The <scp>E3</scp> ubiquitin ligase <scp>UBR5</scp> promotes ubiquitylation and degradation of the chromatin regulator <scp>ATAD2</scp>

UBR5 is a HECT-type E3 ubiquitin ligase that assembles K48-linked ubiquitin chains and generates K48-linked branched chains. UBR4 is another E3 that forms K48-linked chains through an atypical hemi-RING-like domain. To define substrates specific to each ligase, we analyzed tandem mass tag proteomics data and identified candidates that accumulated after UBR5 or UBR4 knockdown, respectively. UBR5 depletion caused a marked delay in turnover of the chromatin regulator ATAD2. We found that ATAD2 associated with UBR5 in co-immunoprecipitation assays, and UBR5 promoted ubiquitylation of ATAD2 in vitro and in cells. RNA-sequencing further showed that the expression of cell cycle-related genes was antagonistically regulated by ATAD2 and UBR5. These findings identify ATAD2 as a UBR5 substrate and reveal a regulatory module controlling gene expression.