The role of histone ubiquitylation and deubiquitylation in gene expression as determined by the analysis of an HTB1 K123R Saccharomyces cerevisiae strain

Abstract

In Saccharomyces cerevisiae histone H2B is ubiquitylated at lysine 123 in a process requiring the E2-ubiquitin conjugase, Rad6. We have analyzed gene expression in a strain containing a variant of histone H2B with lysine 123 converted to arginine to address the mechanisms by which ubiquitylation and deubiquitylation of histone H2B affect gene expression. The SAGA complex component, Ubp8, is one of two proteases that remove the ubiquitin moiety at lysine 123. We show that changes in gene expression observed upon deletion of ubp8 are suppressed by htb1 K123R , which provides genetic evidence that Ubp8 alters gene expression through deubiquitylation of histone H2B. Microarray analyses of the htb1 K123R strain show that loss of histone ubiquitylation results in a twofold or greater change in expression of ∼1.5% of the protein coding genes with ∼75% of these increasing. For genes in which ubiquitylation represses expression, ubiquitylation principally acts through its effects on histone methylation. In contrast, decreased expression of the CWP1 gene was not paralleled by deletions of methyltransferase components and is thus likely independent of methylation. Finally, by comparing gene expression changes in the htb1 K123R strain with those in a strain deleted for rad6, we conclude that lysine 123 affects transcription primarily because of it being a site of ubiquitylation.

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Acknowledgments

We would like to thank Amy Tong and Drs. Brenda Andrews and Charlie Boone for providing reagents as well as Megan Davey, David Edgell, Eric Ball, Kerri Kobryn, and David Haniford for their discussions on this manuscript. Unpublished microarray data was kindly supplied by Drs. F. Devaux and WS Moye-Rowley. Special thanks to Karen Kennedy for technical assistance. This work was supported by a Canadian Institutes of Health Research operating grant to CJB (MT10845). SMTH is supported by a NSERC (Canada) Studentship. AIM and GL were supported by Western Graduate Research Scholarships.

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Correspondence to Christopher J. Brandl.

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Communicated by A. Aguilera.

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Mutiu, A.I., Hoke, S.M.T., Genereaux, J. et al. The role of histone ubiquitylation and deubiquitylation in gene expression as determined by the analysis of an HTB1 K123R Saccharomyces cerevisiae strain. Mol Genet Genomics 277, 491–506 (2007). https://doi.org/10.1007/s00438-007-0212-6

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Keywords

  • Transcription
  • Yeast
  • Ubp8
  • Histone deubiquitylation
  • SAGA complex