Genome-wide profiling of RNA Polymerase II, MITF and DDX21 occupancy in human A375 cells stably expressing either empty vector or HA-tagged PRL3.

To determine the role of PRL3 in gene regulation, empty vector or HA-tagged PRL3 was stably expressed in cultured human melanoma A375 cells. ChIP-seq was used to determine the impact of increased PRL3 expression on the genome-wide distribution of RNA Polymerase II (Total/Ser5-Phosphorylated/Ser2-Phosphorylated), MITF and DDX21. In combination with transcriptional analysis (4sU-seq; GEO accession - GSE127855), this study demonstrated that PRL3 overexpression leads to reduced RNA polymerase processivity at a subset of so called 'restricted' genes which are enriched for endolysosomal functions. ChIP-seq for RNAPII (RNAPII - Total/Ser5-Phospho/Ser2-Phospho), MITF and DDX21 was performed on A375 cells that stably express either PRL3 or an empty vector control. Two independent replicate experiments were prepared for each sample.