PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy [RNA-seq]

Control of gene expression is one of the most complex yet continuous physiological processes impacting cellular homeostasis. RNA polymerase II (Pol II) transcription is tightly regulated at promoter-proximal regions by intricate dynamic processes including Pol II pausing, release into elongation, and premature termination. Here, we identify PTEN interacting with the Pol II transcription machinery and dephosphorylating Pol II C-terminal domain in vitro. PTEN alters the expression of hundreds of genes, and its restoration establishes Pol II promoter-proximal pausing in PTEN null cells. Furthermore, PTEN re-distributes genome-wide Pol II occupancy and possibly impacts Pol II pause duration, release, and elongation rate in order to enable precise gene regulation at genome-wide scale. Our observations demonstrate a direct and imperative role of PTEN in global transcriptional regulation. Total RNA was extracted from cells using the Qiagen RNeasy kit with on-column DNase treatment. RNA quality was assessed via the Agilent 2100 Bioanalyzer. All samples have RIN numbers ≥ 9.5. Two independent biological replicates (each containing two technical replicates) were used for RNA-sequencing. The library was prepared using Illumina TruSeq stranded total RNA kit. Sequencing was performed using Illumina HiSeq 2500 using 100-bp paired-end rapid run format.