Transcriptome-Wide Survey of Mouse CNS-Derived Cells Reveals Monoallelic Expression within Novel Gene Families

Monoallelic expression is an integral component of regulation of a number of essential genes and gene families. To probe for allele-specific expression in cells of CNS origin, we used next-generation sequencing (RNA-seq) to analyze four clonal neural stem cell (NSC) lines derived from Mus musculus C57BL/6 (B6)×Mus musculus molossinus (JF1) adult female mice. We established a JF1 cSNP library, then ascertained transcriptome-wide expression from B6 vs. JF1 alleles in the NSC lines. Validating the assay, we found that 262 of 268 X-linked genes evaluable in at least one cell line showed monoallelic expression (at least 85% expression of the predominant allele, p-value<0.05). For autosomal genes 170 of 7,198 genes (2.4% of the total) showed monoallelic expression in at least 2 evaluable cell lines. The group included eight known imprinted genes with the expected pattern of allele-specific expression. Among the other autosomal genes with monoallelic expression were five members of the glutathione transferase gene superfamily, which processes xenobiotic compounds as well as carcinogens and cancer therapeutic agents. Monoallelic expression within this superfamily thus may play a functional role in the response to diverse and potentially lethal exogenous factors, as is the case for the immunoglobulin and olfactory receptor superfamilies. Other genes and gene families showing monoallelic expression include the annexin gene family and the Thy1 gene, both linked to inflammation and cancer, as well as genes linked to alcohol dependence (Gabrg1) and epilepsy (Kcnma1). The annotated set of genes will provide a resource for investigation of mechanisms underlying certain cases of these and other major disorders.

单等位基因表达（Monoallelic expression）是众多关键基因及基因家族调控机制的核心组成部分。为探究中枢神经系统（Central Nervous System, CNS）来源细胞的等位基因特异性表达情况，我们采用下一代测序技术（RNA-seq），对源自小家鼠C57BL/6（B6）×小家鼠Molossinus（JF1）成年雌性小鼠的4株克隆神经干细胞（NSC）系进行分析。我们构建了JF1编码区单核苷酸多态性（cSNP）文库，随后明确了各NSC系中全转录组范围内B6与JF1等位基因的表达水平。为验证该检测方法的有效性，我们发现在至少1株细胞系中可评估的268个X连锁基因中，有262个呈现单等位基因表达模式（优势等位基因的表达占比不低于85%，p值<0.05）。对于常染色体基因而言，在7198个可评估基因中，有170个（占总数的2.4%）在至少2株可评估细胞系中呈现单等位基因表达。该组基因包含8个已知的印记基因，其等位基因特异性表达模式与预期一致。在其余呈现单等位基因表达的常染色体基因中，包含谷胱甘肽S-转移酶基因超家族的5个成员，该超家族可代谢外源性化合物、致癌物及癌症治疗药物。因此，该超家族内的单等位基因表达可能在机体应对多种潜在致命外源性因素的过程中发挥功能性作用，这与免疫球蛋白超家族及嗅觉受体超家族的情况一致。其他呈现单等位基因表达的基因及基因家族包括膜联蛋白基因家族与Thy1基因，二者均与炎症及癌症相关；此外还有与酒精依赖（Gabrg1）及癫痫（Kcnma1）相关的基因。该注释后的基因集将为探究此类及其他重大疾病部分病例的潜在发病机制提供研究资源。