Direct targeting and regulation of RNA polymerase II by cell signaling kinases Science

Although the functional roles of phospho-Ser2 and phospho-Ser5 and the kinases that place those marks have been extensively studied, the functions of the three so-called "orphan" residues (Tyr1, Thr4, and Ser7) and the identity of kinases that modify those sites remain poorly defined. Unbiased mass spectrometric mapping of the CTD revealed that the orphan sites are phosphorylated, and non-CDK kinases, such as HRR25, PLK3, and ABL1, modify those residues. Notably, unlike Ser2 or Ser5, whose phosphorylation has broad effects, mutations of the orphan residues or inhibition of kinases that act on them selectively disrupt the expression of limited sets of genes. The pathways mapped to those genes suggest that of the 250 phospho-acceptor residues that are densely packed within 360 residues of the human CTD, nearly 150 orphan sites may be used by other kinases to selectively regulate distinct sets of functionally coherent genes. To bridge the knowledge gap and identify previously unknown CTD-active kinases, we used three orthogonal kinome testing platforms in conjunction with machine learning algorithms to predict kinase-substrate pairings.