcripts were classified according to the cell type in which they were mostly expressed, then their significant GO annotations were clustered (also taking into account their parent nodes in the ontology), to calculate the terms abundance log-odds ratio. Comparison of GO categories between transcripts predominantly expressed in X1, X2 or Xin cell fractions revealed significant patterns of enrichment as indicated in Additional file 6 (see also the “Transcriptomes” tables available from the web site—planarian.bio.ub.edu/SmedDGE—for specific GO terms assigned to each transcript).Figure 3


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)

Predicted functional domains for several of the selected transcript candidates. Functional domains annotation based on Pfam hidden Markov models. Legend box shows a classification of the domain hits based on its match to complete domain model; the boxes height is proportional to the E-value score provided for each match. Significant matches were considered for HMMER [117] E-value < 0.001; however, low-significance matches are also shown, as well as hits to Pfam-B models produced by automated alignment protocols. Further annotation over Smed454 transcripts is already available at the GBrowse2 URL planarian.bio.ub.edu/gbrowse/smed454_transcriptome; an example can also be found on Figure 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Predicted functional domains for several of the selected transcript candidates. Functional domains annotation based on Pfam hidden Markov models. Legend box shows a classification of the domain hits based on its match to complete domain model; the boxes height is proportional to the E-value score provided for each match. Significant matches were considered for HMMER [117] E-value < 0.001; however, low-significance matches are also shown, as well as hits to Pfam-B models produced by automated alignment protocols. Further annotation over Smed454 transcripts is already available at the GBrowse2 URL planarian.bio.ub.edu/gbrowse/smed454_transcriptome; an example can also be found on Figure 4.
Mentions: 8,903 contigs from Smed454_90e—Smed454 from now on—[10] showing significant expression changes (p < 0.001) were selected and, from those, 7,735 contigs presented a hit to a Pfam domain model (Figure 3). For those sequences having a significant hit to a known domain/protein, gene ontology (GO) analysis was performed in order to summarize changes on the biological processes and molecular functions due to the observed expression patterns of the enriched sets of transcripts. Those transcripts were classified according to the cell type in which they were mostly expressed, then their significant GO annotations were clustered (also taking into account their parent nodes in the ontology), to calculate the terms abundance log-odds ratio. Comparison of GO categories between transcripts predominantly expressed in X1, X2 or Xin cell fractions revealed significant patterns of enrichment as indicated in Additional file 6 (see also the “Transcriptomes” tables available from the web site—planarian.bio.ub.edu/SmedDGE—for specific GO terms assigned to each transcript).Figure 3

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