Epigenetic Control of Cell Cycle-Dependent Histone Gene Expression Is a Principal Component of the Abbreviated Pluripotent Cell Cycle

Abstract

Self-renewal of human pluripotent embryonic stem cells proceeds via an abbreviated cell cycle with a shortened G₁ phase. We examined which genes are modulated in this abbreviated period and the epigenetic mechanisms that control their expression. Accelerated upregulation of genes encoding histone proteins that support DNA replication is the most prominent gene regulatory program at the G₁/S-phase transition in pluripotent cells. Expedited expression of histone genes is mediated by a unique chromatin architecture reflected by major nuclease hypersensitive sites, atypical distribution of epigenetic histone marks, and a region devoid of histone octamers. We observed remarkable differences in chromatin structure—hypersensitivity and histone protein modifications—between human embryonic stem (hES) and normal diploid cells. Cell cycle-dependent transcription factor binding permits dynamic three-dimensional interactions between transcript initiating and processing factors at 5′ and 3′ regions of the gene. Thus, progression through the abbreviated G₁ phase involves cell cycle stage-specific chromatin-remodeling events and rapid assembly of subnuclear microenvironments that activate histone gene transcription to promote nucleosomal packaging of newly replicated DNA during stem cell renewal.

ACKNOWLEDGMENTS

We thank Judy Rask and Patricia Jamieson for expert assistance with manuscript preparation. We also thank Phyllis Spatrick, David Lapointe, Stephen Baker, and Mei Xu from UMMS for expert advice with microarray and statistical analysis and Wade Harper (Harvard Medical School), Zbigniew Dominski (University of North Carolina at Chapel Hill), Rudolf Jaenisch (The Whitehead Institute), and Vincenzo De Laurenzi (Universita G. d'Annunzio Chieti-Pescara) for generously providing antibodies and/or cell lines. We also thank the members of our research group and especially Kaleem Zaidi and Jason Dobson for stimulating discussions and Margaretha van der Deen for histone H4 primer (1, 2, 3, 5, and 6) sequences.

Studies reported were in part supported by National Institutes of Health grants RC1 AG035886-01 (to G.S.S. and A.J.V.W.) and R01 CA139322-03 (to G.S.S. and J.L.S.), as well as FONDECYT contract grant 1095075 (to M.M.) and FONDAP contract grant 15090007 (to M.M.).

The contents of this paper are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health.

We declare no competing financial interests.