Genome-wide Reprogramming in Hybrids of Somatic Cells and Embryonic Stem Cells

¹ Center for Regenerative Biology, University of Connecticut, 1392 Storrs Road, Storrs, Connecticut; Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
² Department of Genetics and Developmental Biology, University of Connecticut Medical School, Farmington, Connecticut
³ Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
⁴ Center for Regenerative Biology, University of Connecticut, 1392 Storrs Road, Storrs, Connecticut; Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut; Department of Animal Science, University of Connecticut, Storrs, Connecticut

^* To whom correspondence should be addressed. E-mail: Theodore.Rasmussen{at}uconn.edu.

	Abstract

Recent experiments demonstrate that somatic nuclei can be reprogrammed to a pluripotent state when fused to embryonic stem cells (ESCs). The resulting hybrids are pluripotent as judged by developmental assays, but detailed analyses of the underlying molecular-genetic control of reprogrammed transcription in such hybrids are required to better understand fusion-mediated reprogramming. We produced hybrids of mouse ESCs and fibroblasts that, though nearly tetraploid, exhibit characteristics of normal ESCs, including apparent immortality in culture, ESC-like colony morphology, and pluripotency. Comprehensive analysis of the MEF/ESC hybrid transcriptome revealed global patterns of gene expression reminiscent of ESCs. However, combined analysis of variance (ANOVA) and hierarchical clustering analyses revealed at least seven distinct classes of differentially-regulated genes in comparisons of hybrids, ESCs, and somatic cells. The largest class includes somatic genes that are silenced in hybrids and ESCs, but a smaller class includes genes that are expressed at nearly equivalent levels in hybrids and ESCs that contain many genes implicated in pluripotency and chromatin function. Reprogrammed genes are distributed throughout the genome. Reprogramming events include both transcriptional silencing and activation of genes residing on chromosomes of somatic origin. Somatic/ESC hybrid cell lines resemble their pre-fusion ESC partners in terms of behavior in culture and pluripotency. However, they contain unique expression profiles that are similar, but not identical to normal ESCs. ESC fusion-mediated reprogramming provides a tractable system for the investigation of mechanisms of reprogramming.