Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations [RNA-seq]

We find that HTT binds ATF7IP, a regulator of the histone H3 methyltransferase SETDB1. HTT inhibits the interaction of the ATF7IP-SETDB1 complex with other heterochromatin regulators and transcriptional repressors, maintaining low levels of H3K9 trimethylation (H3K9me3) in hESCs. Conversely, loss of HTT promotes global increased H3K9me3 levels. To test whether HTT knockdown also induces enrichment of H3K9me3 marks at specific genes, we performed chromatin immunoprecipitation (ChIP)-sequencing assays of hESCs using an antibody to H3K9me3. We performed RNAseq in pluripotent stem cells and derived NPCs to examine how changes in HTT and ATF7IP levels change transcript levels. We have 19 samples in total: 3 replicate NPCs derived from HD iPSCs expressing Nt shRNA + 3 NPCs derived from HD iPSCs expressing ATF7IP shRNA to be compared with 3 NPCs derived from Control iPSCs expressing Nt shRNA; 2 replicates H9 hESCs expressing ATF7IP shRNA to be compared with 2 replicates H9 hESCs expressing control NT shRNA; 3 replicates NPCs derived from H9 hESCs expressing HTT shRNA to be compared with 3 replicates NPCs derived from H9 hESCs expressing control NT shRNA