Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant

Abstract

Trimethylation of histone H3 lysine 4 (H3K4me3) at the promoters of actively transcribed genes is a universal epigenetic mark and a key product of Trithorax group action. Here, we show that Mll2, one of the six Set1/Trithorax-type H3K4 methyltransferases in mammals, is required for trimethylation of bivalent promoters in mouse embryonic stem cells. Mll2 is bound to bivalent promoters but also to most active promoters, which do not require Mll2 for H3K4me3 or mRNA expression. By contrast, the Set1 complex (Set1C) subunit Cxxc1 is primarily bound to active but not bivalent promoters. This indicates that bivalent promoters rely on Mll2 for H3K4me3 whereas active promoters have more than one bound H3K4 methyltransferase, including Set1C. Removal of Mll1, sister to Mll2, had almost no effect on any promoter unless Mll2 was also removed, indicating functional backup between these enzymes. Except for a subset, loss of H3K4me3 on bivalent promoters did not prevent responsiveness to retinoic acid, thereby arguing against a priming model for bivalency. In contrast, we propose that Mll2 is the pioneer trimethyltransferase for promoter definition in the naïve epigenome and that Polycomb group action on bivalent promoters blocks the premature establishment of active, Set1C-bound, promoters. KEY WORDS: Epigenetics, Epigenome, Histone methylation, Bivalent promoters, Trithorax group, Polycomb group, Kmt2 INTRODUCTIONIn eukaryotes, transcription is regulated not only by transcription factors that bind specific DNA sequences near the regulated gene, but also by post-translational modifications of the nucleosomes that surround and encompass these DNA sequences. The modifications include methylation, acetylation and mono-ubiquitylation of histone tails that project out from the core nucleosome and serve as binding sites for chromatin proteins and complexes (Bannister and Kouzarides, 2011;Suganuma and Workman, 2011). In vertebrates, nucleosome modifications, together with cytosine methylation, influence transcriptional regulation during development, adult life (h.stunnenberg@ncmls.ru.nl; stewart@biotec.tu-dresden.de) This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. RESEARCH ARTICLE STEM CELLS AND REGENERATION Received 20 August 2013; Accepted 17 November 2013and disease (Albert and Helin, 2010;Butler et al., 2012;Reik, 2007). This epigenetic level of transcriptional regulation is crucial to the multiple ways in which a genome is interpreted in multicellular organisms (Goldberg et al., 2007).Metazoan development is regulated by programmed transcriptional hierarchies acting in synergy with epigenetic mechanisms (Fisher and Fisher, 2011; Jaenisch and Bird, 2003;Magnúsdóttir et al., 2012). The first clues about how epigenetic mechanisms regulate gene expression were discovered in Drosophila thro...

Trithorax and Polycomb group-dependent regulation: a tale of opposing activities

“…Whereas Mll2 was bound at both bivalent and active promoters, Cxxc1, a Set1 complex subunit, was found only at active gene promoters. Consistent with the findings from Hu et al (2013), Denissov et al (2014) further showed that the induction of genes with bivalent promoters was not influenced by abrogation of Fig. 3.…”

“…Given that bivalency has been proposed to poise developmental genes for rapid activation (Voigt et al, 2013), this observation was unexpected and calls into question the function of bivalency. Independent evidence for Mll2 being the bivalent domain H3K4 methyltransferase came in 2014 (Denissov et al, 2014), but, in this study, the authors further examined the interplay between the various Set1/Trithorax-type H3K4 methyltransferases.…”

“…2B) (Hu et al, 2013). Curiously, however, Mll2 knockdown had no influence on ESC self-renewal nor did it affect the rapid induction of bivalent genes in response to retinoic acid stimulus (Denissov et al, 2014;Hu et al, 2013). Given that bivalency has been proposed to poise developmental genes for rapid activation (Voigt et al, 2013), this observation was unexpected and calls into question the function of bivalency.…”

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation

“…Loss of H3K4me1 has been proposed to be a key step in enhancer decommissioning (preprint: Agarwal et al , 2017; Cao et al , 2018; Whyte et al , 2012; Yan et al , 2018), though a direct function for this mark remains controversial (Dorighi et al , 2017; Cao et al , 2018; Yan et al , 2018). Since inactivation of various MLL family members fails to ablate H3K4 methylation at most pluripotency enhancers or alter pluripotency gene expression (Denissov et al , 2014; Wang et al , 2016; Cao et al , 2017, 2018; Dorighi et al , 2017; Yan et al , 2018), the importance of this class of histone modification in regulating the activity of the pluripotency network remains to be stringently tested. Our finding that H3K4me1 becomes undetectable at the Esrrb enhancer in committed cells, coincident with loss of TF binding and gain of DNA methylation, might provide a well‐characterized model to address these controversies.…”

Enhancer priming by H3K4 methyltransferase MLL4 controls cell fate transition

“…2E). Interestingly, reanalysis of a published ESC ChIP-Seq dataset on MLL2 (KMT2B) (23) revealed that over 50% of MLL4-independent AEs are also occupied by MLL2. In contrast, only ∼25% of MLL4-dependent AEs are occupied by MLL2 in ESCs (SI Appendix, Fig.…”