Lysine Methylation Regulators Moonlighting outside the Epigenome

Abstract

Landmark discoveries made nearly two decades ago identified known transcriptional regulators as histone lysine methyltransferases. Since then, the field of lysine methylation signaling has been dominated by studies of how this small chemical posttranslational modification regulates gene expression and other chromatin-based processes. However, recent advances in mass-spectrometry-based proteomics have revealed that histones are just a subset of the thousands of eukaryotic proteins marked by lysine methylation. As the writers, erasers, and readers of histone lysine methylation are emerging as a promising therapeutic target class for cancer and other diseases, a key challenge for the field is to define the full spectrum of activities for these proteins. Here we summarize recent discoveries implicating non-histone lysine methylation as a major regulator of diverse cellular processes. We further discuss recent technological innovations that are enabling the expanded study of lysine methylation signaling. Collectively, these findings are shaping our understanding of the fundamental mechanisms of non-histone protein regulation through this dynamic and multi-functional posttranslational modification.

Figure 1.. Lysine methylation writer, eraser, and reader families.

Wheel plots depicting current knowledge of the subcellular localization, substrates, and evaluation status of small molecular inhibitors for (A) lysine methyltransferases; KMTs, (B) lysine demethylases; KDMs, (C) proteins with UniProt-annotated PHD, BAH, CW, and SPIN domains, and (D) the Royal family of methyllysine readers with UniProt-annotated Tudor, MBT, PWWP, and Chromo domains. Data was curated from UniProt (2019) and ChromoHub (Liu et al., 2012).

Figure 2.. Molecular functions associated with lysine methylation.

Radar plot counting the number of PubMed-archived papers assigning the indicated molecular function to lysine methylation.

Figure 3.. Common phenotypes associated with histone and non-histone substrates of KMT activity.

(A) MPP8 chromodomain recognition of G9a/GLP-dependent H3K9 and ATF7IPK16 methylation is associated with gene silencing. (B) UHRF1 tandem Tudor domain recognition of G9a/GLP-dependent H3K9 and LIG1 methylation is associated with DNA methylation inheritance. (C) SETD2-dependent H3K36 and αTubulinK40 methylation contributes to genomic stability. (D) The catalytic subunit of the PRC2 complex, EZH2, methylates H3K27 and ElonginAK754 to promote gene silencing.

Figure 4.. Technologies developed to reveal KMT substrates.

(A) Typical mass spectrometry (MS)-based proteomics pipeline for the identification of lysine methylation sites from cultured cells. (B) SPOT arrays evaluate the sequence tolerance of known KMT peptide substrates. (C) Protein arrays facilitate de novo identification of KMT substrates. (D) Lysine-oriented peptide libraries (K-OPL) reveal the sequence determinants of KMT substrate selectivity.