Protocol matters – reproducibility and rigor of DNA methylation data sets [BiSulfite-seq]

While epigenetics continues to be a burgeoning research area in neuroscience, unaddressed issues related to data reproducibility across laboratories remain. Indeed, separating meaningful experimental changes from background variability is a challenge in epigenomic studies. Genome-wide DNA methylation analysis of hippocampal tissues from wild-type rats across three independent laboratories revealed that seemingly minor protocol differences resulted in significant epigenome profile changes, even in the absence of experimental intervention. Difficult-to-match factors such as animal vendors and a subset of husbandry and tissue extraction procedures produced quantifiable variations between wild-type animals across the three laboratories. To enhance scientific rigor, we conclude that strict adherence to protocols is necessary for the execution and interpretation of epigenetic studies and that protocol-sensitive epigenetic changes, amongst naive animals, may confound experimental results.表观遗传学（epigenetics）始终是神经科学领域蓬勃发展的新兴研究方向，但跨实验室数据可重复性相关的未解决问题依然存在。事实上，在表观基因组学研究中，将具有生物学意义的实验变化与背景变异区分开来仍是一项挑战。对三家独立实验室的野生型大鼠海马组织开展全基因组DNA甲基化分析后发现，即便未施加任何实验干预，看似细微的实验方案差异也会导致表观基因组谱发生显著改变。诸如动物供应商、部分饲养管理流程及组织提取步骤等难以统一管控的因素，导致三家实验室间野生型大鼠样本出现了可量化的差异。为提升科研严谨性，本研究得出结论：开展表观遗传学研究并对其结果进行解读时，必须严格遵循实验方案；同时，未经实验干预的动物中，受实验方案影响的表观遗传变化可能会干扰实验结果。