Molecular Cell
Previews A New Bump in the Epigenetic Landscape Anand S. Bhagwat1 and Christopher R. Vakoc1,* 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.molcel.2014.03.001
In this issue of Molecular Cell, Cheng et al. describe an unexpected role for the histone methyltransferases MLL3 and MLL4 in the repression of tissue-specific promoters, a function that prevents precocious cell differentiation in the skeletal muscle lineage.
The SET1/MLL family of chromatin regulators catalyzes histone H3 lysine 4 (H3K4) methylation and plays fundamental roles in gene regulation, metazoan development, and human disease (Shilatifard, 2012). H3K4 can be mono- (me1), di- (me2), or tri-methylated (me3), with each degree of methylation distributed in a unique pattern across the genome. While H3K4me3 is focally enriched near active promoters, H3K4me1 tends to be found at distal enhancer elements and in the vicinity of active genes (Heintzman et al., 2007). The patterning of H3K4 methylation reflects the localization and product specificity of the individual SET1/MLL proteins: SET1A and SET1B catalyze the majority of H3K4me3, MLL1 and MLL2 maintain H3K4me3 at discrete genomic sites, and MLL3 and MLL4 catalyze the bulk of H3K4me1. MLL3 and MLL4 (and their Drosophila homolog Trr) have been implicated in enhancer-mediated gene regulation through catalysis of H3K4me1 (Herz et al., 2012; Lee et al., 2013; Hu et al., 2013). Depletion of MLL3/4 or Trr from cells results in loss of H3K4me1 and other active chromatin marks from enhancers, rendering these elements incompetent for long-range effects on gene activation. While the link between H3K4me1 and active enhancers is well-established, prior studies have also shown that H3K4me1 can be enriched near promoter regions (Barski et al., 2007; Heintzman et al., 2007). However, the function at H3K4me1 at promoters has not been defined. In this issue, Cheng et al. (2014) describe an unexpected role for MLL3/4 and H3K4me1 at promoters, where they maintain a repressed chromatin state. By performing chromatin immunoprecipitation analysis in a skeletal muscle
myoblast cell line, the authors identify a class of promoters that is bound by both MLL3 and MLL4 and marked by broad enrichment of H3K4me1. Notably, this class of genes lacks active chromatin marks like H3K4me3 and is transcribed at only low levels. These promoters also exhibit high nucleosome density and enrichment for other repressive histone modifications, such as H3K27me3. RNAi-based knockdown of MLL3/4 led to increased transcription of this set of genes, suggesting that H3K4me1 performs a repressive function at promoters (Cheng et al., 2014). This unexpected finding contradicts the prevailing notion of H3K4 methylation as a mark that promotes transcriptional activation, suggesting that the role of MLL3/4 and H3K4me1 at promoters is distinct from their known role at enhancers. Promoter repression by MLL3/4 in myoblast cells was found associated with muscle-specific genes that are destined for later activation upon differentiation into myotubes (Cheng et al., 2014). During differentiation, they observed that MLL3/4 is replaced by MLL1/SET1 as this class of promoters transitions from repressed to fully activated. This methyltransferase switch results in the conversion of H3K4me1 into H3K4me3, followed by recruitment of the H3K4me3-specific reader protein ING1 and its associated protein complex to promote transcriptional activation. Phenotypically, knockdown of MLL3/4 in myoblast cells causes precocious cell differentiation due to aberrant activation of muscle-specific genes. This result suggests that MLL3/4mediated promoter repression acts as an epigenetic barrier that prevents the premature transition from myoblast to myotube (Figure 1). This new class of
H3K4me1-enriched promoters can be observed in a variety of different cell lineages, suggesting that MLL3/4-mediated repression is a general strategy to temporarily restrain gene activity prior to induction (Cheng et al., 2014). A key issue raised by this study is how H3K4me1 can have opposite effects on transcription depending on its location at enhancers versus promoters. In several experimental settings, the authors noted that perturbations that elevate H3K4me1 tend to cause reciprocal reductions of H3K4me3 and ING1 recruitment. Based on this observation, they propose that H3K4me1 might be capable of repressing promoter activity by antagonizing the accumulation and/or function of H3K4me3. Consistent with such a model, the PHD domain of ING1 recognizes H3K4me2/me3 but not H3K4me1 (Pen˜a et al., 2008). Hence, enzymatic activities that raise the level of H3K4me1 at the expense of H3K4me2/me3 would be expected to prevent ING1 recruitment and consequently downregulate transcription. Since H3K4me3 does not accumulate to significant levels near enhancers, such antagonism would preferentially manifest at promoter regions. An alternative mechanism for H3K4me1-mediated repression would be that distinct reader domain proteins interpret the H3K4me1 signal at promoters and enhancers. However, we currently do not know the identity of H3K4me1-specific readers that are relevant for enhancer or promoter function, an issue that clearly warrants further investigation. Another recent study found that MLL3/ 4 are critical for muscle lineage specification from early mesodermal precursor cells in vivo and during transdifferentiation from preadipocytes in vitro, which was
Molecular Cell 53, March 20, 2014 ª2014 Elsevier Inc. 857
Molecular Cell
Previews
attributed to an essential role promoting genes in these Mesodermal for MLL3/4 in activating musother cell lineages. precursor cell cle-specific enhancers (Lee et al., 2013). These obserREFERENCES vations are seemingly contraBarski, A., Cuddapah, S., Cui, K., dictory to Cheng et al. (2014); Roh, T.Y., Schones, D.E., Wang, Myoblast however, it should be noted Z., Wei, G., Chepelev, I., and Zhao, that each study employed K. (2007). Cell 129, 823–837. culture models that recapituCheng, J., Blum, R., Bowman, C., late different stages of myoMyotube Hu, D., Shilatifard, A., Shen, S., genesis. During early myoand Dynlacht, B.D. (2014). Mol. Cell 53, this issue, 979–992. MLL3 MLL1 genesis, the positive role of MLL3/4 at muscle-specific MLL4 SET1 Heintzman, N.D., Stuart, R.K., Hon, enhancers could be essential G., Fu, Y., Ching, C.W., Hawkins, Enhancer Promoter Promoter R.D., Barrera, L.O., Van Calcar, S., to commit a multipotent preActivation Repression Activation Qu, C., Ching, K.A., et al. (2007). H3K4me1 H3K4me1 H3K4me3 cursor cell to the muscle Nat. Genet. 39, 311–318. lineage. Upon reaching the Herz, H.M., Mohan, M., Garruss, intermediate myoblast stage, Figure 1. A Role for H3K4 Methylation in the Epigenetic Control of A.S., Liang, K., Takahashi, Y.H., Myogenesis the role of MLL3/4 in represMickey, K., Voets, O., Verrijzer, Depicted is a model of myogenesis that accommodates the findings of Lee sion of muscle-specific proC.P., and Shilatifard, A. (2012). et al. (2013) and Cheng et al. (2014). The path from mesodermal precursor Genes Dev. 26, 2604–2620. moters might become more cells to differentiated myotubes is represented as a ball rolling down a hill, important to inhibit premature with the activities of various H3K4 methyltransferases either facilitating or Hu, D., Gao, X., Morgan, M.A., Herz, inhibiting transitions through effects at myogenic enhancers and promoters. myotube differentiation. This H.M., Smith, E.R., and Shilatifard, A. (2013). Mol. Cell. Biol. 33, 4745– repressive function of MLL3/ 4754. 4 is ultimately overcome by Recent genome sequencing studies Lawrence, M.S., Stojanov, P., Mermel, C.H., RobinMLL1/SET1 as cells complete terminal differentiation (Figure 1). These two have identified the genes encoding son, J.T., Garraway, L.A., Golub, T.R., Meyerson, M., Gabriel, S.B., Lander, E.S., and Getz, G. important studies reveal a highly dynamic MLL3 and MLL4 as among the most (2014). Nature 505, 495–501. regulatory cascade of H3K4 methylation commonly mutated in all of human cancer at promoters and distal enhancers that (Lawrence et al., 2014). Such mutations Lee, J.E., Wang, C., Xu, S., Cho, Y.W., Wang, L., Feng, X., Baldridge, A., Sartorelli, V., guides proper cell lineage specification are predicted to be loss-of-function Zhuang, L., Peng, W., and Ge, K. (2013). Elife 2, and differentiation (Cheng et al., 2014; and are especially common in lymphoid, e01503. Lee et al., 2013). A clear objective for bladder, and lung malignancies (LawPen˜a, P.V., Hom, R.A., Hung, T., Lin, H., Kuo, A.J., future studies will be to define genetically rence et al., 2014). The newly defined Wong, R.P., Subach, O.M., Champagne, K.S., and biochemically upstream and down- role of MLL3/4 in transcriptional repres- Zhao, R., Verkhusha, V.V., et al. (2008). J. Mol. stream components that operate in sion is likely to be relevant to their tu- Biol. 380, 303–312. conjunction with MLL3/4 at promoters mor suppressor functions, particularly if Shilatifard, A. (2012). Annu. Rev. Biochem. 81, directed toward the promoters of growth 65–95. versus enhancers.
858 Molecular Cell 53, March 20, 2014 ª2014 Elsevier Inc.
Previews A New Bump in the Epigenetic Landscape Anand S. Bhagwat1 and Christopher R. Vakoc1,* 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.molcel.2014.03.001
In this issue of Molecular Cell, Cheng et al. describe an unexpected role for the histone methyltransferases MLL3 and MLL4 in the repression of tissue-specific promoters, a function that prevents precocious cell differentiation in the skeletal muscle lineage.
The SET1/MLL family of chromatin regulators catalyzes histone H3 lysine 4 (H3K4) methylation and plays fundamental roles in gene regulation, metazoan development, and human disease (Shilatifard, 2012). H3K4 can be mono- (me1), di- (me2), or tri-methylated (me3), with each degree of methylation distributed in a unique pattern across the genome. While H3K4me3 is focally enriched near active promoters, H3K4me1 tends to be found at distal enhancer elements and in the vicinity of active genes (Heintzman et al., 2007). The patterning of H3K4 methylation reflects the localization and product specificity of the individual SET1/MLL proteins: SET1A and SET1B catalyze the majority of H3K4me3, MLL1 and MLL2 maintain H3K4me3 at discrete genomic sites, and MLL3 and MLL4 catalyze the bulk of H3K4me1. MLL3 and MLL4 (and their Drosophila homolog Trr) have been implicated in enhancer-mediated gene regulation through catalysis of H3K4me1 (Herz et al., 2012; Lee et al., 2013; Hu et al., 2013). Depletion of MLL3/4 or Trr from cells results in loss of H3K4me1 and other active chromatin marks from enhancers, rendering these elements incompetent for long-range effects on gene activation. While the link between H3K4me1 and active enhancers is well-established, prior studies have also shown that H3K4me1 can be enriched near promoter regions (Barski et al., 2007; Heintzman et al., 2007). However, the function at H3K4me1 at promoters has not been defined. In this issue, Cheng et al. (2014) describe an unexpected role for MLL3/4 and H3K4me1 at promoters, where they maintain a repressed chromatin state. By performing chromatin immunoprecipitation analysis in a skeletal muscle
myoblast cell line, the authors identify a class of promoters that is bound by both MLL3 and MLL4 and marked by broad enrichment of H3K4me1. Notably, this class of genes lacks active chromatin marks like H3K4me3 and is transcribed at only low levels. These promoters also exhibit high nucleosome density and enrichment for other repressive histone modifications, such as H3K27me3. RNAi-based knockdown of MLL3/4 led to increased transcription of this set of genes, suggesting that H3K4me1 performs a repressive function at promoters (Cheng et al., 2014). This unexpected finding contradicts the prevailing notion of H3K4 methylation as a mark that promotes transcriptional activation, suggesting that the role of MLL3/4 and H3K4me1 at promoters is distinct from their known role at enhancers. Promoter repression by MLL3/4 in myoblast cells was found associated with muscle-specific genes that are destined for later activation upon differentiation into myotubes (Cheng et al., 2014). During differentiation, they observed that MLL3/4 is replaced by MLL1/SET1 as this class of promoters transitions from repressed to fully activated. This methyltransferase switch results in the conversion of H3K4me1 into H3K4me3, followed by recruitment of the H3K4me3-specific reader protein ING1 and its associated protein complex to promote transcriptional activation. Phenotypically, knockdown of MLL3/4 in myoblast cells causes precocious cell differentiation due to aberrant activation of muscle-specific genes. This result suggests that MLL3/4mediated promoter repression acts as an epigenetic barrier that prevents the premature transition from myoblast to myotube (Figure 1). This new class of
H3K4me1-enriched promoters can be observed in a variety of different cell lineages, suggesting that MLL3/4-mediated repression is a general strategy to temporarily restrain gene activity prior to induction (Cheng et al., 2014). A key issue raised by this study is how H3K4me1 can have opposite effects on transcription depending on its location at enhancers versus promoters. In several experimental settings, the authors noted that perturbations that elevate H3K4me1 tend to cause reciprocal reductions of H3K4me3 and ING1 recruitment. Based on this observation, they propose that H3K4me1 might be capable of repressing promoter activity by antagonizing the accumulation and/or function of H3K4me3. Consistent with such a model, the PHD domain of ING1 recognizes H3K4me2/me3 but not H3K4me1 (Pen˜a et al., 2008). Hence, enzymatic activities that raise the level of H3K4me1 at the expense of H3K4me2/me3 would be expected to prevent ING1 recruitment and consequently downregulate transcription. Since H3K4me3 does not accumulate to significant levels near enhancers, such antagonism would preferentially manifest at promoter regions. An alternative mechanism for H3K4me1-mediated repression would be that distinct reader domain proteins interpret the H3K4me1 signal at promoters and enhancers. However, we currently do not know the identity of H3K4me1-specific readers that are relevant for enhancer or promoter function, an issue that clearly warrants further investigation. Another recent study found that MLL3/ 4 are critical for muscle lineage specification from early mesodermal precursor cells in vivo and during transdifferentiation from preadipocytes in vitro, which was
Molecular Cell 53, March 20, 2014 ª2014 Elsevier Inc. 857
Molecular Cell
Previews
attributed to an essential role promoting genes in these Mesodermal for MLL3/4 in activating musother cell lineages. precursor cell cle-specific enhancers (Lee et al., 2013). These obserREFERENCES vations are seemingly contraBarski, A., Cuddapah, S., Cui, K., dictory to Cheng et al. (2014); Roh, T.Y., Schones, D.E., Wang, Myoblast however, it should be noted Z., Wei, G., Chepelev, I., and Zhao, that each study employed K. (2007). Cell 129, 823–837. culture models that recapituCheng, J., Blum, R., Bowman, C., late different stages of myoMyotube Hu, D., Shilatifard, A., Shen, S., genesis. During early myoand Dynlacht, B.D. (2014). Mol. Cell 53, this issue, 979–992. MLL3 MLL1 genesis, the positive role of MLL3/4 at muscle-specific MLL4 SET1 Heintzman, N.D., Stuart, R.K., Hon, enhancers could be essential G., Fu, Y., Ching, C.W., Hawkins, Enhancer Promoter Promoter R.D., Barrera, L.O., Van Calcar, S., to commit a multipotent preActivation Repression Activation Qu, C., Ching, K.A., et al. (2007). H3K4me1 H3K4me1 H3K4me3 cursor cell to the muscle Nat. Genet. 39, 311–318. lineage. Upon reaching the Herz, H.M., Mohan, M., Garruss, intermediate myoblast stage, Figure 1. A Role for H3K4 Methylation in the Epigenetic Control of A.S., Liang, K., Takahashi, Y.H., Myogenesis the role of MLL3/4 in represMickey, K., Voets, O., Verrijzer, Depicted is a model of myogenesis that accommodates the findings of Lee sion of muscle-specific proC.P., and Shilatifard, A. (2012). et al. (2013) and Cheng et al. (2014). The path from mesodermal precursor Genes Dev. 26, 2604–2620. moters might become more cells to differentiated myotubes is represented as a ball rolling down a hill, important to inhibit premature with the activities of various H3K4 methyltransferases either facilitating or Hu, D., Gao, X., Morgan, M.A., Herz, inhibiting transitions through effects at myogenic enhancers and promoters. myotube differentiation. This H.M., Smith, E.R., and Shilatifard, A. (2013). Mol. Cell. Biol. 33, 4745– repressive function of MLL3/ 4754. 4 is ultimately overcome by Recent genome sequencing studies Lawrence, M.S., Stojanov, P., Mermel, C.H., RobinMLL1/SET1 as cells complete terminal differentiation (Figure 1). These two have identified the genes encoding son, J.T., Garraway, L.A., Golub, T.R., Meyerson, M., Gabriel, S.B., Lander, E.S., and Getz, G. important studies reveal a highly dynamic MLL3 and MLL4 as among the most (2014). Nature 505, 495–501. regulatory cascade of H3K4 methylation commonly mutated in all of human cancer at promoters and distal enhancers that (Lawrence et al., 2014). Such mutations Lee, J.E., Wang, C., Xu, S., Cho, Y.W., Wang, L., Feng, X., Baldridge, A., Sartorelli, V., guides proper cell lineage specification are predicted to be loss-of-function Zhuang, L., Peng, W., and Ge, K. (2013). Elife 2, and differentiation (Cheng et al., 2014; and are especially common in lymphoid, e01503. Lee et al., 2013). A clear objective for bladder, and lung malignancies (LawPen˜a, P.V., Hom, R.A., Hung, T., Lin, H., Kuo, A.J., future studies will be to define genetically rence et al., 2014). The newly defined Wong, R.P., Subach, O.M., Champagne, K.S., and biochemically upstream and down- role of MLL3/4 in transcriptional repres- Zhao, R., Verkhusha, V.V., et al. (2008). J. Mol. stream components that operate in sion is likely to be relevant to their tu- Biol. 380, 303–312. conjunction with MLL3/4 at promoters mor suppressor functions, particularly if Shilatifard, A. (2012). Annu. Rev. Biochem. 81, directed toward the promoters of growth 65–95. versus enhancers.
858 Molecular Cell 53, March 20, 2014 ª2014 Elsevier Inc.
