Quiescence induces epigenetic changes in bovine fibroblasts and improves their reprogramming into cloned embryos

Abstract

Cloning by somatic cell nuclear transfer (SCNT) forces cells to lose their lineage-specific epigenetic marks and become totipotent again. This reprogramming process often results in epigenetic and transcriptional aberrations that compromise development. Development rates after SCNT can thus serve as a functional assay for genome-wide epigenetic reprogramming. Dolly the sheep, the first mammalian SCNT clone, was derived from a donor cell that was induced into quiescence by serum starvation. We hypothesized that quiescence alters the epigenetic status of donor cells and elevates their reprogrammability. In order to test this idea, we compared chromatin composition and cloning efficiency of serum-starved, quiescent (G₀), bovine fibroblasts vs non-starved, diploid G₁ controls. Mechanically synchronized G₁ cells were generated by mitotic shake-off and harvested within 3 h post-mitosis. Based on morphological assessment and EdU incorporation during continuous labeling, >93% of cells were captured in G₁. Using quantitative confocal immunofluorescence microscopy and fluorometric ELISA, we show that G₀ fibroblasts were significantly hypomethylated at lysines (K) of histone 3 (H3), specifically H3K4me3, H3K9me2, H3K9me3 and H3K27me3, but not H3K9me1. Histone acetylation was reduced at H3K9 and H4K5, increased at H3K12 and remained unchanged at H3K16. G₀ cells also significantly reduced DNAme. In addition, they significantly down-regulated the nuclear abundance of RNA polymerase II, histone variant H2A.Z, as well as Polycomb group (PcG) proteins EED, SUZ12, PHC1 and RING2. Histone variant H3.3, PcG proteins EZH2 and histone deacetylase HDAC1 did not change compared to the G₁ controls. Following NT into metaphase-arrested oocytes, G₀ DNA condensed slower than that of G₁ cells, indicating a more relaxed chromatin configuration. After seven days of in vitro culture, H3K9me3, but not H3K4me3, H3K27me3, SUZ12 and RING2, remained hypomethylated in G₀- vs G₁-derived NT blastocysts, both in the inner cell mass and trophectoderm. Furthermore, G₀ donors significantly improved development into cloned blastocysts. In conclusion, quiescence induced long-term epigenetic changes, specifically H3K9me3 hypomethylation, that correlated with increased donor cell reprogrammability.