Emerging roles for chromatin as a signal integration and storage platform

Abstract

Cells of a multicellular organism, all containing nearly identical genetic information, respond to differentiation cues in variable ways. In addition, cells are plastic, able to execute their specialized function while maintaining the ability to adapt to environmental changes. This is achieved through multiple mechanisms, including the direct regulation of chromatin-based processes in response to stimuli. How signal transduction pathways directly communicate with chromatin to change the epigenetic landscape is poorly understood. The preponderance of covalent modifications on histone tails coupled with a relatively small number of functional outputs raises the possibility that chromatin acts as a site of signal integration and storage.

Figure 1. The histone tails act as a signal storage and converter device

Signals from multiple inputs occurring over time, which are ‘on’ or ‘off’ in nature, can be stored on chromatin through post-translational modifications (PTMs) of histone tails. These inputs may affect the chromatin directly or be transmitted through epigenetic enzymes, including factors that ‘write’ or ‘erase’ particular marks on histones and chromatin-remodelling factors. The chromatin landscape is constantly interpreted by ‘reader’ proteins, which are comprised of various domains. This ‘signal interpretation’ involves a collage of mechanisms whereby the marks present on histones, either directly or through crosstalk, recruit reader proteins and additional enzymes. The crosstalk between different histone modifications can have several effects including: changing the ability of a reader protein to recognize an adjacent mark; recruiting or precluding enzymes that modify additional sites; or creating a combinatorial display for recognition in multivalent binding events. Together, these outcomes can influence the amplitude of a continuous wave of transcriptional output. Ac, acetylation; Me, methylation; P, phosphorylation.

Figure 2. Possible modes of signalling to chromatin

Activated signalling cascades can alter the epigenetic landscape directly or indirectly by communicating with chromatin regulators. a, Metabolites and nutrient availability influence the activity of many enzymes regulating the epigenome, as these small molecules are used as cofactors. Forexample, oxygen is required for the activity of the JumonjiC (JMJC) family of Lys demethylases. The extent to which a hypoxic environment inhibits the various JMJC demethylases is not known. Hypoxia can lead to histone acetylation around hypoxia-inducible factor 1α (HIF1α) and HIF1β target genes via the recruitment of p300. Dietary Met is a precursor of the methyl donor S-adenosylmethionine (SAM), which is required for DNA, Lys or Arg methylation (Me) events, and glucose metabolism through the tricarboxylic acid (TCA) cycle produces α-ketoglutarate, which is also required for JMJC demethylase activity. Glucose metabolism through thehexosamine biosynthetic pathway produces uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), which is used by O-linked β-d-N-acetylglucosamine transferase (OGT) to trigger O-GlcNAcylation of enzymes that regulate chromatin modification, histones and transcription factors (TFs). Acetyl-CoA that is produced from citrate exiting the TCA cycle also provides the donor group for protein acetylation (Ac). b, A simplified and generic kinase cascade that collides with chromatin modifying factors in the nucleus. Signal-induced post-translational modifications (PTMs) of enzymes (such as phosphorylation) may alter enzyme activity in modifying histone or DNA residues. Enzyme modification of ATP-dependent chromatin remodellers can also alter their effects on nucleosome repositioning, changing the modification landscape or DNA accessibility around particular gene promoters or enhancers. Controlling enhancer activity or responsiveness to signals through nearby histone tail modifications and transcription factor binding site accessibility may be a crucial process in cell fate decisions, as enhancer utilization drives tissue-specific gene expression. Phosphorylation–dephosphorylation events on histone chaperones can alter their ability to deposit histone variants into functionally important genomic areas, such as around the transcriptional start sites of genes. Reader proteins may also be direct targets of signalling cascades; changing the ability of these proteins to recognize the PTMs on chromatin and therefore the recruitment of additional regulators can completely switch the biological consequence of a chromatin modification. Another mechanism at work is complex nucleation initiated by a signalling event. In this case, one or a few proteins are maintained on or nearby their target genes, poised but not active, and acting as a ‘placeholder’ for rapid induction. Upon a signalling event, the placeholders nucleate the remaining protein complex and a function is executed. Due to the rapid nature of this response, complex nucleation may be most prevalent during primary response gene (PRG) induction.

Figure 3. AKT signalling to chromatin-modifying enzymes

Chromatin-modifying enzymes are emerging as a new class of AKT phosphorylation targets. A,The AKT signalling cascade is induced by ligand binding and subsequent activation of receptor Tyr kinases, cytokine receptors and integrin receptors, to name a few. This results in activation of PI3K at the intracellular domain of the receptor, followed by PI3K-induced production of phosphatidylinositol-3,4,5-triphosphates (PtdIns(3,4,5)P₃). PtdIns(3,4,5)P₃ production creates docking sites for phosphoinositide-dependent kinase 1 (PDK1) and AKT, thus allowing phosphorylation and activation of AKT by PDK1. Many cellular pathways are regulated by AKT signalling. Depicted are epigenetic enzymes that are targeted by AKT, including the histone methyltransferase EZH2, the histone ubiquitylating enzyme BMI1, the histone acetyltransferase p300 and the DNA methyltransferase DNMT1. AKT-mediated phosphorylation of these enzymes may have several effects, for example altering catalytic activity in the case of EZH2 and p300, altering protein stability or retention at the replication fork in the case of DNMT1, or increasing the ubiquitin ligase activity of BMI1 towards H2A after DNA damage. B, Other chromatin-modifying enzymes contain AKTtarget motifs (that is; R-X-R-X-X-S/T; Arg residues are boxed in blue and Ser/Thr residues in orange). Listed are potential phosphorylation sites for KDM4B (a demethylase for histone H3 Lys 9 dimethylation (H3K9me2) or H3K36me3), SET1A (a H3K4 methyltransferase) and DNMT3B (a denovo DNA methyltransferase). Although more enzymes contain putative AKT sites, each of these highlighted sites has been identified multiple times as phosphorylated peptides in large proteomic studies aimed at identifying new AKT targets ( PhosphoSitePlus). c, The modification state of H3K27 is one major chromatin feature that is highly predictive of enhancer activity. Methylation at this residue by EZH2 marks an inactive, and possibly poised, enhancer, whereas acetylation of H3K27 by p300 marks an active enhancer that is engaged in transcription with promoter regions. AKT phosphorylation of EZH2 limits its ability to methylate H3K27, whereas AKT phosphorylation of p300 promotes transactivation.

Figure 4. Histone-mimic sequences may be an integral part of signal-induced chromatin-mediated processes

A, The amino-terminal tails of histones H3 and H4 are depicted. Basic local alignment search tools predict that several nuclear proteins contain plausible histone-mimic motifs, and notable examples are shown here. Residues that are common with H3 or H4 are depicted in pink. These highly conserved histone tail-like sequences illustrate that it is likely that multiple non-histone proteins modulating chromatin are subject to modification by the same enzymes that modify the histone tails. B, Histone-mimic sequences have been well-characterized within the methyltransferase G9A and the tumour suppressor p53. Examples of respective homologous protein motifs are shown and the common residues highlighted in yellow. C, The reader protein MPP8 (M phase phosphoprotein 8) can recognize methylated histone-mimic motifs within the histone methyltransferase GLP and the de novo DNA methyltransferase DNMT3A, linking dimethylation of Lys9 on histone H3 (H3K9me2) with denovo DNA methylation by DNMT3A. One possibility is that a single signalling event might trigger simultaneous automethylation of GLP and methylation of DNMT3A to coordinate histone and DNA methylation events in close vicinity. ATF7IP, activating transcription factor 7-interacting protein 1; BRWD3, bromodomain and WD repeat-containing protein 3; CREBZF, CREB/ATF bZIP transcription factor; DHX34, DEAH box protein 34; FMR2,fragile X mental retardation 2; FOXC2, forkhead box C2; MLL, mixed-lineage leukaemia; TAF11, transcription initiation factor TFIID subunit 11; ZNF, zinc-finger.