Mother-Specific Signature in the Maternal Transcriptome Composition of Mature,Unfertilized Zebrafish Eggs

Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize technical interference, we used mature, unfertilized eggs from siblings. About half of the number of analyzed genes was found to be expressed as maternal RNA. The expressed and nonexpressed genes showed that maternal mRNA accumulation is a non-random process, as it is related to specific biological pathways and processes relevant in early embryogenesis. Moreover, it turned out that overall the composition of the maternal transcriptome is tightly regulated as about half of the expressed genes display a less than twofold expression range between the observed minimum and maximum expression values of a gene in the experiment. Even more, the maximum gene-expression difference within clutches is for 88% of the expressed genes lower than twofold. This means that expression differences observed in maternally expressed genes are primarily caused by differences between mothers, with only limited variability between eggs from the same mother. This was underlined by the fact that 99% of the expressed genes were found to be differentially expressed between any of the mothers in an ANOVA test. Furthermore, linking chromosome location, transcription factor binding sites, and miRNA target sites of the genes in clusters of distinct and unique mother-specific gene-expression, suggest biological relevance of the mother-specific signatures in the maternal transcriptome composition. Altogether, the maternal transcriptome composition of mature zebrafish oocytes seems to be tightly regulated with a distinct mother-specific signature. GSE72839at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?accGSE72839, and http://rnabiology.nl/Dr-Browser.html 2 papers: Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. Rauwerda H, Wackers P, Pagano JF, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, Breit TM. PLoS One. 2016 Jan 22;11(1):e0147151. doi: 10.1371/journal.pone.0147151. eCollection 2016. PMID: 26799215 Transcriptome data on maternal RNA of 24 individual zebrafish eggs from five sibling mothers. Pagano JF, Rauwerda H, de Leeuw WC, Wackers P, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, Breit TM.Data Brief. 2016 Apr 26;8:69-72. doi: 10.1016/j.dib.2016.04.045. eCollection 2016 Sep. PMID: 27284564All Data are in SILS tape archive 2016_Breit_mother.spec.mat.transcr.zfeggs_Rauwerda_Breit

成熟卵母细胞中存在的母源mRNA（maternal mRNA）对早期胚胎的正常发育具有重要作用。目前针对母源转录组（maternal transcriptome）的研究多采用混合成熟卵子开展，单个卵子之间的潜在表达差异尚未明确。本研究针对来自5条雌鱼产卵群的单个斑马鱼卵子开展转录组分析，重点关注产卵群间以及产卵群内部各基因的母源mRNA丰度差异。为尽可能降低技术干扰，我们使用了同组雌鱼的成熟未受精卵子。

本研究发现，约半数分析的基因可作为母源RNA进行表达。对表达基因与非表达基因的分析显示，母源mRNA的积累属于非随机过程，其与早期胚胎发生相关的特定生物学通路与过程密切相关。此外，整体而言母源转录组受到严格调控：约半数表达基因的实验观测表达量波动范围不足两倍。更值得注意的是，88%的表达基因的同产卵群内最大表达差异低于两倍。这表明，母源表达基因的表达差异主要来源于雌鱼之间的差异，而同一条雌鱼所产卵子之间的表达变异十分有限。方差分析（ANOVA）检验结果进一步验证了这一点：99%的表达基因在任意雌鱼之间均存在差异表达。

此外，对具有独特母本特异性基因表达的聚类基因的染色体位置、转录因子结合位点（transcription factor binding sites）以及微小RNA（miRNA）靶位点进行关联分析，提示母源转录组组成中的母本特异性特征具有生物学相关性。综上，成熟斑马鱼卵母细胞的母源转录组组成似乎受到严格调控，并呈现出鲜明的母本特异性特征。

相关数据集编号GSE72839，可通过以下网址访问：http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72839，以及http://rnabiology.nl/Dr-Browser.html。

本研究相关论文共2篇：
1. 《Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs》，作者为Rauwerda H、Wackers P、Pagano JF等，发表于PLoS One，2016年1月22日；11(1):e0147151。DOI: 10.1371/journal.pone.0147151，2016年卷收录，PMID: 26799215。
2. 《Transcriptome data on maternal RNA of 24 individual zebrafish eggs from five sibling mothers》，作者为Pagano JF、Rauwerda H、de Leeuw WC等，发表于Data Brief，2016年4月26日；8:69-72。DOI: 10.1016/j.dib.2016.04.045，2016年9月卷收录，PMID: 27284564。

所有数据存储于SILS磁带档案库2016_Breit_mother.spec.mat.transcr.zfeggs_Rauwerda_Breit。