Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF

Abstract

Mono-, di- and trimethylated states of particular histone lysine residues are selectively found in different regions of chromatin, thereby implying specialized biological functions for these marks ranging from heterochromatin formation to X-chromosome inactivation and transcriptional regulation. A major challenge in chromatin biology has centred on efforts to define the connection between specific methylation states and distinct biological read-outs impacting on function. For example, histone H3 trimethylated at lysine 4 (H3K4me3) is associated with transcription start sites of active genes, but the molecular 'effectors' involved in specific recognition of H3K4me3 tails remain poorly understood. Here we demonstrate the molecular basis for specific recognition of H3(1-15)K4me3 (residues 1-15 of histone H3 trimethylated at K4) by a plant homeodomain (PHD) finger of human BPTF (bromodomain and PHD domain transcription factor), the largest subunit of the ATP-dependent chromatin-remodelling complex, NURF (nucleosome remodelling factor). We report on crystallographic and NMR structures of the bromodomain-proximal PHD finger of BPTF in free and H3(1-15)K4me3-bound states. H3(1-15)K4me3 interacts through anti-parallel beta-sheet formation on the surface of the PHD finger, with the long side chains of arginine 2 (R2) and K4me3 fitting snugly in adjacent pre-formed surface pockets, and bracketing an invariant tryptophan. The observed stapling role by non-adjacent R2 and K4me3 provides a molecular explanation for H3K4me3 site specificity. Binding studies establish that the BPTF PHD finger exhibits a modest preference for K4me3- over K4me2-containing H3 peptides, and discriminates against monomethylated and unmodified counterparts. Furthermore, we identified key specificity-determining residues from binding studies of H3(1-15)K4me3 with PHD finger point mutants. Our findings call attention to the PHD finger as a previously uncharacterized chromatin-binding module found in a large number of chromatin-associated proteins.

Mechanisms of ATP dependent chromatin remodeling

“…The presence of such an epitope was found to be essential in generating ATP-dependent regularly spaced nucleosome arrays by RSF [141]. Recent reports have shown that H3K9me3 mark can actively recruit the PHD domain of NURF [142,143]. Similarly, the same mark was also shown to recruit Isw1p ATPase to chromatin [144].…”

Structural insights into human KAP1 PHD finger–bromodomain and its role in gene silencing

“…The integrated structure of the KAP1 PHD finger-bromodomain is unique and different from the structure of the PHD finger-bromodomain of human BPTF 14 , or those of the tandem bromodomains of human transcriptional protein TAFII250 (ref. 9) and yeast remodeling protein Rsc4 (ref.…”

“…The domain-domain association is reinforced by interactions between the ZA loops of the two domains. In BPTF or TAFII250, the acetyllysine binding pocket located between the ZA and BC loops is accessible to the solvent, which indicates that the bromodomain and the PHD finger have independent functions in protein-protein interactions even in the tandem motif 9,14 . However, these structural features contrast sharply with the distinct integrated nature of the structure of the KAP1 tandem PHD finger-bromodomain (Fig.…”

“…domains [8][9][10] and the 'royal' family of chromodomains, Tudor and MBT domains [11][12][13] , as well as PHD fingers as methyllysine binding domains [14][15][16] provides support for this hypothesis.…”

“…The new structure reveals a uniquely unified tandem-domain architecture that is completely unlike that of the PHD finger-bromodomain of bromodomain-PHD finger transcription factor (BPTF) 14 . We show that the PHD finger and the bromodomain of KAP1 function interdependently in catalyzing SUMOylation of lysine residues within this tandem module.…”