Renard Thibaut, Aron Serge
Evolutionary Biology and Ecology, Université Libre de Bruxelles, 1050 Brussels, Belgium.
Epigenomes. 2025 Sep 18;9(3):35. doi: 10.3390/epigenomes9030035.
BACKGROUND/OBJECTIVES: The DNA methylome allows environmental signals to be converted into stable and adaptive changes in gene expression. While 5-methylcytosine (5mC) has been extensively studied, alternative epigenetic marks such as N6-methyladenine (6mA) and 5-hydroxymethylcytosine (5hmC) remain poorly understood. Comparative studies of these marks are rare, and their results are often confounded by phylogeny, tissue type, developmental stage, or methodology. Here, we aimed to disentangle the constitutive, somatic- and germline-specific, and/or age-related patterns displayed by 6mA, 5mC, and 5hmC within a single species.
We generated long-read nanopore sequencing data for somatic tissues of buff-tailed bumblebee () males and their sperm, enabling simultaneous detection of 6mA, 5mC, and 5hmC. We used a stepwise approach to successively identify (i) constitutive patterns conserved between somatic tissues and sperm, (ii) differences between the soma and the germline, and (iii) age-related changes between young and old males.
We found distinct constitutive, somatic and sperm, and age-related specific signatures in the genomic contexts, maintenance fidelity, and biological functions associated with 6mA, 5mC, and 5hmC. Sperm cells consistently displayed lower methylation entropy than did somatic tissues, indicating more stable methylation patterns in the germline. 5mC exhibited the greatest variation across all genomic contexts; 6mA and 5hmC displayed less dramatic differences. The influence of age was subtler but revealed context-dependent remodeling of methylation, particularly for 5hmC.
We observed that 6mA, 5mC, and 5hmC displayed constitutive, somatic- and sperm-specific, and age-related differences that were associated with distinct genomic contexts and biological functions, supporting the complementarity of these methylation marks and their diverging epigenetic roles.
背景/目的：DNA甲基化组可使环境信号转化为基因表达中的稳定且适应性的变化。虽然5-甲基胞嘧啶（5mC）已得到广泛研究，但诸如N6-甲基腺嘌呤（6mA）和5-羟甲基胞嘧啶（5hmC）等其他表观遗传标记仍知之甚少。对这些标记的比较研究很少见，其结果常常因系统发育、组织类型、发育阶段或方法学而混淆。在此，我们旨在厘清单个物种内6mA、5mC和5hmC所呈现的组成性、体细胞和生殖系特异性以及/或与年龄相关的模式。
我们生成了雄蜂及其精子的体细胞组织的长读长纳米孔测序数据，能够同时检测6mA、5mC和5hmC。我们采用逐步方法依次识别：（i）体细胞组织和精子之间保守的组成性模式；（ii）体细胞与生殖系之间的差异；以及（iii）年轻和老年雄蜂之间与年龄相关的变化。
我们在与6mA、5mC和5hmC相关的基因组背景、维持保真度和生物学功能中发现了不同的组成性、体细胞和精子特异性以及与年龄相关的特异性特征。精子细胞的甲基化熵始终低于体细胞组织，表明生殖系中的甲基化模式更稳定。5mC在所有基因组背景中表现出最大的变化；6mA和5hmC的差异则不那么显著。年龄的影响较为微妙，但揭示了甲基化的上下文依赖性重塑，尤其是对于5hmC。
我们观察到6mA、5mC和5hmC呈现出组成性、体细胞和精子特异性以及与年龄相关的差异，这些差异与不同的基因组背景和生物学功能相关，支持了这些甲基化标记的互补性及其不同的表观遗传作用。
