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Reconciling Epigenetic Memory and Transcriptional Responsiveness
Cell Systems
Previews Reconciling Epigenetic Memory and Transcriptional Responsiveness Amanda G. Fisher,1,* Michael P.H. Stumpf,2 and Matthias Merkenschlager1 1Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK 2Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW72AZ, UK *Correspondence: [email protected] http://dx.doi.org/10.1016/j.cels.2017.04.005
The molecular basis of cellular memory is important but poorly understood. Using estimates of histone dynamics, Martin Howard and colleagues construct a mathematical model that helps to explain both the stability and flexibility of Polycomb-mediated gene regulation in cellular memory. Polycomb (Pc) and trithorax (Trx) were discovered more than 60 years ago as two opposing multiprotein complexes, required to maintain the expression of developmental regulator genes in an onor off-state that was previously established by the transient activity of sequence-specific DNA binding transcription factors (Lewis, 1978). The broader importance of these observations, originally made in larvae of fruit flies, became clear to cell and developmental biologists almost from the outset. Pc and Trx function offered a theoretical explanation for the phenomenon of cellular memory, in which patterns of gene expression could be passed on as cells divided. In this issue of Cell Systems, Berry et al. (2017) suggest that this well-appreciated cellular memory arises, at least in part, from another process known to impart memory into dynamical systems: bistability. Cellular memory enables developing cells to respond differently to signals that they encounter based on their inherited programs of gene expression and thereby allows the segregation and diversification of multicellular function. Early investigations of how Pc- and Trxbased memory might work relied heavily on genetics. They characterized the impact of deleting Pc and/or Trx and their modifiers on development, focusing on candidate loci and specialized genomic environments, such as facultative and constitutive heterochromatin (Ringrose and Paro, 2007). By the early 2000s, these genetic approaches had laid the foundations for detailed biochemical analysis that in turn provided a step change in understanding Pc and Trx function. A cluster of studies
emerged at this time showing that Pc and Trx complexes interact with chromatin and directly modify histone tails (reviewed in Allis and Jenuwein, 2016). These reports encouraged the idea that Pc and Trx complexes might directly modulate transcription, either by impeding or enhancing RNA polymerase II (PolII) recruitment and function or by altering the physical compaction of target chromatin domains. Although we still know relatively little about what triggers the binding of Pc complexes to chromatin, or exactly how the silent state spreads into surrounding domains, it is now clear that the Polycomb repressor complex 2 (PRC2) can specifically bind histone H3 lysine 27 in its trimethylated state (H3K27me3), as well as catalyze the H3K27 methylation. The ability of PRC2 to both bind and catalyze H3K27me3 provides important insights into the potential mechanism for the spreading and the transmission of H3K27me3 through DNA replication (Margueron et al., 2009; Gaydos et al., 2014) (shown schematically in Figure 1). In this scenario, the ability of PRC2 to act as both a chromatin writer and reader probably serves to reinforce H3K27 methylation and thereby to maintain transcriptional silencing. However, this silenced state is not permanent. H3K27methylation can be reduced or removed by the KDM6 family of histone demethylases, by a process of histone exchange, by experimental reprogramming, or as a result of sustained expression of trans-acting factors that promote gene expression. Recently, quantitative and time-resolved data on H3K27 methylation in
different model organisms have become available, providing an opportunity to mathematically model chromatin dynamics and its relationship to gene expression. The recent study by Berry et al. provides a model that may explain two important and potentially conflicting properties of PRC2-mediated H3K27 methylation; high-fidelity transmission and the need to remain potentially responsive to trans-acting activators. The authors of the present study build upon previous models (Dodd et al., 2007) to hypothesize that transcription antagonizes PRC2 activity and as a consequence generates bi-stability of actively transcribed (low H3K27me3) and poorly transcribed (high H3K27me3) states. Intuitively, this is an attractive hypothesis given that bi-stability is a feature of many reactions that require control and execution of biological functions, as exemplified by signaling pathways. In the model presented by Berry et al., six features are assumed, many of which have strong supporting experimental evidence. Perhaps the weakest surrounds the mechanism of transcriptional repression by PRC2 and whether, as assumed, passage of PolII through a gene results in the stochastic removal of methyl groups from H3K27. This feature is central to the model proposed by Berry et al. and warrants further validation. Nonetheless, the model generates some remarkable features. Simulations show that, provided H3K27 acquisition and removal processes remain balanced, the active and repressive states are maintained (i.e., are bi-stable), providing a capability for the cell’s current
Cell Systems 4, April 26, 2017 ª 2017 Published by Elsevier Inc. 373
Cell Systems
Previews
transcription states to be Drosophila, remain heritably A writer memorized over the course associated with that gene reader of several cell cycles. As this over several rounds of division can operate over a wide and preserve silencing even range of external transcripwhen the ability to copy this tional inputs, the current histone mark is lost (Coleman chromatin state (that is, either and Struhl, 2017), adds weight n1 n2 n3 low H3K27me3 or high to this idea. However, as with H3K27me3) generally permost good things, there is a sists stably and is selfcatch. We still know so little reinforced. about how Pc recruitment However, in addition to beacross the genome operates, ing stable in two states, biaside from handful of loci in stable systems also have the specific organisms. As recent B DNA innate capacity to switch bestudies in fission yeast have replication tween states. Accordingly, highlighted an important role complex simulations predict that from of the DNA sequence for susn4 NEW an initially repressed state taining epigenetic inheritance with high H3K27me3, on histone H3K9 methylation n1 n2 increased traffic of RNA PolII (Wang and Moazed, 2017), would alter chromatin state future models will now need n3 over a few hours and result incorporate such features as in a switch to a low they emerge. That said, in NEW H3K27me3 state that is tracing our progress in undermore permissive of gene standing the molecular basis expression. The mirror-image of cellular memory, from process, the accumulation of early routes in genetics and H3K27me3 upon transcripbiochemistry to mathematical Figure 1. Spreading and Transmission of H3K27me3-Modified Chromatin tional shutdown would be a modeling, the reward of itera(A) Histone H3K27 (orange circles with black rods) methylation of a nucleomuch slower process, howtion between these three discisome template (n1) is copied between adjacent nucleosomes in cis (n2) by the ever taking several cell cycles plines becomes both clear and PRC2 complex; components within the complex provide both chromatin reader (blue) and writer (yellow) functions. to enter the high H3K27me3 compelling. (B) During DNA synthesis, new unmodified histones (black rods without orstate. In total, the model ange circles) are incorporated and redistributed as the replication fork proshows that chromatin states gresses, providing a fresh nucleosome template (pink) for PRC2-mediated REFERENCES can either respond to or methylation of H3K27. instruct gene expression, deAlabert, C., Barth, T.K., Revero´n-Go´pending on the strength of mez, N., Sidoli, S., Schmidt, A., The authors use these results to specu- Jensen, O.N., Imhof, A., and Groth, A. (2015). transactivation via RNA PolII and the initial late on the likely ability of Pc-based epige- Genes Dev. 29, 585–590. H3K27 methylation starting state. Lastly, the authors use their model to netic silencing to be able to filter tran- Allis, C.D., and Jenuwein, T. (2016). Nat. Rev. see just how closely simulations over suc- scriptional noise. This is a natural and Genet. 17, 487–500. cessive rounds of cell division and exper- necessary feature of their model, which Berry, S., Dean, C., and Howard, M. (2017). Cell imental data from chromatin-capture sta- deserves some closer scrutiny. Chro- Systems 4, this issue, 445–457. ble isotope labeling by amino acids in cell matin targets essentially remain bi-stable Coleman, R.T., and Struhl, G. (2017). Science 356, culture (SILAC) experiments compared. unless they encounter situations of strong eaai8236. Quantitative measurements of histone and prolonged activation or repression; Dodd, I.B., Micheelsen, M.A., Sneppen, K., and modifications in human cells before and this essentially filters out all high-fre- Thon, G. (2007). Cell 129, 813–822. after DNA synthesis were used, in which, quency noise in a manner reminiscent of Gaydos, L.J., Wang, W., and Strome, S. (2014). critically, the incorporation of nascent kinetic proofreading. Given the number Science 345, 1515–1518. and pre-existing histones in chromatin of transcription factors under the influ- Lewis, E.B. (1978). Nature 276, 565–570. could be distinguished (Alabert et al., ence of PRC2, the proposed mechanism R., Justin, N., Ohno, K., Sharpe, M.L., 2015). Encouragingly, the experimental would offer a way in which such noise Margueron, Son, J., Drury, W.J., 3rd, Voigt, P., Martin, S.R., data and simulations showed a close cor- could be attenuated effectively, compre- Taylor, W.R., De Marco, V., et al. (2009). Nature respondence and demonstrated that the hensively, and globally. The authors liken 461, 762–767. levels of H3K27me3 dropped by one half this to short-term memory. Ringrose, L., and Paro, R. (2007). Development The recent demonstration that H3K27 134, 223–232. as DNA was replicated and then increased slowly on a timescale longer tri-methylated nucleosomes, once estab- Wang, X., and Moazed, D. (2017). Science lished at a repressed Hox gene in 356, 88–91. than each cell cycle. 374 Cell Systems 4, April 26, 2017
Previews Reconciling Epigenetic Memory and Transcriptional Responsiveness Amanda G. Fisher,1,* Michael P.H. Stumpf,2 and Matthias Merkenschlager1 1Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK 2Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW72AZ, UK *Correspondence: [email protected] http://dx.doi.org/10.1016/j.cels.2017.04.005
The molecular basis of cellular memory is important but poorly understood. Using estimates of histone dynamics, Martin Howard and colleagues construct a mathematical model that helps to explain both the stability and flexibility of Polycomb-mediated gene regulation in cellular memory. Polycomb (Pc) and trithorax (Trx) were discovered more than 60 years ago as two opposing multiprotein complexes, required to maintain the expression of developmental regulator genes in an onor off-state that was previously established by the transient activity of sequence-specific DNA binding transcription factors (Lewis, 1978). The broader importance of these observations, originally made in larvae of fruit flies, became clear to cell and developmental biologists almost from the outset. Pc and Trx function offered a theoretical explanation for the phenomenon of cellular memory, in which patterns of gene expression could be passed on as cells divided. In this issue of Cell Systems, Berry et al. (2017) suggest that this well-appreciated cellular memory arises, at least in part, from another process known to impart memory into dynamical systems: bistability. Cellular memory enables developing cells to respond differently to signals that they encounter based on their inherited programs of gene expression and thereby allows the segregation and diversification of multicellular function. Early investigations of how Pc- and Trxbased memory might work relied heavily on genetics. They characterized the impact of deleting Pc and/or Trx and their modifiers on development, focusing on candidate loci and specialized genomic environments, such as facultative and constitutive heterochromatin (Ringrose and Paro, 2007). By the early 2000s, these genetic approaches had laid the foundations for detailed biochemical analysis that in turn provided a step change in understanding Pc and Trx function. A cluster of studies
emerged at this time showing that Pc and Trx complexes interact with chromatin and directly modify histone tails (reviewed in Allis and Jenuwein, 2016). These reports encouraged the idea that Pc and Trx complexes might directly modulate transcription, either by impeding or enhancing RNA polymerase II (PolII) recruitment and function or by altering the physical compaction of target chromatin domains. Although we still know relatively little about what triggers the binding of Pc complexes to chromatin, or exactly how the silent state spreads into surrounding domains, it is now clear that the Polycomb repressor complex 2 (PRC2) can specifically bind histone H3 lysine 27 in its trimethylated state (H3K27me3), as well as catalyze the H3K27 methylation. The ability of PRC2 to both bind and catalyze H3K27me3 provides important insights into the potential mechanism for the spreading and the transmission of H3K27me3 through DNA replication (Margueron et al., 2009; Gaydos et al., 2014) (shown schematically in Figure 1). In this scenario, the ability of PRC2 to act as both a chromatin writer and reader probably serves to reinforce H3K27 methylation and thereby to maintain transcriptional silencing. However, this silenced state is not permanent. H3K27methylation can be reduced or removed by the KDM6 family of histone demethylases, by a process of histone exchange, by experimental reprogramming, or as a result of sustained expression of trans-acting factors that promote gene expression. Recently, quantitative and time-resolved data on H3K27 methylation in
different model organisms have become available, providing an opportunity to mathematically model chromatin dynamics and its relationship to gene expression. The recent study by Berry et al. provides a model that may explain two important and potentially conflicting properties of PRC2-mediated H3K27 methylation; high-fidelity transmission and the need to remain potentially responsive to trans-acting activators. The authors of the present study build upon previous models (Dodd et al., 2007) to hypothesize that transcription antagonizes PRC2 activity and as a consequence generates bi-stability of actively transcribed (low H3K27me3) and poorly transcribed (high H3K27me3) states. Intuitively, this is an attractive hypothesis given that bi-stability is a feature of many reactions that require control and execution of biological functions, as exemplified by signaling pathways. In the model presented by Berry et al., six features are assumed, many of which have strong supporting experimental evidence. Perhaps the weakest surrounds the mechanism of transcriptional repression by PRC2 and whether, as assumed, passage of PolII through a gene results in the stochastic removal of methyl groups from H3K27. This feature is central to the model proposed by Berry et al. and warrants further validation. Nonetheless, the model generates some remarkable features. Simulations show that, provided H3K27 acquisition and removal processes remain balanced, the active and repressive states are maintained (i.e., are bi-stable), providing a capability for the cell’s current
Cell Systems 4, April 26, 2017 ª 2017 Published by Elsevier Inc. 373
Cell Systems
Previews
transcription states to be Drosophila, remain heritably A writer memorized over the course associated with that gene reader of several cell cycles. As this over several rounds of division can operate over a wide and preserve silencing even range of external transcripwhen the ability to copy this tional inputs, the current histone mark is lost (Coleman chromatin state (that is, either and Struhl, 2017), adds weight n1 n2 n3 low H3K27me3 or high to this idea. However, as with H3K27me3) generally permost good things, there is a sists stably and is selfcatch. We still know so little reinforced. about how Pc recruitment However, in addition to beacross the genome operates, ing stable in two states, biaside from handful of loci in stable systems also have the specific organisms. As recent B DNA innate capacity to switch bestudies in fission yeast have replication tween states. Accordingly, highlighted an important role complex simulations predict that from of the DNA sequence for susn4 NEW an initially repressed state taining epigenetic inheritance with high H3K27me3, on histone H3K9 methylation n1 n2 increased traffic of RNA PolII (Wang and Moazed, 2017), would alter chromatin state future models will now need n3 over a few hours and result incorporate such features as in a switch to a low they emerge. That said, in NEW H3K27me3 state that is tracing our progress in undermore permissive of gene standing the molecular basis expression. The mirror-image of cellular memory, from process, the accumulation of early routes in genetics and H3K27me3 upon transcripbiochemistry to mathematical Figure 1. Spreading and Transmission of H3K27me3-Modified Chromatin tional shutdown would be a modeling, the reward of itera(A) Histone H3K27 (orange circles with black rods) methylation of a nucleomuch slower process, howtion between these three discisome template (n1) is copied between adjacent nucleosomes in cis (n2) by the ever taking several cell cycles plines becomes both clear and PRC2 complex; components within the complex provide both chromatin reader (blue) and writer (yellow) functions. to enter the high H3K27me3 compelling. (B) During DNA synthesis, new unmodified histones (black rods without orstate. In total, the model ange circles) are incorporated and redistributed as the replication fork proshows that chromatin states gresses, providing a fresh nucleosome template (pink) for PRC2-mediated REFERENCES can either respond to or methylation of H3K27. instruct gene expression, deAlabert, C., Barth, T.K., Revero´n-Go´pending on the strength of mez, N., Sidoli, S., Schmidt, A., The authors use these results to specu- Jensen, O.N., Imhof, A., and Groth, A. (2015). transactivation via RNA PolII and the initial late on the likely ability of Pc-based epige- Genes Dev. 29, 585–590. H3K27 methylation starting state. Lastly, the authors use their model to netic silencing to be able to filter tran- Allis, C.D., and Jenuwein, T. (2016). Nat. Rev. see just how closely simulations over suc- scriptional noise. This is a natural and Genet. 17, 487–500. cessive rounds of cell division and exper- necessary feature of their model, which Berry, S., Dean, C., and Howard, M. (2017). Cell imental data from chromatin-capture sta- deserves some closer scrutiny. Chro- Systems 4, this issue, 445–457. ble isotope labeling by amino acids in cell matin targets essentially remain bi-stable Coleman, R.T., and Struhl, G. (2017). Science 356, culture (SILAC) experiments compared. unless they encounter situations of strong eaai8236. Quantitative measurements of histone and prolonged activation or repression; Dodd, I.B., Micheelsen, M.A., Sneppen, K., and modifications in human cells before and this essentially filters out all high-fre- Thon, G. (2007). Cell 129, 813–822. after DNA synthesis were used, in which, quency noise in a manner reminiscent of Gaydos, L.J., Wang, W., and Strome, S. (2014). critically, the incorporation of nascent kinetic proofreading. Given the number Science 345, 1515–1518. and pre-existing histones in chromatin of transcription factors under the influ- Lewis, E.B. (1978). Nature 276, 565–570. could be distinguished (Alabert et al., ence of PRC2, the proposed mechanism R., Justin, N., Ohno, K., Sharpe, M.L., 2015). Encouragingly, the experimental would offer a way in which such noise Margueron, Son, J., Drury, W.J., 3rd, Voigt, P., Martin, S.R., data and simulations showed a close cor- could be attenuated effectively, compre- Taylor, W.R., De Marco, V., et al. (2009). Nature respondence and demonstrated that the hensively, and globally. The authors liken 461, 762–767. levels of H3K27me3 dropped by one half this to short-term memory. Ringrose, L., and Paro, R. (2007). Development The recent demonstration that H3K27 134, 223–232. as DNA was replicated and then increased slowly on a timescale longer tri-methylated nucleosomes, once estab- Wang, X., and Moazed, D. (2017). Science lished at a repressed Hox gene in 356, 88–91. than each cell cycle. 374 Cell Systems 4, April 26, 2017