Crosstalk between the RNA methylation and histone binding activities of MePCE regulates P-TEFb activation on chromatin

The switch of RNAP II from the paused to the productive transcription elongation state is a pivotal regulatory step requiring specific phosphorylations catalyzed by the P-TEFb kinase. Nucleosolic P-TEFb activity is inhibited by its interaction with the ribonuclear protein complex built around the 7SK small nuclear RNA (7SK snRNP). MePCE is the RNA methyltransferase that methylates and stabilizes 7SK in the nucleosol. Here we report that MePCE also binds chromatin through the tail of histone H4 to serve as a P-TEFb activator at specific genes important for cellular identity. Notably, this histone binding abolishes MePCE’s RNA methyltransferase activity towards 7SK, explaining why MePCE-bound P-TEFb on chromatin may not be associated with the full 7SK snRNP and is competent for RNAP II activation. Overall, our results suggest that a crosstalk between the histone binding and RNA methylation activities of MePCE regulates P-TEFb activation on chromatin in a 7SK- and Brd4-independent manner. RNA-Seq was performed in MDA-MB-231 shNC (Negative Control) and shMePCE cells. Concomitantly, ChIP-seq was performed in these same cells with antibodies specifically recognizing RNA Polymerase II phosphorylated at S2 or S5 of its CTD, the N-ter of MePCE, as well as GFP (Negative Control) and H3K4me3 (Positive Control). Because, the ChIP-Seq with the MePCE antibody does not work well for single gene inspection, we performed additional ChIP-seq with the MePCE antibody in HeLa-S3-FlpIn cells.