The Nucleosome Acidic Patch Regulates the H2B K123 Monoubiquitylation Cascade and Transcription Elongation in Saccharomyces cerevisiae

Abstract

Eukaryotes regulate gene expression and other nuclear processes through the posttranslational modification of histones. In S. cerevisiae, the mono-ubiquitylation of histone H2B on lysine 123 (H2B K123ub) affects nucleosome stability, broadly influences gene expression and other DNA-templated processes, and is a prerequisite for additional conserved histone modifications that are associated with active transcription, namely the methylation of lysine residues in H3. While the enzymes that promote these chromatin marks are known, regions of the nucleosome required for the recruitment of these enzymes are undefined. To identify histone residues required for H2B K123ub, we exploited a functional interaction between the ubiquitin-protein ligase, Rkr1/Ltn1, and H2B K123ub in S. cerevisiae. Specifically, we performed a synthetic lethal screen with cells lacking RKR1 and a comprehensive library of H2A and H2B residue substitutions, and identified H2A residues that are required for H2B K123ub. Many of these residues map to the nucleosome acidic patch. The substitutions in the acidic patch confer varying histone modification defects downstream of H2B K123ub, indicating that this region contributes differentially to multiple histone modifications. Interestingly, substitutions in the acidic patch result in decreased recruitment of H2B K123ub machinery to active genes and defects in transcription elongation and termination. Together, our findings reveal a role for the nucleosome acidic patch in recruitment of histone modification machinery and maintenance of transcriptional integrity.

Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6–Bre1

“…This result is also observed upon mutating H2A Glu93, a residue located toward the center of the NCP disk (Figs. 1C and 5D, lanes 2 and 6), and is consistent with a previous report (23). In marked contrast, H2A Glu57 and Glu65 mutations showed increased H2B Lys123∼Ub levels.…”

“…It was previously suggested that acidic histone residues are required to maintain normal cellular H2B∼Ub levels in Saccharomyces cerevisiae (22,23). However, it has remained unclear whether those residues mediate a direct physical interaction with Rad6-Bre1, or whether their mutation indirectly perturbs chromatin architecture or affects other transcription components.…”

Quantitative Analysis of Dynamic Protein Interactions during Transcription Reveals a Role for Casein Kinase II in Polymerase-associated Factor (PAF) Complex Phosphorylation and Regulation of Histone H2B Monoubiquitylation

“…6A). No changes in histone H3K4 methylation levels were observed, which is in line with studies that show that reduced H2B-K123ub1 levels can occur without significant effects on H3K4 methylation (56). Taken together, these data show that CKII is an important regulator of histone H2B-K123ub1, likely through its regulation of PAF-C and FACT.…”

Recognition of the nucleosome by chromatin factors and enzymes

“…Another E3 ligase, RNF168, may not bind directly to the H2A/H2B acidic patch, but nonetheless requires an intact H2A/H2B acidic patch for nucleosome and H2A/H2B dimer ubiquitylation [33,34]. In S. cerevisiae , acidic patch mutations disrupt histone modification patterns including H2B K123 ubiquitylation and downstream H2A K4 and K79 methylation [54,55]. It remains to be determined whether arginine anchors are used by these histone modifying enzymes in establishing these marks.…”