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 regulation1,2,3. 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 function4. For example, histone H3 trimethylated at lysine 4 (H3K4me3) is associated with transcription start sites of active genes5,6,7, 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 β-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.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
D.J.P. is supported by funds from the Abby Rockefeller Mauze Trust, and the Dewitt Wallace and Maloris Foundations. C.D.A. is supported by an NIH MERIT award and funds from Rockefeller University. S.I. holds a Ruth Kirschstein NIH postdoctoral fellowship and J.W. holds a Damon-Runyon CRF Fellowship. We thank the Peptide Core Facilities at Sloan-Kettering (S. S. Yi at Microchemistry and Proteomics) and Rockefeller University for the synthesis and purification of K4-methylated H3 peptides. We would like to thank the staff at beam line X25 at the Brookhaven National Laboratory and beam lines 23ID-D and 24ID-C of the Advanced Photon Source at the Argonne National Laboratory, supported by the US Department of Energy, for assistance with data collection. D.J.P. is a member of the New York Structural Biology Center, supported in part by funds from the NIH. Author Contributions H.L. is responsible for the X-ray and surface plasmon resonance studies, S.I. for the NMR studies, W.W. for the calorimetric studies, B.D. for fluorescence polarization studies and J.W. for identification and functional characterization of the BPTF PHD finger as a H3K4me3 reader. D.J.P. and C.D.A. supervised the structural and functional (see companion paper) aspects of the project, respectively, and take overall responsibility for their joint research. All authors discussed the results and commented on the manuscript.
This file contains Supplementary Methods, Supplementary Notes, Supplementary Figures 1–13 and Supplementary Tables 1–3.