Abstract
Hexim proteins are RNA-dependent regulators whose main target is 7SK long non-coding RNA, a major regulator of eukaryotic mRNA transcription. 7SK RNPs control available intracellular concentrations of the kinase P-TEFb (Cdk9-CyclinT1/2) by sequestering it in an inactive form. Active P-TEFb phosphorylates NELF, DSIF, and the RNA polymerase II CTD to transition it from promoter-proximal pausing to productive elongation. P-TEFb associates with 7SK RNP via Hexim, which directly binds 7SK RNA. However, free Hexim is in an autoinhibited state that cannot inactivate P-TEFb, and how Hexim autoinhibition is released by 7SK remains unknown. Here, we show that one Hexim1 homodimer binds two sites on linear 7SK RNA in a manner that exposes the Cdk9 binding sites, which are otherwise masked within the autoinhibited dimer. These results provide mechanistic insights into Hexim-RNA specificity and explain how P-TEFb can be effectively regulated to respond to changing levels of transcriptional signaling.