Molecular basis for chromatin binding and regulation of MLL5

Abstract

The human mixed-lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle, and survival; however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its plant homeodomain finger with the histone mark H3K4me3. The 1.48-Å resolution crystal structure of MLL5 plant homeodomain in complex with the H3K4me3 peptide reveals a noncanonical binding mechanism, whereby K4me3 is recognized through a single aromatic residue and an aspartate. The binding induces a unique His-Asp swapping rearrangement mediated by a C-terminal α-helix. Phosphorylation of H3T3 and H3T6 abrogates the association with H3K4me3 in vitro and in vivo, releasing MLL5 from chromatin in mitosis. This regulatory switch is conserved in the Drosophila ortholog of MLL5, UpSET, and suggests the developmental control for targeting of H3K4me3. Together, our findings provide first insights into the molecular basis for the recruitment, exclusion, and regulation of MLL5 at chromatin.T he mixed-lineage leukemia 5 (MLL5) protein was initially identified as a candidate tumor suppressor and more recently has been shown to play a critical role in hematopoiesis and lymphopoiesis (1). The MLL5 gene-containing region of chromosome 7 is frequently deleted in patients with hematological disorders, including acute myeloid and therapy-induced leukemias and myeloid dysplastic syndrome (MDS). Depletion of Mll5 in mice causes mild postnatal lethality, with some of the surviving animals showing retarded growth, male sterility, and decreased size of thymus, spleen, and lymph nodes (2-4). Genetic analyses of these Mll5 deficiencies reveals a 30% decrease in the number of hematopoietic stem cells (HSC) and progenitors, defects in HSC self-renewal mechanisms, and impaired myeloid differentiation (2-4). In addition to being an essential mediator of HSC homeostasis, MLL5 has been implicated in cytokinesis, the DNA damage response, and genome maintenance (5-7). Overexpression and knockdown of MLL5 both induce cell cycle arrest at various phases, suggesting a versatile function of MLL5 throughout the cell cycle (5).MLL5 belongs to the MLL family of methyltransferases that regulate gene expression during developmental processes. These enzymes catalyze the addition of methyl groups to the e-amino moiety of lysine and are highly specific for lysine 4 of histone H3. Along with MLL5, also known as a lysine methyltransferase 2E (KMT2E), the MLL family contains MLL1-4, SET1A, and SET1B (KMT2A-KMT2D, KMT2F, and KMT2G, respectively) (8). Full-length MLL5 is ∼200 kDa and is evolutionarily distant from the more canonical and better-characterized members of this family. Unlike the other multimodular MLL proteins, MLL5 consists of only two conserved motifs near the N terminus, a plant homeodomain (PHD) finger, followed by a catalytic Su(var)3-9, enhancer of zeste, trithorax (SET) domain. A long, ∼1,000-residue C-terminal region of MLL5 displays no apparent homology to...

Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins

“…3, B and F). The overall histone binding mode observed in the ZCWPW2 and MORC3 structures is similar to those of the previously reported ZCWPW1-H3K4me3 (8) and PHD-H3K4me3 complex structures, such as BPTF (31), ING2 (32), JARID1A (33), and MLL5 (34).…”

“…These results indicate that the invariant tryptophan cage residue (Trp-41 in ZCWPW2, right wall) is a strong determinant for binding methylated H3K4, similar to the MLL5 PHD domain (Fig. 6D), which uses a cage of a single aromatic residue, Trp, to accommodate H3K4me3 (34). As far as we know, MLL5 is the only identified histone binder that naturally uses a cage with a single aromatic residue to recognize methylated histones.…”

“…Although the sequences and structures of the CW and PHD domains are diverse, they have similar cores (Fig. 8A), and the Lys-4/Arg-2-separating tryptophan is also highly conserved in the PHD domains, where it plays a similarly important role, such as in BPTF (31), ING2 (32), PHF2 (38), and MLL5 (34) (Fig. 8B).…”

“…The corresponding loop is also conserved in the PHD domain, where it is located between the fifth and sixth zinc-coordinating cysteine residues (Fig. 8A) (31)(32)(33)(34)38). In these binding pockets, the free N terminus is essential for H3K4me3 recognition.…”

The essential role of acetyllysine binding by the YEATS domain in transcriptional regulation

“…28,29 A similar switch has been shown to eject the H3K4me3-interacting PHD fingers when neighboring H3T3 or H3T6 are phosphorylated. [30][31][32][33] To assess whether 'phospho-acetyl' switches can regulate the function of Taf14, we evaluated binding activity of the Taf14 YEATS domain toward histone peptides harboring S10ph and T6ph modifications along with H3K9ac ( Fig. 2a and ref 4 ).…”