Multivalent engagement of chromatin modifications by linked binding modules

Abstract

Various chemical modifications on histones and regions of associated DNA play crucial roles in genome management by binding specific factors that, in turn, serve to alter the structural properties of chromatin. These so-called effector proteins have typically been studied with the biochemist's paring knife--the capacity to recognize specific chromatin modifications has been mapped to an increasing number of domains that frequently appear in the nuclear subset of the proteome, often present in large, multisubunit complexes that bristle with modification-dependent binding potential. We propose that multivalent interactions on a single histone tail and beyond may have a significant, if not dominant, role in chromatin transactions.

Figure 1. Thermodynamics of multivalent binding

a | Monovalent association of a hypothetical effector module (purple) to a chromatin substrate (yellow tail with green diamond) is simplistically compared to a bivalent association of the same effector in a complex, representing the lowest order of multivalent interactions. The change in free energy ΔG_i for the monovalent system undergoing binding is indicated by the change in enthalpy ΔH_i minus the change in entropy ΔS_i, scaled by the temperature (T). b | By tethering the two effector modules, the entropy term may be, to a first approximation, similar for each of the binding equilibria in panels a and b (TΔS_complex ≈ TΔS_i). For our purposes, this example assumes that hydrogen-bonding electrostatic interactions dominate and desolvation is negligible, so that ΔS for the system will be negative. Thus, the entropic penalty to binding is lessened approximately twofold by pre-organizing the effector domains in a complex (TΔS_complex ≈ TΔS_i), while the enthalpy of the bivalent domain interaction is effectively double that of the monovalent case (∼2ΔH_i, if enthalpic penalties due to the strain induced by bivalent binding are negligible). In this manner, the reduced net entropy loss for the binding process can be a significant determinant of free energy, especially in low-binding enthalpy regimes. Losses of entropy on the substrate side would be expected to be minimal due to the low intrinsic rotational and translational freedom of chromatin; however, conformational entropy losses here are assumed to be negligible for simplicity.

Figure 2. Polypeptides with many putative effector modules and representative complexes

a | The coexistence of possible effector module domains within single polypeptides is depicted schematically, with the number of instances of linkage for any two domains within the human proteome listed near the line connecting them. The SMART database was used as the source of these linkages, and redundant entries were removed. b | A structurally characterized example of two linked effector domains is provided by the structure of a BPTF module that comprises a PHD finger, a helical linker and a bromodomain, with a trimethylated Lys4 of histone H3 (H3K4me3) peptide bound to the PHD finger. The acetyl-Lys (Kac)-binding pocket on the bromodomain is shown, as well as residues R2 and K4me3 of the H3 peptide. c | Chromatin metabolism complexes, exemplified by the MLL1 (ref. 122), NURF^, and CtBP core complexes, have multiple putative effector domains. The predicted domain structure of subunits of the complex members are shown as a linear arrangement from N to C terminus. Chromatin-associated domains, most of which are modification sensitive, are coloured as in panel a, and are shown with additional predicted domains given in the key. The portion of the MLL1 protein that is cleaved by taspase-1 to yield two functional fragments (MLL1-N and MLL1-C) is shown. A frequent breakpoint at which fusion partners are appended and a domain deletion (Δ) that causes certain leukaemias are also depicted on the MLL1 domain structure. Ash2L, Set1–Ash2 histone methyltransferase complex subunit; BAH, bromo-adjacent homology domain; BPTF, bromodomain PHD finger transcription factor; Bromo, bromodomain; Chromo, chromodomain; CoREST, corepressor to the RE1 silencing transcription factor; CtBP, C-terminal binding protein; EHMT1, euchromatic histone-Lys N-methyltransferase-1; HCFC1, host cell factor C1; HDAC1, histone deacetylase-1; LSD1, Lys-specific demethylase-1; MBD, methyl-CpG binding domain; MEN1, multiple endocrine neoplasia-1; MLL1, mixed lineage leukaemia; MOF, males absent on first histone acetyltransferase; NURF, nucleosome remodelling factor; PHD, plant homeodomain; PWWP, PWWP motif protein of the Royal superfamily; RBBP, retinoblastoma binding protein; RREB1, Ras responsive element binding protein-1; SNF2L, sucrose non-fermenting-2-like ATPase; WD40r, WD40 repeat; WDR5, WD repeat domain-5; ZEB1/2, zinc finger E-box binding homeobox-1/2; ZnF217, zinc finger protein-217.

Figure 3. Modes of multivalent chromatin engagement

To distinguish among several potential mechanisms of multivalent association, we propose the following nomenclature. a | Intranucleosomal association can be subdivided into two distinct classes: cis-histone, when more than one discrete binding contact is made to a single histone, in particular the same tail; and trans-histone, whereby contacts are made to different histone protomers or attendant DNA within the same nucleosome. b | By contrast, internucleosomal binding modes crosslink two nucleosomes that are either adjacent or discontinuous in DNA sequence. Most of these crucial interactions are envisioned as modification dependent; however, DNA interactions and modification-independent contacts may have a vital energetic role. BPTF, bromodomain PHD finger transcription factor; HP1, heterochromatin protein-1; TAF1, TATA-binding protein-associated factor-1.

Figure 4. Models of nucleosomal engagement

a | A model of the LSD1–CoREST complex docked with the nucleosome in a bipartite manner with the second SANT domain binding to DNA and the AOD and SWIRM domains binding an H3 tail bearing Lys methylation. LSD1 is shown in green and CoREST in red. Adapted from REF. . b | A model of the PHD–bromodomain module of BPTF (green) binding a nucleosome with modifications in the tails of two different histones, H3K4me3 and H4ac (the precise site is unknown but H4K16ac is modelled here). The remaining portion of the NURF complex is shown as green ovals, including the N terminus of BPTF, SNF2L and RBBP4 and -7. In both panels, core histones are pink with tail cartoons in dark blue. The modification recognition epitope is shown in space-filling spheres (carbon, yellow; nitrogen, blue; oxygen, red) with DNA in grey. AOD, amine oxidase domain; BPTF, bromodomain PHD finger transcription factor; Bromo, bromodomain; CoREST, corepressor to the RE1 silencing transcription factor; LSD1, Lys-specific demethylase-1; NURF, nucleosome remodelling factor; PHD, plant homeodomain; RBBP, retinoblastoma binding protein; SNF2L, sucrose non-fermenting-2-like ATPase.