The Deubiquitylase Ubp15 Couples Transcription to mRNA Export

The nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed and exported. The role of ubiquitylation in this process is increasingly recognized as the ubiquitylation of many key players have been shown to affect mRNA nuclear export. While a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here, we identified the deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts both with RNA polymerase II and with the nuclear pore complex, and its deletion reverts the nuclear export defect of mutants of the E3 ligase Rsp5. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export. We profiled RNAPII (Rpb3) in WT, ubp15Δ, dst1Δ and ubp15Δ/dst1Δ cells treated or not with 100 µg/mL of 6-azauracil for 60 min in yeast Saccharomyces cerevisiae by ChIP-chip on tiling arrays. All ChIP samples were labeled with Cy5 and hybridized against Input DNA (labeled with Cy3). The microarrays used were described before (Jeronimo and Robert, 2014). The data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384). Each experiment was done in duplicate, except for the Rpb3 ChIP in non-treated ubp15Δ/dst1Δ cells.