GSE173176
Determine the chromatin association change of H3K27me3 and PRC2  in response to CTR9 inducible loss as well as genome-wide mapping of Flag-CTR9 binding sites in MCF7 cells
CTR9 is the scaffold subunit in PAFc (Polymerase associated factor complex), a multifunctional complex employed in multiple steps of RNA Pol II-mediated transcription. CTR9/PAFc is well known as an evolutionarily conserved elongation factor regulating gene activation via coupling with histone modifications enzymes. However, little is known about its function to restrain repressive histone markers. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the amount of H3K27me3 is strictly controlled by CTR9. Quantitative profiling on histone modifications revealed a striking increase of H3K27me3 level upon loss of CTR9. Moreover, loss of CTR9 leads to genome-wide expansion of H3K27me3, as well as increased recruitment of PRC2 on chromatin, which can be reversed by CTR9 restoration. Moreover, CTR9 depletion triggers a PRC2 subtype switch from less active PRC2.2 to PRC2.1 with higher methyltransferase activity. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution provide a unique mechanism of transition from transcriptionally active to repressive chromatin states and shed light on the biological functions of CTR9 in development and cancer. Overall design: 1. ChIP-Rx of H3K27me3 and PRC2 subunits (SUZ12/JARID2/MTF2) in MCF7-tet-on-shCTR9 cells (Dox inducible CTR9 KD) -- 2 replicates  2. ChIP-Rx of Flag (2 different vendors) in MCF7-3xFlag-KI-CTR(9 cells (CTR9 with 3xFlag epitope tag knock in) -- 2 replicates (PS: every ChIP reaction was incorportated with same amount of spike-in control)