4sU-seq of EV vs PRL3 expressing melanoma cells

We report the use of 4sU-seq to determine the role of PRL3 in transcriptional processivity in human melanoma cells overexpressing either PRL3 or empty vector control. Genome-wide analysis of read coverage across length of equalised genes revealed a distinct accumulation of transcripts towards the 5’ end in PRL3 overexpressing cells. Furthermore, we identify the genes that were enriched with 5’ transcripts in the PRL3 expressing cells by comparing the intronic read counts (normalized for length) at the 5’ and 3’ end of the gene and termed this metric the transcriptional processivity ratio (TPR). Comparing the TPRs for each gene between control cells and cells expressing PRL3, we found 1745 genes that were enriched for transcripts at the 5’ end and 40 genes that were enriched at the 3’ end in the PRL3 expressing melanoma cells compared with controls. Over 62% of the genes with altered TPRs showed a significantly altered change in total RNA differential expression analysis between PRL3 cells and control cells. These data illustrate a function for PRL3 in the regulation of transcriptional processivity that is enough to substantially alter steady-state mRNA levels. 4sU labelled nascent RNA was profiled in stably transfected A375 human melanoma cells overexpressing PRL and empty vector (EV), in triplicates, using Illumina HiSeq 4000.