Dynamic And Stable Epigenomic Profiles In Mammalian Cell Fate Conversion

A mammalian cell with defined developmental potency can be converted to a pluripotent stem cell that has the potential to differentiate into any of the three germ layers: endoderm, mesoderm, or ectoderm. This reprogramming phenomenon offers a number of potential clinical applications, especially for diseases with a genetic basis. Several strategies have been applied to achieve cell reprogramming, including somatic cell nuclear transfer (SCNT), cell fusion, inducing pluripotent stem (iPS) with overexpression of several key pluripotency-associated transcription factors. However, these current approaches are limited in cell source, reprogramming efficiency, or application safety, which rescrict their potential applications in research and clinical treatment. Besides, the underlying reprogramming mechanisms remain largely unknown. And it is unclear whether intrinsic genetic and epigenetic characteristics of a lineage-restricted cell can affect reprogramming process. This thesis is focused on the impact of the epigenome on mammalian cell fate conversion from unipotency to multi-/pluri-potency. In Chapter one, we studied the spontaneous conversion from cultured mouse spermatogonial stem and progenitor cells (SSCs) to multipotent adult spermatogonial-derived stem cells (MASCs). In Chapter two, we performed time-series study on transcription factor-induced mouse embryonic fibroblasts (MEFs) reprogramming. In each model system, we applied high throughput sequencing and bioinformatics analyses to dissect both transcriptome and epigenome defined by transcription-associated histone modifications and histone variant exchange. We found in SSCs that many genes essential to pluripotent stem cell maintenance and differentiation were enriched with both histone H3 lysine 4 and lysine 27 trimethylation modifications (K4me3+K27me3) at promoter regions. After SSC conversion, promoter histone modifications were restrictively changed at pluripotency- or germline-specific genes but remained repressive for most somatic genes, bestowing MASCs with pluripotency-associated promoter chromatin states. At enhancer regions, the core pluripotency circuitry was activated partially in SSCs and completely in MASCs, concomitant with global erasure of germ cell-specific enhancer activity and initiation of an embryonic-like program. In addition, histone variant H3.3, which is specifically enriched at core pluripotency genes in SSCs, was potentially involved in chromatin remodeling and pluripotency gene reactivation during the reprogramming of differentiated MEFs. These results suggest that unipotent SSCs encode their innate developmental flexibility by means of the epigenome and that both the promoter chromatin state, and the activity of cell-type-specific enhancers are prominent features of SSC reprogramming. Besides, our finding of the gene-specific epigenetic conversion during mammalian cell reprogramming provides insights into the development of new strategies to achieve pluripotency