SAGE identification of differentiation responsive genes in P19 embryonic cells induced to form cardiomyocytes in vitro

Abstract

Transcriptome profiling facilitates the identification of developmentally regulated genes. To quantify the functionally active genome of P19 embryonic carcinoma (EC) cells induced to form cardiomyocytes, we employed serial analysis of gene expression (SAGE) to sequence and compare a total of 171,735 SAGE tags from three libraries (undifferentiated P19 EC cells, differentiation days 3+0.5 and 3+3.0). After in vitro differentiation, only 3.1% of the gene products demonstrated significant (P<0.05) changes in expression. The most highly significant changes (P<0.01) involved altered expression of 410 genes encoding predominantly transcription factors, differentiation factors and growth regulators. Quantitative polymerase chain reaction analysis and in situ hybridization revealed five growth regulators (Dlk1, Igfbp5, Hmga2, Podxl and Ptn) and two unknown ESTs with expression profiles similar to known cardiac transcription factors, implicating these growth regulators in cardiac differentiation. These SAGE libraries thus serve as a reference resource for understanding the role of differentiation-dependent genes in embryonic stem cell models induced to form cardiomyocytes in vitro.