INO80 Chromatin Remodeler Facilitates Release of RNA Polymerase II from Chromatin for Ubiquitin-Mediated Proteasomal Degradation

Abstract

SUMMARY Stalling of RNA Polymerase II (RNAPII) on chromatin during transcriptional stress results in polyubiquitination and degradation of the largest subunit of RNAPII, Rpb1, by the ubiquitin proteasome system (UPS). Here, we report that the ATP-dependent chromatin remodeling complex INO80 is required for turnover of chromatin-bound RNAPII in yeast. INO80 interacts physically and functionally with Cdc48/p97/VCP, a component of UPS required for degradation of RNAPII. Cells lacking INO80 are defective in Rpb1 degradation and accumulate tightly bound ubiquitinated Rpb1 on chromatin. INO80 forms a ternary complex with RNAPII and Cdc48 and targets Rpb1 primed for degradation. The function of INO80 in RNAPII turnover is required for cell growth and survival during genotoxic stress. Our results identify INO80 as a bona fide component of the proteolytic pathway for RNAPII degradation and suggest that INO80 nucleosome remodeling activity promotes the dissociation of ubiquitinated Rpb1 from chromatin to protect the integrity of the genome.

Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress

“…On the other hand, INO80C is found at ARS elements and may play a role in normal fork elongation through chromatin (Shimada et al 2008). Our data suggest that INO80C contributes to RNAPII eviction and degradation following HU treatment and extend a study that links INO80C to Cdc48 and the proteasome for the removal of RNAPII from chromatin in the presence of MMS (Lafon et al 2015). Interestingly, DNA damageindependent degradation of RNAPII seems to occur on chromatin, since Cdc48 and several subunits of the proteasome are recruited to transcribed genes (Verma et al 2011;Karakasili et al 2015).…”

“…It has recently been proposed that damage-stalled RNAPII is stably associated to chromatin and requires both INO80 and the proteasome to be removed from the DNA template (Lafon et al 2015). To investigate whether the RNAPII degradation that we scored upon replicative stress is proteasome-mediated, we measured RNAPII association to chromatin after HU treatment in a pre1-1 pre2-2 strain, which has severe defects in the 26S-mediated proteolysis.…”

“…Based on the observation that eviction and degradation of RNAPII are coupled upon HU treatment and the fact that both Mec1 and INO80 deal with damage-stalled RNAPII (Taschner et al 2010;Lafon et al 2015), we next checked whether Mec1 was required for RNAPII degradation upon HU treatment. Indeed, consistent with its role in RNAPII removal, Mec1 was also required for degradation of RNAPII in HU (Fig.…”

Rescue from replication stress during mitosis

“…A recent study has shown that the yeast ortholog of ATR, Mec1, together with the chromatin remodeler INO80 trigger the removal of RNA polymerase II from chromatin in HU-treated cells to avoid collisions between the transcription and replication machineries 101 . An independent study has also highlighted the role of INO80 in RNA polymerase II release from chromatin under conditions of transcriptional stress 102 . Interference between transcription and replication may also result in complementary binding between the newly synthesized RNA and one of the 2 replicating DNA strands 103, 104 .…”

The INO80 complex activates the transcription of S‐phase genes in a cell cycle‐regulated manner

“…The INO80 chromatin remodeling complex has roles in the regulation of transcription, DNA repair and DNA replication [14][15][16][17]. The Ino80 ATPase is a member of the SNF2 family of ATPases and functions as an integral component of a multisubunit ATPdependent chromatin remodeling complex [18].…”