Transcriptional Repression in ES Cells Clara Y. Cheong and Thomas Lufkin * Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore ABSTRACT The dynamics of embryonic stem cell pluripotency is orchestrated by an interplay of transcriptional and epigenetic regulation in a systematic and modular manner. While the ES cell stage is marked by multiple loci with bivalent chromatin marks that prepare genes for imminent activation on differentiation, this open chromatin conformation is tempered by repressive machinery that prevent premature expression of key developmental genes. This review serves to highlight key ES transcription factors and their known links to the epigenetic machinery via known protein complexes. J. Cell. Biochem. 110: 288–293, 2010. ß 2010 Wiley-Liss, Inc. KEY WORDS: STEM CELLS; EPIGENETICS; TRANSCRIPTIONAL REPRESSION; METHYLATION; HISTONE MODIFICATION T he biology of embryonic stem (ES) cells has captured the imagination of both the scientific and general community alike, and the promise it holds for our understanding of early development and future medicine lies in its pluripotent capacity to self-renew or differentiate into almost any cell type. ES cells are derived from the inner cell mass (ICM) of the pre-implantation embryo at the blastocyst stage, therefore represent an in vitro culture equivalent of the developmental processes at this embryonic stage. Importantly, when introduced into a similarly staged blastocyst, mouse ES cells can contribute to the development of all tissues of the resultant animal, demonstrating the relevance of ES cells to our understanding of early development and is the basis for their usefulness in regenerative medicine [Boiani and Scholer, 2005]. The maintenance of ES cell pluripotency engages multiple levels of cellular machinery, and highlights a conundrum faced in ES cell regulation. While self-renewal requires the suppression of genes involved at later developmental time points, the pluripotency stage in vivo is a short-lived one, and differentiation to specific lineages of endoderm, mesoderm, and ectoderm requires a rapid but tightly controlled regulation of gene expression. Our understanding of these processes in recent years has been buffeted by the emerging role of epigenetics in influencing the regulation of gene expression through processes such as DNA methylation, histone and chromatin modification [Farthing et al., 2008]. The specific application of these processes to relevant genes is likely to lay with core transcription factors active in ES cells that are known to bind to many sites across the genome. Furthermore, these binding sites are often found in proximity to each other especially at key developmental regulators [Chen et al., 2008; Kim et al., 2008], and may suggest a modular approach to transcriptional control by multiple transcription factors that also serve as recruitment platforms for a secondary level of control through epigenetic modifiers. Indeed, the role for epigenetics in ES cells is potentially large— unlike somatic cells, ES cells are known to hold a greater proportion of their genome as euchromatin with significant nucleosome-free regions and trimethylated histone 3 lysine 4 (H3K4me3) and acetylated histone 4 (H4Ac) marks typically associated with transcriptionally active regions [Lee et al., 2004; Azuara et al., 2006; Yaragatti et al., 2008]. As such, the extent of regulation necessary to prevent untimely differentiation of ES cells is dependent upon both epigenetic mechanisms and transcription factors alike. Trimethylated Histone 3 Lysine 27 (H3K27me3), unlike H3K4me3, is a transcriptionally repressive histone mark and both typically occur in mutually exclusive domains [Cao and Zhang, 2004]. In ES cells however, the presence of bivalent chromatin domains serves to balance the high degree of transcrip- tional activity in an ES cell, and to prime the cell for its imminent role in a differentiated lineage by the confluence of the activating H3K4me3 and repressive H3K27me3 marks along regions typically associated with highly conserved regions of developmentally important factors [Bernstein et al., 2006; Mikkelsen et al., 2007]. In this review, we highlight key transcription factors and their links with various protein complexes that enable the recruitment of epigenetic modifying proteins for the silencing of genes not involved in pluripotency. Journal of Cellular Biochemistry PROSPECT Journal of Cellular Biochemistry 110:288–293 (2010) 288 *Correspondence to: Prof. Thomas Lufkin, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore. E-mail: lufkin@gis.a-star.edu.sg Received 3 February 2010; Accepted 11 February 2010  DOI 10.1002/jcb.22576  ß 2010 Wiley-Liss, Inc. Published online 24 March 2010 in Wiley InterScience (www.interscience.wiley.com).