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Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish.

Borchardt T, Looso M, Bruckskotten M, Weis P, Kruse J, Braun T - BMC Genomics (2010)

Bottom Line: Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs.Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms.We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles.

View Article: PubMed Central - HTML - PubMed

Affiliation: Max-Planck-Institute for Heart and Lung Research, Parkstr, 1, 61231 Bad Nauheim, Germany.

ABSTRACT

Background: The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration.

Results: A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish.

Conclusion: We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.

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Expression profiles of selected mRNAs during newt heart regeneration. Expression of RNF 7, SFRP 1, Thioredoxin-like protein 4B and TCTP 1 was analysed by RT-PCR at 4, 7, 14 and 21 days after mechanical injury of newt ventricles (n = 3 for each time point). Expression of ribosomal protein S21 was analyzed as a non-modulated control. A more than 2 fold change in expression level was detected for all 4 selected genes during the newt heart regeneration. Statistically significant changes in expression (p < 0.05 by paired students t-test) were detected for RNF 7 and SFRP 1 at 14 and 21 days after injury and 7 and 14 days after injury for Thioredoxin-like protein 4B. Error bars are shown as ± STDEV. Please note that selected newt genes were so far not identified in regenerating zebrafish hearts.
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Figure 6: Expression profiles of selected mRNAs during newt heart regeneration. Expression of RNF 7, SFRP 1, Thioredoxin-like protein 4B and TCTP 1 was analysed by RT-PCR at 4, 7, 14 and 21 days after mechanical injury of newt ventricles (n = 3 for each time point). Expression of ribosomal protein S21 was analyzed as a non-modulated control. A more than 2 fold change in expression level was detected for all 4 selected genes during the newt heart regeneration. Statistically significant changes in expression (p < 0.05 by paired students t-test) were detected for RNF 7 and SFRP 1 at 14 and 21 days after injury and 7 and 14 days after injury for Thioredoxin-like protein 4B. Error bars are shown as ± STDEV. Please note that selected newt genes were so far not identified in regenerating zebrafish hearts.

Mentions: To detect transcriptional changes during newt heart regeneration, we performed RT-PCR analysis for the selected candidates as described above. Although most candidate genes did not show major changes in expression, we monitored a more than 2 fold change in the levels of RNF 7, SFRP 1, Thioredoxin-like protein 4B and TCTP 1 during newt heart regeneration (Figure 6). These changes were statistically significant for RNF 7 and SFRP 1 at 14 and 21 days after injury and 7 and 14 days after injury for Thioredoxin-like protein 4B (p < 0.05 by paired students t-test). We concluded that our functional annotation based screen identified dynamically regulated candidate genes that have not been implicated in cardiac regeneration before. Although a functional analysis is pending, the changes in the expression of cell cycle control genes and of regulators of programmed cell death suggest an important role of these processes for newt heart regeneration.


Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish.

Borchardt T, Looso M, Bruckskotten M, Weis P, Kruse J, Braun T - BMC Genomics (2010)

Expression profiles of selected mRNAs during newt heart regeneration. Expression of RNF 7, SFRP 1, Thioredoxin-like protein 4B and TCTP 1 was analysed by RT-PCR at 4, 7, 14 and 21 days after mechanical injury of newt ventricles (n = 3 for each time point). Expression of ribosomal protein S21 was analyzed as a non-modulated control. A more than 2 fold change in expression level was detected for all 4 selected genes during the newt heart regeneration. Statistically significant changes in expression (p < 0.05 by paired students t-test) were detected for RNF 7 and SFRP 1 at 14 and 21 days after injury and 7 and 14 days after injury for Thioredoxin-like protein 4B. Error bars are shown as ± STDEV. Please note that selected newt genes were so far not identified in regenerating zebrafish hearts.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2823690&req=5

Figure 6: Expression profiles of selected mRNAs during newt heart regeneration. Expression of RNF 7, SFRP 1, Thioredoxin-like protein 4B and TCTP 1 was analysed by RT-PCR at 4, 7, 14 and 21 days after mechanical injury of newt ventricles (n = 3 for each time point). Expression of ribosomal protein S21 was analyzed as a non-modulated control. A more than 2 fold change in expression level was detected for all 4 selected genes during the newt heart regeneration. Statistically significant changes in expression (p < 0.05 by paired students t-test) were detected for RNF 7 and SFRP 1 at 14 and 21 days after injury and 7 and 14 days after injury for Thioredoxin-like protein 4B. Error bars are shown as ± STDEV. Please note that selected newt genes were so far not identified in regenerating zebrafish hearts.
Mentions: To detect transcriptional changes during newt heart regeneration, we performed RT-PCR analysis for the selected candidates as described above. Although most candidate genes did not show major changes in expression, we monitored a more than 2 fold change in the levels of RNF 7, SFRP 1, Thioredoxin-like protein 4B and TCTP 1 during newt heart regeneration (Figure 6). These changes were statistically significant for RNF 7 and SFRP 1 at 14 and 21 days after injury and 7 and 14 days after injury for Thioredoxin-like protein 4B (p < 0.05 by paired students t-test). We concluded that our functional annotation based screen identified dynamically regulated candidate genes that have not been implicated in cardiac regeneration before. Although a functional analysis is pending, the changes in the expression of cell cycle control genes and of regulators of programmed cell death suggest an important role of these processes for newt heart regeneration.

Bottom Line: Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs.Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms.We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles.

View Article: PubMed Central - HTML - PubMed

Affiliation: Max-Planck-Institute for Heart and Lung Research, Parkstr, 1, 61231 Bad Nauheim, Germany.

ABSTRACT

Background: The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration.

Results: A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish.

Conclusion: We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.

Show MeSH
Related in: MedlinePlus