Targeted Profiling of Epitranscriptomic Reader, Writer, and Eraser Proteins Regulated by H3K36me3

Trimethylation of lysine 36 on histoneH3 (H3K36me3), an epigeneticmark associated with actively transcribed genes, plays an importantrole in multiple cellular processes, including transcription elongation,DNA methylation, DNA repair, etc. Aberrant expression and mutationsof the main methyltransferase for H3K36me3, i.e., SET domain-containing2 (SETD2), were shown to be associated with various cancers. Here,we performed targeted profiling of 154 epitranscriptomic reader, writer,and eraser (RWE) proteins using a scheduled liquid chromatography-parallel-reactionmonitoring (LC-PRM) method coupled with the use of stable isotope-labeled(SIL) peptides as internal standards to investigate how H3K36me3 modulatesthe chromatin occupancies of epitranscriptomic RWE proteins. Our resultsshowed consistent changes in chromatin occupancies of RWE proteinsupon losses of H3K36me3 and H4K16ac and a role of H3K36me3 in recruitingMETTL3 to chromatin following induction of DNA double-strand breaks.In addition, protein-protein interaction network and Kaplan-Meiersurvival analyses revealed the importance of METTL14 and TRMT11 inkidney cancer. Taken together, our work unveiled cross-talks betweenhistone epigenetic marks (i.e., H3K36me3 and H4K16ac) and epitranscriptomicRWE proteins and uncovered the potential roles of these RWE proteinsin H3K36me3-mediated biological processes.