Every cell in the human body contains almost the same genetic material, therefore, cellular identity is derived from the selection of genes transcribed into RNA and the mRNAs that are made into proteins. To achieve precise control of gene expression, the transcription of messenger RNAs by RNA polymerase II is regulated at multiple checkpoints. A major control point within this system is the P-TEFb dependent transition from paused to productive elongating polymerase complexes. Reversible inhibition of P-TEFb by the 7SK small nuclear ribonucleoprotein (snRNP) is the key step in the control of transcription elongation.
Due to the importance of the regulation of P-TEFb, this research investigates the structure of 7SK RNA and the interactions within the 7SK snRNP. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) was used to demonstrate a magnesium-dependent conformational change of in vitro transcribed 7SK RNA folding including a switch in the pairing of the 7SK motif, which is required for P-TEFb regulation. SHAPE was also used to determine that the 5′ end of 7SK pairs alternatively with two different regions within the RNA resulting in open and closed conformations. Moreover, SHAPE was used to show a similar conformational change in cellular 7SK snRNP complexes after the loss of P-TEFb. Assembly of the 7SK snRNP in vitro, using recombinant HEXIM1, P-TEFb, LARP7, MEPCE, and in vitro transcribed 7SK RNA were combined under optimized conditions, resulted in a complete and functional complex. These complexes demonstrated a reversible inhibition of the activity of P-TEFb as well as a similar structure to cellular complexes. LARP7 was found to contain a C-terminal MEPCE interaction domain (MID) that associates with and inhibits MEPCE after binding to the 3′ stem loop of 7SK. The inhibition of MEPCE was determined to be dependent on the overall conformation of 7SK and structural elements of the 3′ stem loop. Use of a highly selective degrader of Brd4, dBET6, also revealed a possible alternative mechanism for P-TEFb sequestration into the 7SK snRNP. Collectively, these findings aid in the understanding of gene regulation through the control of P-TEFb by the 7SK snRNP.