The interplay of histone H2B ubiquitination with budding and fission yeast heterochromatin

Abstract

Mono-ubiquitinated histone H2B (H2B-Ub) is important for chromatin regulation of transcription, chromatin assembly, and also influences heterochromatin. In this review, we discuss the effects of H2B-Ub from nucleosome to higher-order chromatin structure. We then assess what is currently known of the role of H2B-Ub in heterochromatic silencing in budding and fission yeasts (S. cerevisiae and S. pombe), which have distinct silencing mechanisms. In budding yeast, the SIR complex initiates heterochromatin assembly with the aid of a H2B-Ub deubiquitinase, Ubp10. In fission yeast, the RNAi-dependent pathway initiates heterochromatin in the context of low H2B-Ub. We examine how the different silencing machineries overcome the challenge of H2B-Ub chromatin and highlight the importance of using these microorganisms to further our understanding of H2B-Ub in heterochromatic silencing pathways.

Keywords: Epigenetics; Heterochromatin; SIR complex; Silencing; Ubiquitination; Ubp10.

Figure 1. The influence of H2B-Ub on chromatin structure and higher-order folding

a. Ubiquitination and deubiquitination regulates H2B-Ub on nucleosomes. (Top) Rad6/Bre1 conjugates ubiquitin onto H2B. (Bottom) In vitro H2B-Ub nucleosomes are stable and resist interactions within a chromatin array (sideways arrows) and between chromatin arrays (up and down arrows). H2B-Ub chromatin exhibits characteristics of an open chromatin structure. Bulk ubiquitinated chromatin in ubp10• and ubp8• cells resists salt-dependent solubilization and exhibits disrupted telomeric silencing. b. (Top) Deubiquitinases, Ubp10 or Ubp8 in budding yeast, cleave H2B-Ub. (Bottom) Lack of ubiquitination results in decreased nucleosome occupancy on chromatin. This phenotype is observed in htb-K123R (budding yeast) or htb-K119R (fission yeast) cells. In vitro unmodified nucleosomes tend to interact within a chromatin array (sideways arrows) and between chromatin arrays (up and down arrows). c. It is unclear if H2B-Ub chromatin can directly influence silencing machinery binding or if Rad6/Bre1 is specifically excluded from silent chromatin.

Figure 2. The role of H2B-Ub in yeast heterochromatic silencing

a. In budding yeast, SIR complex can deacetylate H4K16 but it cannot silence chromatin with H3 methylation present. H2B-Ub promotes downstream methylation of H3K4 and H3K79, thereby indirectly antagonizing SIR complex-dependent silencing. This presents a problem for SIR complex de novo heterochromatin formation of an active region. b. At sub-telomeric regions SIR complex nucleates near the telomeres from recruitment factors (RF). The sub-telomeric regions experience more dynamic forces than at the silent mating-type loci, including occasional transcription by Pol II. Competition between factors that promote silencing (ex. Ubp10) and those that promote transcription (ex. Rad6/Bre1) are constantly at play. c. The silent mating-type is a region of natural or “strong” silencing due to flanking silencer sequences that promote nucleation of SIR complex towards each other. This is a region of established heterochromatin that prevents transcriptional events, limiting the need to recruit Ubp10. D. A schematic of the pathways involved in RNAi-dependent silencing in fission yeast and the interplay with H2B-Ub. Complexes and activities are color-coded to match functional analogs/homologs found in budding yeast. These pathways are described in more detail in the text. Panels A-C adapted from (Zukowski et al. 2017).