Epigenetic modifiers, enzymes that catalyze covalent modifications on chromatin, play a pivotal role in establishing stable states for gene expression and cellular identity. Mutations in these modifiers have been linked to a variety of human diseases, including developmental disorders and cancers, highlighting the importance of understanding how these mutations impact the functions of epigenetic modifiers in development and disease. Recent findings suggest that some epigenetic modifiers may have noncatalytic functions, independent of their catalytic activities, which raises questions about the determinants of their dependency on catalytic activity and the implications for chromatin modifications. In this context, a comment by Chen et al. provides valuable insights into the catalytic and noncatalytic functions of the histone methyltransferase SETD2, a protein responsible for histone H3 lysine 36 trimethylation (H3K36me3) and frequently mutated in clear cell renal cell carcinoma.

The comment begins with a screening of SETD2 mutations in clear cell renal cell carcinoma, identifying a single-nucleotide mutation that results in a catalytically dead (CD) SETD2 protein. This mutation abolishes the enzyme's catalytic activity while retaining its interaction with RNA polymerase II. By generating a Setd2-CD knockin mouse model, the researchers compared it with a Setd2 knockout (KO) model to understand the physiological functions of SETD2 in mouse embryonic development. Both Setd2-CD and Setd2-KO mice exhibited embryonic lethality with similar vascular defects, indicating that the catalytic activity of SETD2 is essential for embryonic development. Western blot analysis and gene expression profiling revealed comparable decreases in H3K36me3 levels and gene expression alterations in both models. Notably, many collagen genes, which are often long and highly interrupted, were downregulated in the Setd2-CD and Setd2-KO yolk sacs, suggesting a role for SETD2 in regulating these genes, which may be relevant to vascular remodeling defects.

Comparative analyses of the Setd2-CD and Setd2-KO embryos revealed that the Setd2-CD embryos showed slightly milder developmental defects, particularly in chorioallantoic attachment, a critical event in mammalian embryonic development. Single-cell transcriptomic analysis revealed that the 5′ Hoxa cluster genes, specifically expressed in the allantois, were downregulated in the Setd2-KO but not in the Setd2-CD allantois cells, suggesting a role for SETD2 in regulating these genes in specific developmental contexts.

The comment suggests that SETD2 represents a different example from other epigenetic modifiers, as its physiological functions in mouse embryonic development require its catalytic activity. This contrasts with some epigenetic modifiers whose major functions are independent of catalytic activities and are often involved in multi-protein complexes, mediating functionally redundant chromatin modifications. The findings emphasize the importance of SETD2's catalytic activity and its role in mouse embryonic development, providing a clear example of an epigenetic modifier whose functions are dependent on its catalytic activity.

To determine the catalytic versus noncatalytic functions of epigenetic modifiers, the generation of point mutation CD knockin animal models and direct comparison with KO models is considered an objective standard, although technically challenging and time-consuming. The development of advanced, precise, and efficient single-nucleotide genome editing methodologies is anticipated to enable comprehensive studies of disease-causing mutations in the human genome. The comment also highlights the need for cross-species comparative studies to address discrepancies in the significance of epigenetic modifiers across species and to unveil the increasing importance of epigenetic modifications during evolution.
DOI: 10.1007/s11684-024-1104-4