Decoding a combinatorial RNA polymerase II CTD grammar that specifies protein-coding gene transcription and mRNA export [ChIP-seq]

The C-terminal domain (CTD) of RNA polymerase II orchestrates transcription via specific post-translational modifications (PTMs), notably phosphorylation. The combinatorial phosphorylation of CTD can potentially encode the precise recruitment of transcription machinery, but lacks robust evidence. Addressing the challenge of detecting combinatorial CTD phosphorylation in cells without specific antibodies, we developed a novel genome-wide approach exploiting antibody masking and selective interference removal to identify dual phosphorylation patterns. Using this method, we uncovered pT4pS5 phosphosites occurring exclusively during protein-coding gene transcription but excluded in non-coding genes. Using multiple sequencing methods, the role of T4 phosphorylation in elongation is highlighted. Particularly, pT4pS5 marks recruit the Transcription and Export complex to facilitate mRNA export. These findings provide robust evidence that CTD operates as a combinatorial, gene-specific coding system, encoding precise transcriptional instructions. Our approach offers a versatile framework for mapping all combinatorial PTMs on RNA polymerase II, advancing molecular insights into gene-specific transcriptional regulation.