De novo profiling of long non-coding RNAs involved in MC-LR–induced liver injury in whitefish: discovery and perspectives

Microcystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap in knowledge persists regarding the underlying molecular mechanisms of liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have been extensively studied in model organisms, our knowledge concerning the role of lncRNAs in liver injury is limited. Given that lncRNAs show low levels of sequence conservation, their role becomes even more unclear in non-model organisms without an annotated genome, like whitefish (Coregonus lavaretus). The objective of this study was to discover and profile aberrantly expressed polyadenylated lncRNAs that are involved in MC-LR-induced liver injury in whitefish. Using RNA sequencing (RNA-Seq) data, we de novo assembled a high-quality whitefish liver transcriptome. This enabled us to find 94 differentially expressed (DE) putative evolutionary conserved lncRNAs, such as MALAT1, HOTTIP, HOTAIR or HULC, and 4429 DE putative novel whitefish lncRNAs, which differed from annotat...微囊藻毒素-LR（Microcystin-LR, MC-LR）是一种强效肝毒素，目前其介导肝脏毒性与损伤的潜在分子机制仍存在显著认知空白。尽管长链非编码RNA（long non-coding RNAs, lncRNAs）在模式生物中已得到广泛研究，但我们对其在肝脏损伤中的作用认知仍十分有限。鉴于lncRNAs的序列保守性普遍较低，对于缺乏注释基因组的非模式生物（如白鲑（Coregonus lavaretus））而言，lncRNAs的功能机制愈发难以阐明。本研究旨在发掘并分析参与MC-LR诱导的白鲑肝脏损伤的异常表达聚腺苷酸化长链非编码RNA。通过利用RNA测序（RNA-Seq）数据，我们从头组装获得了高质量的白鲑肝脏转录组。借此，我们共鉴定出94个差异表达（DE）的、推测具有进化保守性的lncRNAs，例如MALAT1、HOTTIP、HOTAIR及HULC，同时还发现了4429个差异表达的、推测为白鲑特异性的新型lncRNAs，其与（原文此处未完成）。