ENLightening YEATS in antagonizing polycomb repression

In this issue of Blood, Hetzner et al demonstrate that the YEATS domain–containing protein, eleven-nineteen leukemia (ENL), antagonizes polycomb-mediated silencing by recruiting polymerase-associated factor 1 (PAF1).¹ 

Chromosomal rearrangements at 11q23, which result in the fusion of the N terminus of mixed-lineage leukemia (MLL) to a large number of partner genes, are found in a subset of leukemia patients with poor prognosis. Among the MLL fusion partners, ENL is one of the most frequently found partner genes, producing the MLL-ENL fusion protein that confers aberrant transcriptional elongation activity to leukemia cells.²  A notable feature of the ENL protein is the presence of the YEATS domain (from Yaf9, ENL, AF9, Taf14, Sas5), an acyl-lysine reader module.³  Recent findings revealed a critical function of wild-type ENL in MLL-rearranged leukemias. ENL recognizes acetylated histone H3 through the YEATS domain and tethers the super elongation complex (SEC) and the Dot1L complex, promoting gene expression by these complexes.^4,5  ENL has also been shown to interact with another transcription elongation complex, human polymerase-associated factor complex (PAFc), through its interaction with PAF1. In addition to the aforementioned complexes that promote transcriptional elongation and gene expression, ENL also interacts with the polycomb-repressive complex 1 (PRC1) component CBX8, which, as the name indicates, is a major mediator of gene repression. The interaction between ENL and CBX8 nonetheless appears to promote gene expression because ENL has been shown to counteract the repressive function of CBX8.⁶  ENL, through the interaction with transcriptional elongation complexes as well as the polycomb complex, therefore has a multifaceted role in gene expression, but how these ENL interactors coordinate gene expression remains unclear.

By taking a biochemical domain-deletion approach, Hetzner et al demonstrated that ENL depends on its interaction with PAF1 through the YEATS domain to antagonize the gene-repressive function of CBX8. The authors recognize that some patients with MLL-ENL fusion lack the YEATS domain within ENL, arguing against the importance of the ENL YEATS domain in transformation. However, the MLL moiety of the fusion protein also contains a PAF1-interacting domain, overlapping with the CXXC domain. As a consequence, some MLL-ENL fusions have 2 sites of PAF1-binding capacity (1 in MLL, the other in the ENL YEATS domain) and some have only 1 (in MLL). Interestingly, the number of PAF1-binding sites correlated directly to the transformation potential of the MLL-ENL fusion gene, with MLL-ENL with 2 times the PAF1-binding capacity exhibiting significantly stronger transformation potential, increased target gene expression such as Hoxa9 and Meis1, and also in vivo disease progression compared with MLL-ENL with only 1 times the PAF1-binding capacity.

Hetzner et al then turned to 2 ENL YEATS mutations found in Wilms tumors. ENL mutations in Wilms tumors may be an insertion/duplication at p.L117_R118insNHL, which duplicates the NHL tripeptide (called ENL_ins), or a deletion at the position 111-114, disrupting the PPV tripeptide motif (called ENL_del).³  They found that both of the ENL YEATS mutations augmented the ability of ENL to counteract CBX8, suggesting that these YEATS mutations promote gene expression. Interestingly, the NHL tripeptide duplication (ENL_ins mutation) significantly increased the ability of ENL to transform hematopoietic progenitor cells, and caused fully penetrant myeloid leukemia. Although the identical mutation has not been reported in hematological malignancies, a similar duplication was reported in pediatric acute myeloid leukemia (AML), suggesting that ENL YEATS mutations may have important implications in hematological malignancies.

With this new biochemical information, several questions emerge from this study. How does the ENL YEATS mutants found in Wilms tumors gain oncogenic potential? Does it increase the affinity of ENL to PAF1 or other ENL-interacting complexes such as SEC or Dot1L? How do the YEATS domains of ENL and the structurally similar AF9 differ in terms of PAF1 recruitment? Can any of the biochemical differences between ENL and AF9 shed light on the difference in the disease phenotypes brought by the 2 MLL fusion partners, with MLL-AF9 being found more frequently in AML compared with MLL-ENL, particularly in adults?^7,8  Comprehensive approaches encompassing biochemistry, gene regulation, and disease modeling should bring novel insights into the unique roles exerted by the different YEATS domain proteins and the fusion products found in leukemias.