Structural Basis for Lower Lysine Methylation State-Specific Readout by MBT Repeats of L3MBTL1 and an Engineered PHD Finger

Abstract

Human L3MBTL1, which contains three malignant brain tumor (MBT) repeats, binds monomethylated and dimethylated lysines, but not trimethylated lysines, in several histone sequence contexts. In crystal structures of L3MBTL1 complexes, the monomethyl- and dimethyllysines insert into a narrow and deep cavity of aromatic residue-lined pocket 2, while a proline ring inserts into shallower pocket 1. We have also engineered a single Y to E substitution within the aromatic cage of the BPTF PHD finger, resulting in a reversal of binding preference from trimethyl- to dimethyllysine in an H3K4 sequence context. In both the "cavity insertion" (L3MBTL1) and "surface groove" (PHD finger) modes of methyllysine recognition, a carboxylate group both hydrogen bonds and ion pairs to the methylammonium proton. Our structural and binding studies of these two modules provide insights into the molecular principles governing the decoding of lysine methylation states, thereby highlighting a methylation state-specific layer of histone mark readout impacting on epigenetic regulation.

Chromatin reader L(3)mbt requires the Myb–MuvB/DREAM transcriptional regulatory complex for chromosomal recruitment

“…1A), including those with which L(3)mbt has the reported highest affinity, H3K9 and H4K20 mono-and dimethyl ( Fig. 1 A and B) (15,16). In datasets with the largest overlap (H3K4 mono-and dimethyl), L(3)mbt peaks fall into large regions (rather than peaks) of methylated histone enrichment (Fig.…”

“…A potential clue into how repression might be exerted comes from biochemical studies by Reinberg and coworkers, stating that the human L(3)mbt can, once bound to DNA, act as a chromatin compaction agent; the bound protein condenses chromatin and thus prevents the expression of the underlying genes (14). This model, supported by studies in the homolog L3MBTL1, elaborates that the MBT repeats may form higher order structures with nucleosomes through the binding to modified histone tails (15)(16)(17).…”

“…19). L(3)mbt has intrinsic chromatin binding capabilities, which require the integrity of its second MBT repeat (14)(15)(16). To establish a contributing mode for vertebrate L(3)mbt recruitment, several studies have provided evidence consistent with L(3)mbt preferentially, albeit promiscuously, interacting with most mono-and dimethylated lysine residues of histones, with very low affinity for the non-or trimethylated forms (15,20,21).…”

“…L(3)mbt has intrinsic chromatin binding capabilities, which require the integrity of its second MBT repeat (14)(15)(16). To establish a contributing mode for vertebrate L(3)mbt recruitment, several studies have provided evidence consistent with L(3)mbt preferentially, albeit promiscuously, interacting with most mono-and dimethylated lysine residues of histones, with very low affinity for the non-or trimethylated forms (15,20,21). The available crystal structures provide evidence of how this methylated-lysine histone binding may be mediated and suggest that the arrangement of MBT repeats is required for protein stability, even if only one repeat performs the actual binding (15,16,22).…”

“…To establish a contributing mode for vertebrate L(3)mbt recruitment, several studies have provided evidence consistent with L(3)mbt preferentially, albeit promiscuously, interacting with most mono-and dimethylated lysine residues of histones, with very low affinity for the non-or trimethylated forms (15,20,21). The available crystal structures provide evidence of how this methylated-lysine histone binding may be mediated and suggest that the arrangement of MBT repeats is required for protein stability, even if only one repeat performs the actual binding (15,16,22). However, biochemical experiments have shown the methylated histone-L(3)mbt interaction to be weak, suggesting that it may only be partly responsible for recruitment (17).…”