Regulation of the human RNA Polymerase III transcriptome in stem and cancer cells

RNA Polymerase III (Pol III) transcribes small noncoding RNAs that are important in protein synthesis. Genome-wide analysis of Pol III and associated transcription factors (TFIIIC, BRF1, and BRF2) localization in various human cell lines was performed using chromatin immunoprecipitation followed by highthroughput sequencing (ChIP-seq). These analyses show that Pol III binds only to a fraction of all its annotated target genes. Comparison of Pol III-bound regions to known chromatin and transcription factor data shows that Pol III localization in a cell is guided by the chromatin landscape setup by Pol II. We believe Pol III binding is opportunistic and relies on a cell's pool of transcription factors and chromatin landscapes to bind its target genes. To understand Pol III localization in a cell line of high interest, human embryonic stem cells (hESCs), we performed Pol III and TFIIIC ChIP-seq analyses in H1 cells. We hoped to understand the role of open chromatin and pluripotency transcription factors in hESC, on Pol III occupancy. We observed that there are significantly more Pol III-bound regions in hESCs when compared to differentiated cells types. We also observe that these Pol III-bound regions correlated positively with active chromatin marks and Pol II. Interestingly, we also observed that pluripotency transcription factors, NANOG (in hESCs) and OCT4 ! iv! (in mESCs), correlated with Pol III-bound regions. We also observed regional H3K27me3 at Pol III-bound regions. We observe Pol II and H3K4me3 peaks situated in between the Pol III and H3K27me3 peaks. We postulate that active chromatin setup by Pol II insulates the Pol III transcription unit from H3K27me3 repression. We also identified several novel Pol III-bound regions in hESCs. This is the first analysis of Pol III in hESCs and our results are consistent with Pol III binding and activity being regulated by active chromatin that is shaped in part by the pluripotency transcription factor network.