Comprehensive kinase atlas uncovers new layers of gene regulation

RNA polymerase II is a molecular machine that all eukaryotic cells require to read the genome and transcribe genetic instructions into messenger RNA. Regulation of this process, transcription, is central to cellular fate and function. The activity of RNA polymerase II is guided by the addition of phosphate groups onto its “tail” by proteins called kinases.

RNA polymerase II’s tail, also known as the C-terminal domain, or CTD, is composed of nearly 52 sequential repeats of the same seven amino acids. Cells control distinct steps of gene transcription using kinases to attach phosphate groups onto different positions of this repeated amino acid sequence, particularly at positions two and five. The relevance of the other positions of the repeat to RNA polymerase II function has long been debated, so St. Jude scientists conducted a study to understand their role better.

“We knew there were CTD kinases beyond the canonical ones, but appreciated that specificity often comes from proximity,” said Aseem Ansari, Department of Chemical Biology & Therapeutics chair. “Many kinases can phosphorylate the tail, so we wanted to sort through them to determine which are meaningful.”

The researchers tested 427 kinases, approximately 80% of all human kinases, to see if, how, and where they could phosphorylate the CTD tail. They identified 117 kinases that could specifically phosphorylate different positions within the seven-residue repeats of the tail. This included previously disregarded positions, which were surprising as 54 of the tested 62 tyrosine kinases acted exclusively at the first position.

The findings, published in Science, greatly expand upon the small set of kinases previously known to phosphorylate RNA polymerase II. Within this comprehensive kinase atlas were some unexpected findings relating to cell signaling. Extensive experiments confirmed that RNA polymerase II, which resides in the nucleus, is phosphorylated by the cell-surface receptor tyrosine kinase EGFR. This effect is essential for transcription of a set of first-responder genes, demonstrating that cell-surface signaling can directly influence gene expression in the nucleus through the direct activity of these kinases.

These findings challenge traditional views of cell signaling and highlight a previously underappreciated layer of regulation, which carries significant implications for how cell signaling may drive signal-responsive outcomes.

The work also links kinase activity to disease; EGFR is frequently mutated in cancer. “Some aggressive cancers have untethered kinases in the nucleus, disrupting transcriptional programs,” said Ansari. “We’ve been ignoring the presence of these cell surface kinases in the nucleus because it’s a small fraction of the signal; the expectations were that signaling is happening at the cell surface. But shifting where we perceive the basis of pathological function changes how we think about therapeutic vulnerability.”

The study expands the research community’s understanding of RNA polymerase II phosphorylation patterns and supports further exploration of the roles of individual cell signaling kinases in regulating different genes. It also provides new insights into how aberrant signaling pathways may contribute to disease.