Enhancer priming by H3K4 methyltransferase MLL4 controls cell fate transition

Abstract

Transcriptional enhancers control cell-type-specific gene expression. Primed enhancers are marked by histone H3 lysine 4 (H3K4) mono/di-methylation (H3K4me1/2). Active enhancers are further marked by H3K27 acetylation (H3K27ac). Mixed-lineage leukemia 4 (MLL4/KMT2D) is a major enhancer H3K4me1/2 methyltransferase with functional redundancy with MLL3 (KMT2C). However, its role in cell fate maintenance and transition is poorly understood. Here, we show in mouse embryonic stem cells (ESCs) that MLL4 associates with, but is surprisingly dispensable for the maintenance of, active enhancers of cell-identity genes. As a result, MLL4 is dispensable for cell-identity gene expression and self-renewal in ESCs. In contrast, MLL4 is required for enhancer-binding of H3K27 acetyltransferase p300, enhancer activation, and induction of cell-identity genes during ESC differentiation. MLL4 protein, rather than MLL4-mediated H3K4 methylation, controls p300 recruitment to enhancers. We also show that, in somatic cells, MLL4 is dispensable for maintaining cell identity but essential for reprogramming into induced pluripotent stem cells. These results indicate that, although enhancer priming by MLL4 is dispensable for cell-identity maintenance, it controls cell fate transition by orchestrating p300-mediated enhancer activation.enhancer | MLL4/KMT2D | H3K4 methyltransferase | cell fate transition | p300 I n mammalian cells, enhancers coordinate with promoters to precisely control cell-type-specific gene transcription, which determines the cell identity (1, 2). Comprehensive genome-wide studies have provided insights into the chromatin signatures of enhancers. Primed enhancers are marked by H3K4me1/2. Active enhancers (AEs) are further marked by the histone acetyltransferases CBP/p300-mediated H3K27ac (3). Recent studies classify AEs into typical enhancers and superenhancers. Superenhancers are clusters of AEs bound by lineage-determining transcription factors (TFs). Compared with typical enhancers, superenhancers are more cell-lineage-specific and control cell identity (4). Enhancer activation is orchestrated through a regulatory network involving lineage-determining TFs and chromatinmodifying complexes (2). However, how chromatin-modifying complexes regulate enhancer activation and cell fate transition is poorly understood.Embryonic stem cells (ESCs) derived from blastocysts are capable of unlimited replication in vitro, a property known as ESC self-renewal. ESC identity is maintained during self-renewal. ESC self-renewal is controlled by a core circuitry of TFs including Oct4, Sox2, and Nanog (4). ESCs can rapidly respond to environmental cues and differentiate into three germ layers-ectoderm, endoderm, and mesoderm-which consist of all cell lineages within days (5). Differentiated somatic cells can also be converted back to the pluripotent stage by ectopic expression of Oct4 and Sox2 together with Klf4 and c-Myc, a process known as somatic cell reprogramming into induced pluripotent stem cells (iPSCs) (6). The dramatic changes of ce...

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.…”

H3K4 Methyltransferase Activity Is Required for MLL4 Protein Stability

“…PCR genotyping was performed using the following primers: P1 (5′-GGCCTTGGGGAAGACCTC-3′) and P2 (5′-AAGCTGAGACCCAGATGCCT-3′). MLL4 conditional KO ( Mll4 f/f ) and KO ( Mll4 −/− ) ES cells were generated as described [13]. ES cells were cultured on mouse embryonic fibroblast feeder cells and lentiviral vector-mediated stable gene expression of FLAG-tagged histone H3.3 in ES cells was performed as described [23].…”

“…MLL3 and MLL4 are required for enhancer activation and cell type-specific gene expression during cell differentiation [2, 13]. MLL3 and MLL4 are dispensable for cell identity maintenance but are required for cell fate transition [13].…”

“…MLL3 and MLL4 are required for enhancer activation and cell type-specific gene expression during cell differentiation [2, 13]. MLL3 and MLL4 are dispensable for cell identity maintenance but are required for cell fate transition [13]. Mll3 knockout (KO) mice die around birth with no obvious morphological abnormalities, whereas Mll4 KO mice show early embryonic lethality around E9.5 [2].…”

MLL3/MLL4 are required for CBP/p300 binding on enhancers and super-enhancer formation in brown adipogenesis

“…MLL3/MLL4 are essential for enhancer activation and cell-type-specific gene expression during cell differentiation (5,6). We also identified the functionally redundant CBP and p300 as site-specific histone acetyltransferases responsible for H3K27ac in mammalian cells (7).…”