Understanding how mRNA levels are controlled in eukaryotes requires dissection of the intricate pathways responsible for the synthesis and processing of mRNA. Previously, we uncovered evidence for a regulatory process in higher eukaryotes that controls the fraction of initiated RNA polymerase II (Pol II) molecules able to produce full-length mRNAs. We then discovered P-TEFb, a cyclin dependent kinase that plays a key role in this elongation control process. The kinase activity of P-TEFb is generally required for eukaryotic gene expression and thus P-TEFb function is highly regulated. We are currently engaged in projects to more fully understand the mechanisms utilized in Pol II elongation control. In this regard we continue to employ viruses that infect human cells because they reveal unexpected ways to exploit elongation control. For example, the AIDS retrovirus, HIV, encodes a protein, Tat, that enables the virus to take over the control of P-TEFb. We have begun to work with Jeff Meier (Internal Medicine) to examine the transcriptional life cycle of the human cytomegalovirus (HCMV). Transcription and RNA processing are temporally and mechanistically intertwined and we persist in investigating how the two processes affect each other. We are also collaborating with Donal Luse (Cleveland Clinic) concerning the interplay of the elongation control machinery and chromatin. We employ in vitro assays in which the function of specific factors can be evaluated and have recently taken advantage of isolated nuclei to accurately report on transcription and RNA processing in cells. Using CRISPR genome editing technology and small molecules that inhibit or degrade specific proteins we can manipulate cells and follow up with nucleotide-resolution bioinformatics analysis of the pattern of transcription in the isolated nuclei. These and other innovative techniques provide us with unique opportunities to advance our understanding of the molecular mechanisms that control gene expression. The studies are useful in the development of therapies for viral infections and cancer.