Garg Jyoti, Saettone Alejandro, Nabeel-Shah Syed, Dang Steven, Khalid Abdul Hadi, Loehr Jérémy, Petrova Alexandra, Burns James D, Karabatsos Peter, Shibin Sherin, Wahab Suzanne, Taverna Sean D, Greenblatt Jack F, Lambert Jean-Philippe, Fillingham Jeffrey
Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada.
Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Epigenetics Chromatin. 2025 Aug 6;18(1):51. doi: 10.1186/s13072-025-00614-5.
INO80 and SWR1 are evolutionarily related ATP-dependent chromatin remodeling complexes that regulate the chromatin occupancy of the histone variant H2A.Z, playing critical roles in transcriptional regulation, genome replication, and DNA repair. While the H2A.Z-related functions of INO80 and SWR1 are well characterized in budding yeast and metazoans, much less is known about their composition and chromatin-targeting mechanisms outside of the Opisthokonts. We previously found that a distinct bromodomain-containing protein, IBD1, is involved in multiple chromatin-related complexes, including the SWR1-complex, in the ciliate protozoan Tetrahymena thermophila.
Here, we report that a closely related bromodomain-containing protein, IBD2, functions as an acetyl lysine reader module within a putative INO80 complex. Through iterative proteomic analyses, we show that the Tetrahymena INO80 complex retains several conserved subunits found in its yeast and metazoan counterparts. In vitro binding assays reveal that recombinant IBD2 preferentially recognizes acetylated histone H3 tails. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) demonstrates that IBD2 is enriched near transcription start sites and promoter regions. Notably, the IBD1 and IBD2 genomic binding profiles strongly correlate with that of H2A.Z (Hv1), supporting their functional association with the SWRI- and INO80-complexes.
Together, our findings support a model in which H2A.Z chromatin dynamics are modulated by SWR1- and INO80-complexes that are differentially recruited to chromatin via distinct bromodomain proteins that recognize specific histone acetylation marks.
INO80和SWR1是进化相关的ATP依赖性染色质重塑复合物，可调节组蛋白变体H2A.Z在染色质上的占据情况，在转录调控、基因组复制和DNA修复中发挥关键作用。虽然INO80和SWR1与H2A.Z相关的功能在芽殖酵母和后生动物中已得到充分表征，但在 opisthokonts之外，它们的组成和染色质靶向机制却知之甚少。我们之前发现，一种独特的含溴结构域蛋白IBD1参与了纤毛原生动物嗜热四膜虫中多种与染色质相关的复合物，包括SWR1复合物。
在此，我们报告一种密切相关的含溴结构域蛋白IBD2在一个假定的INO80复合物中作为乙酰赖氨酸读取模块发挥作用。通过迭代蛋白质组学分析，我们表明嗜热四膜虫INO80复合物保留了在其酵母和后生动物对应物中发现的几个保守亚基。体外结合试验表明，重组IBD2优先识别乙酰化组蛋白H3尾巴。染色质免疫沉淀结合高通量测序（ChIP-seq）表明，IBD2在转录起始位点和启动子区域附近富集。值得注意的是，IBD1和IBD2的基因组结合图谱与H2A.Z（Hv1）的图谱高度相关，支持它们与SWRI和INO80复合物的功能关联。
总之，我们的研究结果支持一个模型，即H2A.Z染色质动力学由SWR1和INO80复合物调节，这些复合物通过识别特定组蛋白乙酰化标记的不同溴结构域蛋白被差异性招募到染色质上。
