MRG Proteins Are Shared by Multiple Protein Complexes With Distinct Functions

MRG15 (MORF-related gene on chromosome 15)/MORF4L1 is a highly conserved protein in eukaryotes that contains a chromodomain (CHD) recognizing methylation of lysine 36 on histone H3 in chromatin. Intriguingly, it has been reported in the literature to interact with several different factors involved in chromatin modifications, gene regulation, alternative mRNA splicing, and DNA repair by homologous recombination. In order to get a complete and reliable picture of associations in physiological conditions, we used genome editing and tandem affinity purification to analyze the stable native interactome of human MRG15, its paralog MRGX/MORF4L2 that lacks the CHD, and MRGBP (MRG-binding protein) in isogenic K562 cells. We found stable interchangeable association of MRG15 and MRGX with the NuA4 (nucleosome acetyltransferase of H4)–Tat interactive protein 60 kDa (TIP60) histone acetyltransferase/chromatin remodeler, Sin3B histone deacetylase/demethylase, ASH1L (absent, small, or homeotic discs 1-like) histone methyltransferase, and PALB2–BRCA2 DNA repair protein complexes. These associations were further confirmed and analyzed by CRISPR tagging of endogenous proteins and comparison of expressed isoforms. Importantly, based on structural information, point mutations could be introduced that can specifically disrupt MRG15 association with some complexes but not others. Most interestingly, we also identified a new abundant native complex formed by MRG15–X-MRGBP-BRD8-EP400NL (EP400 N-terminal like) that is functionally similar to the yeast TINTIN (Trimer Independent of NuA4 for Transcription Interactions with Nucleosomes) complex. Our results show that EP400NL, being homologous to the N-terminal region of NuA4–TIP60 subunit EP400, creates TINTIN by competing for BRD8 association. Functional genomics indicate that human TINTIN plays a role in transcription of specific genes. This is most likely linked to the H4ac-binding bromodomain of BRD8 along the methylation of lysine 36 on histone H3–binding CHD of MRG15 on the coding region of transcribed genes. Taken together, our data provide a complete detailed picture of human MRG protein–associated protein complexes, which are essential to understand and correlate their diverse biological functions in chromatin-based nuclear processes. [Display omitted] •MRG15 and MRGX are stably associated with several different protein complexes important for genome expression and stability.•Several MRG-containing complexes are chromatin m