SpermBase: A Database for Sperm-Borne RNA Contents.
SpermBase: A Database for Sperm-Borne RNA Contents.
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DOI：
10.1095/biolreprod.116.142190
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发表时间：
2016-11-01
影响因子：
3.6
通讯作者：
Yan W
中科院分区：
文献类型：
--
作者：
Schuster A;Tang C;Xie Y;Ortogero N;Yuan S;Yan W
自从大约三十年前被发现以来，精子携带的 RNA（无论大/小还是编码/非编码）已在多种生物体中被报道，其中一些与精子发生、早期发育和表观遗传有关。尽管取得了这些进展，精子携带的 RNA 的分离、定量和注释仍然很重要。从精子中分离的精子携带的 RNA 的产量和亚种可能因所使用的方法而有很大差异，而且尚未使用标准化的精子 RNA 分离方案对精子 RNA 含量进行跨物种分析。为了解决这些问题，我们开发了一种简单的 RNA 分离方法，适用于不同物种的精子，从而可以进行可靠的种间比较。基于 RNA-Seq 分析，我们建立了 SpermBase ( )，这是一个专门用于多个物种精子携带的 RNA 分析的数据库。目前，SpermBase 包含小鼠、大鼠、兔子和人类总精子和精子头的大小 RNA 表达数据。通过分析大小 RNA 的保守特征，我们发现许多精子携带的 RNA 物种在所分析的所有四个物种中都是保守的，并且在保守的小 RNA 中，精子携带的 tRNA 衍生的小非编码 RNA 和 miRNA 可以靶向大量已知对早期发育至关重要的基因。
Since their discovery approximately three decades ago, sperm-borne RNAs, both large/small and coding/noncoding, have been reported in multiple organisms, and some have been implicated in spermatogenesis, early development, and epigenetic inheritance. Despite these advances, isolation, quantification, and annotation of sperm-borne RNAs remain nontrivial. The yields and subspecies of sperm-borne RNAs isolated from sperm can vary drastically depending on the methods used, and no cross-species analyses of sperm RNA contents have ever been conducted using a standardized sperm RNA isolation protocol. To address these issues, we developed a simple RNA isolation method that is applicable to sperm of various species, thus allowing for reliable interspecies comparisons. Based on RNA-Seq analyses, we established SpermBase ( ), a database dedicated to sperm-borne RNA profiling of multiple species. Currently, SpermBase contains large and small RNA expression data for mouse, rat, rabbit, and human total sperm and sperm heads. By analyzing large and small RNAs for conserved features, we found that many sperm-borne RNA species were conserved across all four species analyzed, and among the conserved small RNAs, sperm-borne tRNA-derived small noncoding RNAs and miRNAs can target a large number of genes known to be critical for early development.
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