Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE-derived transcriptional units expressed across tissues. Finally, we show that novel TE-derived promoters can initiate tissue-specific transcription of alternate gene isoforms. This work provides a comprehensive profile of TE activity across normal zebrafish tissues, shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.

中文翻译：

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表观基因组分析揭示了斑马鱼中转座元件对顺式调控元件、组织特异性表达和替代启动子的普遍贡献


转座元件（TE）编码影响多个物种基因表达的调控元件，但缺乏在基因调控背景下对斑马鱼 TE 的全面分析。在这里，我们使用多维测序数据系统地研究了 11 种成年斑马鱼组织中 TE 的表观基因组和转录组景观。我们发现 TE 对斑马鱼基因组中的多种调控元件做出了重大贡献，并且 37% 的 TE 在成年斑马鱼组织中处于活跃调控状态。我们鉴定了不同组织中富含高度特异性调控元件的 TE 亚家族。我们使用转录本组装来发现跨组织表达的 TE 衍生转录单位。最后，我们证明新型 TE 衍生启动子可以启动替代基因亚型的组织特异性转录。这项工作提供了正常斑马鱼组织中 TE 活性的全面概况，揭示了这种广泛使用的模型生物中基因表达调控的机制。