ABSTRACT
Although the mammalian heart is one of the least regenerative organs in the body, recent evidence indicates that the myocardium undergoes a certain degree of renewal to maintain homeostasis during normal aging. However, the cellular origin of cardiomyocyte renewal has remained elusive due to lack of lineage tracing experiments focusing on putative adult cardiac precursor cells. We have generated triple-transgenic mice based on the tet-cre system to identify descendants of cells that have expressed the stem cell marker Sca1. We found a significant and lasting contribution of Sca1-derived cells to cardiomyocytes during normal aging. Ischemic damage and pressure overload resulted in increased differentiation of Sca1-derived cells to the different cell types present in the heart. Our results reveal a source of cells for cardiomyocyte renewal and provide a possible explanation for the limited contribution of Sca1-derived cells to myocardial repair under pathological conditions.
Subject(s)
Antigens, Ly/metabolism , Cell Differentiation , Cell Lineage , Heart/growth & development , Membrane Proteins/metabolism , Myocytes, Cardiac/cytology , Stem Cells/cytology , Animals , Antigens, Ly/genetics , Cell Proliferation , Membrane Proteins/genetics , Mice , Mice, Inbred C57BL , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/physiology , Stem Cells/metabolism , Stem Cells/physiologyABSTRACT
Exon arrays are regularly used to analyze differential splicing events. GeneChip Gene 1.0 ST Arrays (gene arrays) manufactured by Affymetrix, Inc. are primarily used to determine expression levels of transcripts, although their basic design is rather similar to GeneChip Exon 1.0 ST Arrays (exon arrays). Here, we show that the newly developed Gene Array Analyzer (GAA), which evolved from our previously published Exon Array Analyzer (EAA), enables economic and user-friendly analysis of alternative splicing events using gene arrays. To demonstrate the applicability of GAA, we profiled alternative splicing events during embryonic heart development. In addition, we found that numerous developmental splicing events are also activated under pathological conditions. We reason that the usage of GAA considerably expands the analysis of gene expression based on gene arrays and supplies an additional level of information without further costs and with only little effort.
Subject(s)
Alternative Splicing , Gene Expression Profiling/methods , Oligonucleotide Array Sequence Analysis/methods , Software , Animals , Cell Differentiation , Cell Line , Exons , Heart/embryology , Heart/growth & development , Heart Diseases/genetics , Heart Diseases/metabolism , Mice , Mice, Inbred C57BL , Myocardium/metabolism , Myocytes, Cardiac/cytology , Myocytes, Cardiac/metabolismABSTRACT
MOTIVATION: Due to the development of high-throughput technologies such as microarrays, it has become possible to determine genome-wide expression changes in a single experiment. Although much attention has been paid to identify differentially expressed genes, the functions of tens of thousands of genes in different species still remain unknown. RESULTS: C-It is a knowledge database that has its focus on 'uncharacterized genes'. C-It contains expression profiles of various tissues from human, mouse, rat, chicken and zebrafish. By applying our previously introduced algorithm DGSA (Database-Dependent Gene Selection and Analysis), it is possible to screen for uncharacterized, tissue-enriched genes in the species mentioned above. C-It is designed to include further expression studies, which might provide more comprehensive coverage of gene expression patterns and tissue-enriched splicing isoforms. We propose that C-It will be an excellent starting point to study uncharacterized genes. AVAILABILITY: C-It is freely available online without registration at http://C-It.mpi-bn.mpg.dehttp://C-It.mpi-bn.mpg.de.
Subject(s)
Algorithms , Databases, Genetic , Animals , Expressed Sequence Tags , Gene Expression , Gene Expression Profiling , Humans , Internet , Mice , Oligonucleotide Array Sequence Analysis , Rats , User-Computer Interface , ZebrafishABSTRACT
BACKGROUND: High throughput techniques have generated a huge set of biological data, which are deposited in various databases. Efficient exploitation of these databases is often hampered by a lack of appropriate tools, which allow easy and reliable identification of genes that miss functional characterization but are correlated with specific biological conditions (e.g. organotypic expression). RESULTS: We have developed a simple algorithm (DGSA = Database-dependent Gene Selection and Analysis) to identify genes with unknown functions involved in organ development concentrating on the heart. Using our approach, we identified a large number of yet uncharacterized genes, which are expressed during heart development. An initial functional characterization of genes by loss-of-function analysis employing morpholino injections into zebrafish embryos disclosed severe developmental defects indicating a decisive function of selected genes for developmental processes. CONCLUSION: We conclude that DGSA is a versatile tool for database mining allowing efficient selection of uncharacterized genes for functional analysis.
