A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress
Verena Hurst, Kiran Challa, Felix Jonas, Romain Forey, Ragna Sack, Jan Seebacher, Christoph D. Schmid, Naama Barkai, Kenji Shimada, Susan M. Gasser, Jérôme Poli
Abstract
Upon replication stress, budding yeast checkpoint kinase Mec1ATR triggers the downregulation of transcription, thereby reducing the level of RNA polymerase (RNAP) on chromatin to facilitate replication fork progression. Here, we identify a hydroxyurea‐induced phosphorylation site on Mec1, Mec1‐S1991, that contributes to the eviction of RNAPII and RNAPIII during replication stress. The expression of the non‐phosphorylatable mec1‐S1991A mutant reduces replication fork progression genome‐wide and compromises survival on hydroxyurea. This defect can be suppressed by destabilizing chromatin‐bound RNAPII through a TAP fusion to its Rpb3 subunit, suggesting that lethality in mec1‐S1991A mutants arises from replication–transcription conflicts. Coincident with a failure to repress gene expression on hydroxyurea in mec1‐S1991A cells, highly transcribed genes such as GAL1 remain bound at nuclear pores. Consistently, we find that nuclear pore proteins and factors controlling RNAPII and RNAPIII are phosphorylated in a Mec1‐dependent manner on hydroxyurea. Moreover, we show that Mec1 kinase also contributes to reduced RNAPII occupancy on chromatin during an unperturbed S phase by promoting degradation of the Rpb1 subunit. Transcriptional downregulation upon replication stress through the yeast Mec1/ATR kinase helps to limit replication‐transcription conflicts. We show here that this involves the removal of chromatin‐bound RNA polymerases (RNAP) triggered by hydroxyurea‐induced Mec1 phosphorylation on Serine 1991. Hydroxyurea directly triggers a checkpoint kinase Mec1/ATR function for limiting replication‐transcription conflicts in budding yeast.