MCDB noon seminar will be presented by Sreejita Dutta from the Craig Kaplan Lab and Douglas Swango from the Kane Lab. 

Friday, September 25, 2026
A219B Langley Hall
12:00PM EST

Seminar title and abstract:

Title: How RNA polymerase II activity alters the transcriptome?
Abstract: In eukaryotes, RNA polymerase II (Pol II) transcribes all protein-coding genes. During transcription, initiation generally determines where the 5′ end of the mRNA transcript will be, while the mRNA 3′ end is determined by where 3′-end processing happens. It has been previously established that both transcription start site (TSS) selection, which determines the position of Pol II initiation at the RNA 5′-end, and selection of the cleavage and polyadenylation site (PAS), which determines the position of the RNA 3′-end, are both sensitive to changes in Pol II activity. In collaboration with the Struhl lab at Harvard, we are using transcript end profiling to investigate how distinct Pol II mutants in regions across the enzyme alter either mRNA 5′ or 3′ ends. Profiling both ends of mRNA transcripts provides a high resolution readout to infer if individual Pol II mutants may have distinct biochemical defects, as reflected by distinct initiation or 3′ processing effects or both. Previous experiments established that Pol II catalytic mutants shift both TSS selection and 3′ processing site selection but do so in opposite directions. For instance, fast catalytic mutants shift TSSs upstream but shift PASs downstream and vice versa for slow catalytic mutants. In new work, we have now found some Pol II mutants that are selective for effects on one end of the transcript or the other, consistent with initiation (5′-end selective) or elongation (3′-end selective) effects. Our lab had previously established the use of specific growth phenotypes on plates that are predictive of TSS selection phenotypes. If a mutant shifts the TSS usage upstream, it will show sensitivity to a GTP depleting drug Mycophenolic Acid (MPA) and mutants which use downstream TSS will not show sensitivity to MPA. Intriguingly, one specific mutant in the Pol II subunit Rpb2, rpb2 H1141R, that showed strong downstream shifts to TSS selection exhibited strong sensitivity to MPA, which would have predicted upstream TSS shifts. Among 100s of mutants tested before in our lab we have never ever found a downstream mutant that is also MPA sensitive. I have fully validated this MPA sensitivity, suggesting that rpb2 H1141R has unique genetic phenotypes not previously observed in any other Pol II mutant. In addition, I have also characterized the classical rpb2-7 MPA sensitive allele of RPB2 by TSS profiling (TSS-seq2) and shown that it is highly selective for TSS selection effects but does not alter 3′ end formation. Using published Pol II structures, we suggest models for the biochemical defects of Pol II mutants that are selective for initiation and/or 3′ formation to understand what interactions are leading to the selectivity.