Guan Yalin, Chen Xiaomei, Zhu Xuan, Liu Fuyun, Ma Yuanting, Han Wentao, Yang Rui, Li Yuli, Bao Lisui, Wang Shi, Bao Zhenmin, Wang Jing
Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding & Shandong Key Laboratory of Marine Seed Industry, Ocean University of China, Qingdao, 266003, China.
Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
BMC Genomics. 2025 Jul 1;26(1):594. doi: 10.1186/s12864-025-11776-7.
Histones are the basic packaging units of eukaryotic DNA and are essential for the dynamics of chromatin and the regulation of epigenetics. Canonical histones and their variants exhibit important functional differences in biological processes. However, little is known about the role of histone family members in molluscs, which are known for their ecological and morphological diversity.
Core histone families of 28 molluscan species (12 bivalves, 8 gastropods, 6 cephalopods, 1 scaphopod and 1 polyplacophora) were systematically identified. The evolutionary conservation and lineage-specific innovations were discovered using phylogenomic and transcriptomic analyses. Cephalopods showed a striking expansion of canonical histone genes with brain-enriched expression patterns. Synteny analyses revealed conserved, collinear histone clusters unique to cephalopods. Histone variants, specially H2A and H3 paralogs, display conserved motifs potentially involved in nucleosome stability and lineage-specific residues involved in functional specialization. Developmental transcriptomics revealed the dynamic expression of histone variants in early embryogenesis and the gonads, suggesting that H2A and H3 variants are involved in chromatin remodeling, pluripotency maintenance and germline regulation. Macro-H2A was highly expressed during larval neurodevelopment and in sensory organs, suggesting important roles in neural plasticity.
This study represents the first comprehensive inventory and characterization of core histone genes in molluscs, and will facilitate understanding of the evolutionary patterns and functional properties of core histones in relation to neurogenesis of molluscs. These findings advance our understanding of chromatin evolution and its contribution to phenotypic innovation in non-model taxa.
组蛋白是真核生物DNA的基本包装单位，对染色质动态变化和表观遗传调控至关重要。经典组蛋白及其变体在生物学过程中表现出重要的功能差异。然而，对于以生态和形态多样性著称的软体动物中组蛋白家族成员的作用知之甚少。
系统鉴定了28种软体动物（12种双壳类、8种腹足类、6种头足类、1种掘足类和1种多板类）的核心组蛋白家族。通过系统发育基因组学和转录组学分析发现了进化保守性和谱系特异性创新。头足类显示出经典组蛋白基因的显著扩增，且具有大脑富集的表达模式。共线性分析揭示了头足类特有的保守、共线组蛋白簇。组蛋白变体，特别是H2A和H3旁系同源物，显示出可能参与核小体稳定性的保守基序以及参与功能特化的谱系特异性残基。发育转录组学揭示了组蛋白变体在早期胚胎发育和性腺中的动态表达，表明H2A和H3变体参与染色质重塑、多能性维持和生殖系调控。巨H2A在幼虫神经发育和感觉器官中高表达，表明其在神经可塑性中起重要作用。
本研究首次全面盘点和表征了软体动物中的核心组蛋白基因，将有助于理解核心组蛋白与软体动物神经发生相关的进化模式和功能特性。这些发现推进了我们对染色质进化及其对非模式类群表型创新贡献的理解。
