Genomewide gene expression analysis of murine Sirt1 wild-type or knock-out embryonic stem cells (ESCs)

Stem-cells and transformed cancer cells specifically express a polycomb repressive complex subtype, PRC4 which characteristically contains Sirt1 (Sirtuin-1), a NAD+ dependent class III histone deacetylase (HDAC) and Eed2 isoform as specific members. Analyzing the transcriptiome and methylome analysis of Sirt1 deficient murine ESCs (Sirt1-/- ESC), we demonstrate that these cells repressed specifically on some genomic imprinted and germ-line related genes. We used microarrays to characterize the programm of gene expression affected by Sirt1 in murine ESCs and identified distinct classes of down-regulated genes upon Sirt1 deficiency Total RNA were prepared from the Sirt1 wild-type and mutant ESCs and hybridization on Affymetrix microarrays were performed. The Wild-type and Sirt1 deficient murine R1 ESCs were grown in ESC medium supplemented with 100 IU/ml ESGRO/LIF under 0.1% gelatin coated tissue culture dish.