SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18[S]

Endogenous immunoprecipitation was used to investigate protein interactions of SETD1A complex subunits. An unexpected interaction with the DNA damage protein RAD18 was confirmed for SETD1A but not for other subunits. SETD1A and RAD18 evoked a DNA damage repair phenotype and influenced each other's mRNA and protein expression. [Display omitted] Highlights •Protein interaction screen of SETD1A/COMPASS complex subunits.•Unexpected interaction with DNA damage protein RAD18 was confirmed for SETD1A, but not for other subunits.•SETD1A and/or RAD18 influence each other's mRNA and protein expression levels, and disruption of either gene elicits a similar DNA damage sensitivity phenotype. SETD1A is a SET domain-containing methyltransferase involved in epigenetic regulation of transcription. It is the main catalytic component of a multiprotein complex that methylates lysine 4 of histone H3, a histone mark associated with gene activation. In humans, six related protein complexes with partly nonredundant cellular functions share several protein subunits but are distinguished by unique catalytic SET-domain proteins. We surveyed physical interactions of the SETD1A-complex using endogenous immunoprecipitation followed by label-free quantitative proteomics on three subunits: SETD1A, RBBP5, and ASH2L. Surprisingly, SETD1A, but not RBBP5 or ASH2L, was found to interact with the DNA damage repair protein RAD18. Reciprocal RAD18 immunoprecipitation experiments confirmed the interaction with SETD1A, whereas size exclusion and protein network analysis suggested an interaction independent of the main SETD1A complex. We found evidence of SETD1A and RAD18 influence on mutual gene expression levels. Further, knockdown of the genes individually showed a DNA damage repair phenotype, whereas simultaneous knockdown resulted in an epistatic effect. This adds to a growing body of work linking epigenetic enzymes to processes involved in genome stability.