Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa.
Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa.
PLoS One. 2022 May 27;17(5):e0268760. doi: 10.1371/journal.pone.0268760. eCollection 2022.
We have performed a comprehensive analysis of the involvement of histone H3 and H4 residues in the regulation of chronological lifespan in yeast and identify four structural groups in the nucleosome that influence lifespan. We also identify residues where substitution with an epigenetic mimic extends lifespan, providing evidence that a simple epigenetic switch, without possible additional background modifications, causes longevity. Residues where substitution result in the most pronounced lifespan extension are all on the exposed face of the nucleosome, with the exception of H3E50, which is present on the lateral surface, between two DNA gyres. Other residues that have a more modest effect on lifespan extension are concentrated at the extremities of the H3-H4 dimer, suggesting a role in stabilizing the dimer in its nucleosome frame. Residues that reduce lifespan are buried in the histone handshake motif, suggesting that these mutations destabilize the octamer structure. All residues exposed on the nucleosome disk face and that cause lifespan extension are known to interact with Sir3. We find that substitution of H4K16 and H4H18 cause Sir3 to redistribute from telomeres and silent mating loci to secondary positions, often enriched for Rap1, Abf1 or Reb1 binding sites, whereas H3E50 does not. The redistribution of Sir3 in the genome can be reproduced by an equilibrium model based on primary and secondary binding sites with different affinities for Sir3. The redistributed Sir3 cause transcriptional repression at most of the new loci, including of genes where null mutants were previously shown to extend chronological lifespan. The transcriptomic profiles of H4K16 and H4H18 mutant strains are very similar, and compatible with a DNA replication stress response. This is distinct from the transcriptomic profile of H3E50, which matches strong induction of oxidative phosphorylation. We propose that the different groups of residues are involved in binding to heterochromatin proteins, in destabilizing the association of the nucleosome DNA, disrupting binding of the H3-H4 dimer in the nucleosome, or disrupting the structural stability of the octamer, each category impacting on chronological lifespan by a different mechanism.
我们对组蛋白 H3 和 H4 残基在酵母生物钟寿命调控中的作用进行了全面分析，确定了核小体中影响寿命的四个结构群。我们还确定了用表观遗传模拟物取代可以延长寿命的残基，这为简单的表观遗传开关提供了证据，而无需可能的额外背景修饰，从而导致长寿。导致寿命显著延长的取代残基都位于核小体的暴露面上，除了位于两个 DNA 旋回之间侧向表面的 H3E50 外。对延长寿命有更适度影响的其他残基集中在 H3-H4 二聚体的末端，这表明它们在稳定二聚体在核小体框架中的作用。减少寿命的残基埋藏在组蛋白握手结构域中，表明这些突变会使八聚体结构不稳定。暴露在核小体盘面上并导致寿命延长的所有残基都已知与 Sir3 相互作用。我们发现，H4K16 和 H4H18 的取代导致 Sir3 从端粒和沉默交配位点重新分布到次要位置，这些位置通常富含 Rap1、Abf1 或 Reb1 结合位点，而 H3E50 则不会。基于对 Sir3 具有不同亲和力的初级和次级结合位点的平衡模型可以再现 Sir3 在基因组中的再分布。重新分布的 Sir3 可导致大多数新基因座的转录抑制，包括先前显示缺失突变可延长生物钟寿命的基因。H4K16 和 H4H18 突变株的转录组谱非常相似，与 DNA 复制应激反应兼容。这与 H3E50 的转录组谱明显不同，后者与氧化磷酸化的强烈诱导相匹配。我们提出，不同组的残基参与与异染色质蛋白的结合，破坏核小体 DNA 的缔合，破坏核小体中 H3-H4 二聚体的结合，或破坏八聚体的结构稳定性，每个类别都通过不同的机制影响生物钟寿命。
