Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression

Allele-specific expression is important in development and disease, but a complete picture is lacking. Therefore, we mapped allelic-specific expression in 23 tissues during mouse development, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. By using rRNA depleted RNA-seq we were able to map allelic expression of lncRNAs that may be lowly expressed or non-polyadenylated. Analysis of this data together with ChIP-seq and genetic models reveals previously unappreciated aspects of the regulation of allelic expression. We demonstrate that allelic expression arising from genetic differences between the alleles, or from the epigenetic processes XCI and genomic imprinting, is surprisingly highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We detect a higher rate of XCI escapers than most previous mouse studies, (∼10% genes escaping per tissue similar to reports in human), while leg muscle shows an unexpectedly high rate of ∼50% escapers. By surveying a range of tissues during development, and by performing extensive validation including an embryo transfer experiment to exclude false positives from placental maternal contamination, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This increases the proportion of imprinted genes that are clustered (>90%), and shows that cluster size varies dynamically during development, and can be substantially larger than previously thought, with the Igf2r cluster extending over 10Mb in placenta, making it the largest autosomal cis-regulated region in mammals. Defining allele-specific genome features from the mouse in 23 tissues and developmental stages

等位基因特异性表达 (allele-specific expression) 在发育与疾病进程中发挥关键作用，但目前尚未形成完整的研究图景。为此，我们对小鼠发育过程中的23种组织开展了等位基因特异性表达图谱绘制，其中包含19份雌性组织样本，可同时用于检测X染色体失活 (X chromosome inactivation, XCI) 逃逸基因。通过采用核糖体RNA去除的RNA测序 (rRNA depleted RNA-seq) 技术，我们可对低表达或非多聚腺苷酸化的长链非编码RNA (long non-coding RNAs, lncRNAs) 的等位基因表达情况进行精准定位分析。结合染色质免疫共沉淀测序 (Chromatin Immunoprecipitation sequencing, ChIP-seq) 数据与遗传模型开展的整合分析，揭示了此前未被认知的等位基因表达调控维度。本研究证实，由等位基因间遗传差异，或XCI、基因组印记 (genomic imprinting) 等表观遗传过程所产生的等位基因特异性表达，具有超乎预期的高度组织特异性。研究发现，组织特异性品系偏倚性基因表达，可通过组织特异性增强子或等位基因间转录后稳定性差异实现调控。我们检测到的XCI逃逸基因比例，高于多数既往小鼠相关研究（每组织约10%的逃逸基因，与人类相关研究报道结果相近）；而腿部肌肉组织的逃逸基因比例更是高达约50%，这一结果超出预期。通过对发育过程中的多种组织进行系统性调研，并开展包括胚胎移植 (embryo transfer) 实验在内的多重验证以排除胎盘母体污染导致的假阳性结果，我们成功构建了一份高置信度的小鼠印记基因 (imprinted genes) 列表，其中包含18个全新的印记基因。该列表使已发现的成簇印记基因占比提升至90%以上，同时揭示出印记基因簇的大小在发育进程中呈动态变化，且可远大于此前认知：在胎盘中，胰岛素样生长因子2受体 (insulin-like growth factor 2 receptor, Igf2r) 基因簇的调控范围可延伸至10Mb以上，是哺乳动物中已知规模最大的常染色体顺式调控区域 (autosomal cis-regulated region)。本数据集基于小鼠23种组织及发育阶段样本，明确了小鼠的等位基因特异性基因组特征。