Exploring synthetic lethality between the PP6 phosphatase and SETDB1

Genome wide CRISPR/Cas9 screening identified SETDB1 and the HUSH complex as a synthetic lethal interactor of the PP6 phosphatase. Here, we sought to discover the molecular basis for this synthetic lethality. SETDB1 is a histone H3 lysine 9 methyltransferase, reported to be important in the establishment and maintenance of heterochromatin, and the silencing of repeats and incoming viral elements. We undertook RNA sequencing to explore differences in the transcriptome in HeLa and hTERT-RPE-1 cells devoid of PP6, SETDB1 or both proteins together. Overall design: HeLa or hTERT-RPE-1 cells, either stably knocked out for PPP6C and SETDB1, or depleted for PPP6C and SETDB1 using siRNA interference, were subjected to RNA isolation and purification. Total cellular RNA was submitted to the Oxford genomics centre for ribosomal RNA removal, library preparation and Illumina sequencing. [contributor] Oxford Genomics Centre