SpermBase - A database for sperm-borne RNA contents

Purpose: Sperm-borne RNA are particularly sensitive to degradation and methodology-induced bias, thus necessitating the use of a consistent, effective RNA extraction protocol for inter-species comparisons. To this end, we established SpermBase, an RNA expression database consisting of small and large RNA expression data obtained using consistent methodologies. Methods: Total RNA was extracted from total sperm and sperm head samples using an RNA extraction protocol that required only slight, species-specific alterations at the lysis stage. Total RNA was subjected to either RNA-Seq (large RNA) or sncRNA-Seq (small RNA). Results: By using a consistent methodology, we were able to perform a cross-species analysis on the conserved features of large and small sperm-borne RNAs. We identified conserved features in both populations of RNAs in the four mammalian species (i.e., mouse, rabbit, rat, and human) surveyed. Conclusions: Our study demonstrates an effective, near-universal approach to the study of sperm-borne RNAs, and identifies conserved characteristics in the large and small RNA populations of mammalian sperm. Total RNA was extracted from total sperm and sperm head samples and subjected to sncRNA-Seq or RNA-Seq.研究背景：精子源性RNA极易发生降解，且易受实验方法引入的偏倚影响，因此跨物种比较研究亟需一套统一且高效的RNA提取方案。为此，我们构建了SpermBase数据库——该数据库为RNA表达数据库，收录了采用统一实验方法获取的大RNA与小RNA表达数据。 方法：采用仅在裂解阶段需进行少量物种特异性调整的RNA提取方案，从完整精子及精子头部样本中提取总RNA。随后将总RNA分别进行RNA-Seq（针对大RNA）或小非编码RNA测序（sncRNA-Seq，针对小RNA）。 结果：通过采用统一的实验方法，我们得以对精子源性大RNA与小RNA的保守特征开展跨物种分析。在所调研的四种哺乳动物（小鼠、家兔、大鼠与人类）中，我们均在两类RNA群体中鉴定出了保守特征。 结论：本研究证实了一套高效且近乎通用的精子源性RNA研究方案，并明确了哺乳动物精子中大RNA与小RNA群体的保守特性。本研究从完整精子及精子头部样本中提取总RNA，并分别进行sncRNA-Seq或RNA-Seq。