Sex-biased miRNA expression in mouse, opossum and chicken

Sexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing dataset to analyse male and female miRNA expression profiles in mouse, opossum and chicken. Our analyses uncovered numerous cases of somatic sex-biased miRNA expression, especially in the mouse heart and liver. Sex-biased expression is explained by miRNA-specific regulation, including sex-biased chromatin accessibility at promoters, rather than piggybacking of intronic miRNAs on sex-biased protein-coding genes. In mouse, but not opossum and chicken, sex bias is coordinated across tissues such that autosomal testis-biased miRNAs tend to be somatically male-biased, whereas autosomal ovary-biased miRNAs are female-biased, possibly due to broad hormonal control. In chicken, which has a Z/W sex chromosome system, expression output of genes on the Z chromosome is expected to be male-biased, since there is no global dosage compensation mechanism that restores expression in ZW females after almost all genes on the W chromosome decayed. Nevertheless, we found that the dominant liver miRNA, miR-122-5p, is Z-linked but expressed in an unbiased manner, due to the unusual retention of a W-linked copy. Another Z-linked miRNA, the male-biased miR-2954-3p, shows conserved preference for dosage-sensitive genes on the Z chromosome, based on computational and experimental data from chicken and zebra finch, and acts to equalise male-to-female expression ratios of its targets. Unexpectedly, our findings thus establish miRNA regulation as a novel gene-specific dosage compensation mechanism. Small RNA sequencing of 72 tissue samples from mouse, opossum and chicken. Libraries were prepared with the NEXTflex Small RNA-Seq Kit (NF). For two of the samples, libraries were also prepared with the lllumina TruSeq Small RNA Library Prep Kit (IL) and the HD protocol (HD) developed by Sorefan et al, 2012 (DOI: 10.1186/1758-907X-3-4).性二态性（Sexual dimorphism）依赖于性别偏向性基因表达，但microRNAs（miRNAs，微小RNA）的相关贡献尚未在全局层面得到评估。为此，我们构建了一套大规模的小RNA测序数据集，用以分析小鼠、负鼠和鸡的雌雄miRNA表达谱。我们的分析揭示了大量体细胞性别偏向性miRNA表达的案例，尤其在小鼠心脏与肝脏中。性别偏向性表达可通过miRNA特异性调控得以解释，包括启动子区域的性别偏向性染色质可及性，而非由内含子miRNA随性别偏向性蛋白编码基因一同“搭便车”表达。在小鼠中（而非负鼠与鸡中），性别偏向性在不同组织间存在协同效应：常染色体上的睾丸偏向性miRNA往往表现为体细胞雄性偏向性，而常染色体卵巢偏向性miRNA则呈雌性偏向性，这可能源于广泛的激素调控。对于拥有Z/W性染色体系统的鸡而言，Z染色体上基因的表达输出本应呈现雄性偏向性——因为在几乎所有W染色体基因发生退化后，并不存在全局剂量补偿机制以恢复ZW型雌性的基因表达水平。然而我们发现，肝脏中占主导的miRNA——miR-122-5p，虽为Z连锁基因，却以无偏向性的方式表达，这源于其W连锁拷贝的异常保留。另一类Z连锁miRNA——雄性偏向性的miR-2954-3p，基于鸡与斑胸草雀的计算及实验数据，表现出对Z染色体上剂量敏感基因的保守偏好性，其作用是使靶基因的雌雄表达比值趋于均衡。出乎意料的是，我们的研究结果确立了miRNA调控作为一种全新的基因特异性剂量补偿机制。本数据集包含来自小鼠、负鼠与鸡的72份组织样本的小RNA测序数据。文库构建采用NEXTflex小RNA测序试剂盒（NEXTflex Small RNA-Seq Kit，NF）。其中两份样本的文库还分别使用Illumina TruSeq小RNA文库制备试剂盒（Illumina TruSeq Small RNA Library Prep Kit，IL）以及Sorefan等人2012年开发的HD实验方案（HD，DOI: 10.1186/1758-907X-3-4）完成构建。