The duality of PRDM proteins: epigenetic and structural perspectives

Abstract

PRDF1 and RIZ1 homology domain containing (PRDMs) are a subfamily of Krüppel-like zinc finger proteins controlling key processes in metazoan development and in cancer. PRDMs exhibit unique dualities: (a) PR domain/ZNF arrays-their structure combines a SET-like domain known as a PR domain, typically found in methyltransferases, with a variable array of C2H2 zinc fingers (ZNF) characteristic of DNA-binding transcription factors; (b) transcriptional activators/repressors-their physiological function is context- and cell-dependent; mechanistically, some PRDMs have a PKMT activity and directly catalyze histone lysine methylation, while others are rather pseudomethyltransferases and act by recruiting transcriptional cofactors; (c) oncogenes/tumor suppressors-their pathological function depends on the specific PRDM isoform expressed during tumorigenesis. This duality is well known as the 'Yin and Yang' of PRDMs and involves a complex regulation of alternative splicing or alternative promoter usage, to generate full-length or PR-deficient isoforms with opposing functions in cancer. In conclusion, once their dualities are fully appreciated, PRDMs represent a promising class of targets in oncology by virtue of their widespread upregulation across multiple tumor types and their somatic dispensability, conferring a broad therapeutic window and limited toxic side effects. The recent discovery of a first-in-class compound able to inhibit PRDM9 activity has paved the way for the identification of further small molecular inhibitors able to counteract PRDM oncogenic activity.

Keywords: yin-yang; PRDM; epigenetic regulation; methyltransferase; pseudomethyltransferase; transcription factor.

Fig. 1.

Domain structure of human PRDMs. PR domains are highlighted in red and C2H2 zinc fingers in green. Additional relevant domains are depicted including KRAB domains in blue, Q-rich regions in purple, and RBBP4 binding domain in orange. FOG-1 and FOG-2 proteins have been renamed respectively PRDM18 and PRDM19.

Fig. 2.

Summary of the experimental evidence of PRDM’s methyltransferase activity. PRDMs have been classified into three categories: (a) methyltransferases (PRDM2, PRDM7, PRDM9, and PRDM16); (b) methyltransferases with unclear/indirect evidence (PRDM3, PRDM8); and (c) pseudomethyltransferases (PRDM1, PRDM3, PRDM5, PRDM6, PRDM10, PRDM14, PRDM15).

Fig. 3.

3D molecular models highlighting PR/SET domain interactions. (A) Comparison of the PR/SET domain of mPRDM9 (magenta) in complex with H3K4me2 peptide (red) and SAH (green) (PDB code 4C1Q), unbound hPRDM9 (orange) (PDB code 4IJD), and SAM (yellow) and bound hPRDM9 (green) (PDB code 6NM4). (B) Superposition of the PR/SET domain of mPRDM9-SAH (magenta) onto unbound hPRDM9 (orange). (C) PRDM2 (yellow) (PDB code 2QPW). (D) PRDM4 (gray) (PDB code 3DB5). (E) PRDM10 (cyan) (PDB code 3IHX). (F) PRDM12 (red) (PDB code 3EP0). (G) PRDM14 (blue) (PDB code 5ECJ). (H) PRDM1 (purple) (PDB code 3DAL). Residues interacting with SAH are highlighted. PYMOL (https://pymol.org/2/), an open-source molecular visualization system, has been used to generate the reported structures.

Fig. 4.

Sequence alignment of PRDMs’ PR domains and representative human canonical SET domain containing methyltransferases (KMT2/MLL, EHMT2/G9a, Su(var)3–9H1, and EZH2 highlighted in the turquoise box). The green boxes refer to the PRDMs with demonstrated methyltransferase activity (PRDM9, PRDM3, and PRDM16). The red box highlights the exclusive PR domain motif that is associated with putative methyltransferase activity. The purple boxes denote key amino acidic residues critical for methyltransferase activity (identified in Fig. 3). The alignment has been generated by using the T-Coffee multiple sequence alignment algorithm (https://www.ebi.ac.uk/Tools/msa/tcoffee/) accessible through Jalview open-source software (http://www.jalview.org/). The amino acid sequences were downloaded from the publicly accessible database UniProt (https://www.uniprot.org/); their accession numbers are as follows: Q03164 (KMT2A_MLL), Q96KQ7 (EHMT2_G9A), Q15910 (EZH2), O43463 (SUV39H1), O75626 (PRDM1), Q13029 (PRDM2), Q03112 (PRDM3), Q9UKN5 (PRDM4), Q9NQX1 (PRDM5), Q9NQX0 (PRDM6), Q9NQW5 (PRDM7), Q9NQV8 (PRDM8), Q9NQV7 (PRDM9), Q9NQV6 (PRDM10), Q9NQV5 (PRDM11), Q9H4Q4 (PRDM12), Q9H4Q3 (PRDM13), Q9GZV8 (PRDM14), P57071 (PRDM15), Q9HAZ2 (PRDM16), Q9H9D4 (PRDM17), Q8IX07 (PRDM18/FOG1), and Q8WW38 (PRDM19/FOG2).

Fig. 5.

Summary of predicted and experimentally demonstrated PRDM zinc finger binding sites. A comparative analysis has been performed between predicted binding sites by using Princeton online tool (http://zf.princeton.edu/) and either experimentally demonstrated binding sites or binding sites deposited in JASPAR database.