Somatic transposon expression in neural tissue is commonly considered as a measure of mobilization and has therefore been linked to neuropathology and organismal individuality. We combined genome sequencing data with single-cell mRNA sequencing of the same inbred fly strain to map transposon expression in the Drosophila midbrain and found that transposon expression patterns are highly stereotyped. Every detected transposon is resident in at least one cellular gene with a matching expression pattern. Bulk RNA sequencing from fly heads of the same strain revealed that coexpression is a physical link in the form of abundant chimeric transposon–gene mRNAs. We identified 264 genes where transposons introduce cryptic splice sites into the nascent transcript and thereby significantly expand the neural transcript repertoire. Some genes exclusively produce chimeric mRNAs with transposon sequence; on average, 11.6% of the mRNAs produced from a given gene are chimeric. Conversely, most transposon-containing transcripts are chimeric, which suggests that somatic expression of these transposons is largely driven by cellular genes. We propose that chimeric mRNAs produced by alternative splicing into polymorphic transposons, rather than transposon mobilization, may contribute to functional differences between individual cells and animals.

中文翻译：

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果蝇大脑中的转座子表达由邻近基因驱动并使神经转录组多样化

神经组织中的体细胞转座子表达通常被认为是动员的一种衡量标准，因此与神经病理学和生物体个性有关。我们将基因组测序数据与相同近交系果蝇品系的单细胞 mRNA 测序相结合，以绘制果蝇中的转座子表达图中脑，发现转座子表达模式是高度刻板的。每个检测到的转座子都存在于至少一个具有匹配表达模式的细胞基因中。来自同一品系果蝇头部的大量 RNA 测序表明，共表达是一种以丰富的嵌合转座子基因 mRNA 形式存在的物理联系。我们确定了 264 个基因，其中转座子将神秘的剪接位点引入新生的转录物中，从而显着扩展了神经转录物的全部内容。一些基因专门产生带有转座子序列的嵌合 mRNA；平均而言，从给定基因产生的 mRNA 中有 11.6% 是嵌合的。相反，大多数含有转座子的转录物是嵌合的，这表明这些转座子的体细胞表达在很大程度上是由细胞基因驱动的。