A non-catalytic function of SETD1A regulates Cyclin K and the DNA damage response [RNA-seq]

MLL/SET methyltransferases catalyze methylation of histone 3 lysine 4 and play critical roles in development and cancer. We assessed MLL/SET proteins and found that SETD1A is required for survival of acute myeloid leukemia (AML) cells. Mutagenesis studies and CRISPR-Cas9 domain screening, showed the enzymatic SET domain is not necessary for AML cell survival but that a newly identified region, termed the FLOS (Functional Location on SETD1A) domain, is indispensable. FLOS disruption suppresses DNA damage response genes and induces p53-dependent apoptosis. The FLOS domain acts as a Cyclin K-binding site that is required for chromosomal recruitment of Cyclin K, and for DNA repair-associated gene expression in S phase. These data identify a connection between the chromatin regulator SETD1A and the DNA damage response that is independent of histone methylation, and suggests that targeting SETD1A and Cyclin K complexes may represent a therapeutic opportunity for AML and potentially other cancers. RNA-seq of Setd1a knockout mouse MLL-AF9 leukemia cells and Ccnk shRNA-expressing mouse MLL-AF9 leukemia cells. Setd1aflox/flox;CreER and Setd1a+/+;CreER leukemia cells were analyzed at day 4 post-tamoxifen. shRNA-expressing mouse MLL-AF9 leukemia cells were analyzed at day 4 post-doxycycline.