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Recruitment of Saccharomyces cerevisiae Cmr1/Ydl156w to coding regions promotes transcription genome wide

ABSTRACT: Cmr1 (changed mutation rate 1) is a largely uncharacterized nuclear protein that has recently emerged in several global genetic interaction and protein localization studies. It clusters with proteins involved in DNA damage and replication stress response, suggesting a role in maintaining genome integrity. Under conditions of proteasome inhibition or replication stress, this protein localizes to distinct sub-nuclear foci termed as intranuclear quality control (INQ) compartments, which sequester proteins for their subsequent degradation. Interestingly, it also interacts with histones, chromatin remodelers and modifiers, as well as with proteins involved in transcription including subunits of RNA Pol I and Pol III, but not with those of Pol II. It is not known whether Cmr1 plays a role in regulating transcription of Pol II target genes. Here, we show that Cmr1 is recruited to the coding regions of transcribed genes of S. cerevisiae. Cmr1 occupancy correlates with the Pol II occupancy genome-wide, indicating that it is recruited to coding sequences in a transcription-dependent manner. Cmr1-enriched genes include Gcn4 targets and ribosomal protein genes. Furthermore, our results show that Cmr1 recruitment to coding sequences is stimulated by Pol II CTD kinase, Kin28, and the histone deacetylases, Rpd3 and Hos2. Finally, our genome-wide analyses implicate Cmr1 in regulating Pol II occupancy at transcribed coding sequences. However, it is dispensable for maintaining co-transcriptional histone occupancy and histone modification (acetylation and methylation). Collectively, our results show that Cmr1 facilitates transcription by directly engaging with transcribed coding regions. ChIp-chip experiments were perfomed to determine genome-wide distribution of Cmr1 in WT and gcn4Δ cells (S. cerevisiae). Rpb3 occupancy in WT and cmr1Δ cells was also determined to reveal the changes in Pol II occupancy in the absence of Cmr1.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE77016 | GEO | 2016/07/01

SECONDARY ACCESSION(S): PRJNA309286

REPOSITORIES: GEO

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Project description:Cmr1 (changed mutation rate 1) is a largely uncharacterized nuclear protein that has recently emerged in several global genetic interaction and protein localization studies. It clusters with proteins involved in DNA damage and replication stress response, suggesting a role in maintaining genome integrity. Under conditions of proteasome inhibition or replication stress, this protein localizes to distinct sub-nuclear foci termed as intranuclear quality control (INQ) compartments, which sequester proteins for their subsequent degradation. Interestingly, it also interacts with histones, chromatin remodelers and modifiers, as well as with proteins involved in transcription including subunits of RNA Pol I and Pol III, but not with those of Pol II. It is not known whether Cmr1 plays a role in regulating transcription of Pol II target genes. Here, we show that Cmr1 is recruited to the coding regions of transcribed genes of S. cerevisiae. Cmr1 occupancy correlates with the Pol II occupancy genome-wide, indicating that it is recruited to coding sequences in a transcription-dependent manner. Cmr1-enriched genes include Gcn4 targets and ribosomal protein genes. Furthermore, our results show that Cmr1 recruitment to coding sequences is stimulated by Pol II CTD kinase, Kin28, and the histone deacetylases, Rpd3 and Hos2. Finally, our genome-wide analyses implicate Cmr1 in regulating Pol II occupancy at transcribed coding sequences. However, it is dispensable for maintaining co-transcriptional histone occupancy and histone modification (acetylation and methylation). Collectively, our results show that Cmr1 facilitates transcription by directly engaging with transcribed coding regions. ChIp-chip experiments were perfomed to determine genome-wide distribution of Cmr1 in WT and gcn4Î cells (S. cerevisiae). Rpb3 occupancy in WT and cmr1Î cells was also determined to reveal the changes in Pol II occupancy in the absence of Cmr1. The WT and mutant strains were grown in Synthetic complete and cells were indcued for Gcn4 by treating with Sulfometuron methyl for 30 minutes and processed for chromatin immunoprecipitation using antibodies against Myc and Rpb3 (subunit of Pol II).

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Recruitment of Saccharomyces cerevisiae Cmr1/Ydl156w to coding regions promotes transcription genome wide

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