Enhancer malfunction in cancer

Abstract

Why certain point mutations in a general transcription factor are associated with specific forms of cancer has been a major question in cancer biology. Enhancers are DNA regulatory elements that are key regulators of tissue-specific gene expression. Recent studies suggest that enhancer malfunction through point mutations in either regulatory elements or factors modulating enhancer-promoter communication could be the cause of tissue-specific cancer development. In this Perspective, we will discuss recent findings in the identification of cancer-related enhancer mutations and the role of Drosophila Trr and its human homologs, the MLL3 and MLL4/COMPASS-like complexes, as enhancer histone H3 lysine 4 (H3K4) monomethyltransferases functioning in enhancer-promoter communication. Recent genome-wide studies in the cataloging of somatic mutations in cancer have identified mutations in intergenic sequences encoding regulatory elements-and in MLL3 and MLL4 in both hematological malignancies and solid tumors. We propose that cancer-associated mutations in MLL3 and MLL4 exert their properties through the malfunction of Trr/MLL3/MLL4-dependent enhancers.

Figure 1. A model for transcriptional activation by cis-regulatory elements

(A) Metazoan cis-regulatory elements also called ‘enhancers’ can activate gene expression over more than hundreds of Kbs, but can also function over very short distances. Enhancers contain binding sites for activating or repressing transcription factors (TFs) that are often recruited in response to environmental or developmental signals. (B) TFs often recruit chromatin-modifying co-activators or co-repressors. Co-activators such as CBP/p300 and MLL3/MLL4 have been demonstrated to acetylate histone H3 on lysine 27 (H3K27ac, highlighted in pink) or monomethylate histone 3 on lysine 4 (H3K4me1, highlighted in green) around enhancers, respectively. (C) A looping mechanism mediated by factors such as cohesin and the Mediator complex can bring enhancers into close proximity to promoters. Long-range interactions between enhancers and promoters have been shown to be stabilized by members of the cohesin complex; and the Mediator complex supports the interaction of enhancer-bound transcription factors and co-activators such as MLL3/MLL4 and CBP/p300 with the basal transcription machinery on promoters.

Figure 2. Trr/MLL3/MLL4 COMPASS-like complex-dependent enhancers

Coverage profiles arranged for enrichment of H3K4 monomethylation (H3K4me1) at the promoter-distal sites (> 1 kilobase [kb]) in human colorectal carcinoma cell-line, HCT116 (MLL3^Δset, column 1) or HCT116 cells with a MLL4 deletion (MLL3^Δset/4^Δset, column 2). Sites are arranged in a vertical gradient with a higher enrichment of H3K4 monomethylation at the top, and lower levels of H3K4me1 toward the bottom. A large percentage (~70%) of putative enhancers exhibits a significant loss in H3K4 monomethylation (p<1e-3) in the absence of both MLL3 and MLL4 (compare column 2 with column 1 in first panel), while a minority of putative enhancers (~30%) is independent of MLL3/MLL4 for their H3K4me1 status (we call these enhancers Trr/MLL3/MLL4-independent enhancers, compare column 2 with column 1 in second panel). Data for this figure was adopted from Hu et al., 2013 (Mol Cell Bio 33, 4745-4654) with permission from the American Society for Microbiology.

Figure 3. Misregulation of MLL3/MLL4-dependent enhancer function in cancer pathogenesis

Two models proposing how MLL3/MLL4 mutations can either result in inappropriate enhancer-mediated inactivation of tumor suppressor genes or activation of oncogenes are described here. (A) MLL3/MLL4 loss-of-function scenario on the enhancer of a tumor suppressor gene. MLL3/MLL4 mutations could either result in a destabilization of MLL3/MLL4; reduced association of MLL3/MLL4 with recruiting transcription factors (TFs) on enhancers; or catalytic inactivation of MLL3/MLL4. In any case, the outcome would be diminished or eliminated enhancer activation of tumor suppressor genes. (B) MLL3/MLL4 gain-of-function scenario on the enhancer of oncogenes. MLL3/MLL4 mutations could either result in increased MLL3/MLL4 stability, increased affinity of MLL3/MLL4 towards MLL3/MLL4-recruiting TFs, or catalytic hyperactivation of MLL3/MLL4 on enhancers regulating the expression of oncogenes.