Gan Yuli, Wang Lingyan, Liu Guoxian, Guo Xiruo, Zhou Yiming, Chang Kexin, Zhang Zhonghui, Yan Fang, Liu Qi, Chen Bing
College of Life Science, Hebei University, Baoding 071002, China.
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
Insects. 2024 Nov 30;15(12):950. doi: 10.3390/insects15120950.
: Transposable elements (TEs) and noncoding sequences are major components of the genome, yet their functional contributions to long noncoding RNAs (lncRNAs) are not well understood. Although many lncRNAs originating from TEs (TE-lncRNAs) have been identified across various organisms, their characteristics and regulatory roles, particularly in insects, remain largely unexplored. This study integrated multi-omics data to investigate TE-lncRNAs in , focusing on the influence of transposons across different omics levels. : We identified 16,118 transposons overlapping with lncRNA sequences that constitute 2119 TE-lncRNAs (40.4% of all lncRNAs) using 256 public RNA-seq samples and 15 lncRNA-seq samples of S2 cells treated with heavy metals. Of these, 67.2% of TE-lncRNAs contain more than one TE. The LTR/Gypsy family was the most common transposon insertion. Transposons preferred to insert into promoters, transcription starting sites, and intronic regions, especially in chromosome ends. Compared with lncRNAs, TE-lncRNAs showed longer lengths, a lower conservation, and lower levels but a higher specificity of expression. Multi-omics data analysis revealed positive correlations between transposon insertions and chromatin openness at the pre-transcriptional level. Notably, a total of 516 TE-lncRNAs provided transcriptional factor binding sites through transposon insertions. The regulatory network of a key transcription factor was rewired by transposons, potentially recruiting other transcription factors to exert regulatory functions under heavy metal stress. Additionally, 99 TE-lncRNAs were associated with mA methylation modification sites, and 115 TE-lncRNAs potentially provided candidate small open reading frames through transposon insertions. : Our data analysis demonstrated that TEs contribute to the regulation of lncRNAs. TEs not only promote the transcriptional regulation of lncRNAs, but also facilitate their post-transcriptional and epigenetic regulation.
转座元件（TEs）和非编码序列是基因组的主要组成部分，然而它们对长链非编码RNA（lncRNAs）的功能贡献尚未得到充分理解。尽管在各种生物体中已经鉴定出许多源自转座元件的lncRNAs（TE-lncRNAs），但其特征和调控作用，尤其是在昆虫中的情况，在很大程度上仍未被探索。本研究整合多组学数据以研究[具体物种]中的TE-lncRNAs，重点关注转座子在不同组学水平上的影响。我们使用256个公共RNA测序样本和15个经重金属处理的S2细胞的lncRNA测序样本，鉴定出16118个与lncRNA序列重叠的转座子，这些转座子构成了2119个TE-lncRNAs（占所有lncRNAs的40.4%）。其中，67.2%的TE-lncRNAs包含不止一个转座元件。LTR/Gypsy家族是最常见的转座子插入类型。转座子倾向于插入启动子、转录起始位点和内含子区域，尤其是在染色体末端。与lncRNAs相比，TE-lncRNAs显示出更长的长度、更低的保守性以及更低的表达水平但更高的表达特异性。多组学数据分析揭示了转录前水平上转座子插入与染色质开放性之间的正相关关系。值得注意的是，共有516个TE-lncRNAs通过转座子插入提供转录因子结合位点。关键转录因子的调控网络被转座子重新连接，可能在重金属胁迫下招募其他转录因子发挥调控功能。此外，99个TE-lncRNAs与mA甲基化修饰位点相关，115个TE-lncRNAs可能通过转座子插入提供候选小开放阅读框。我们的数据分析表明，转座元件有助于lncRNAs的调控。转座元件不仅促进lncRNAs的转录调控，还促进其转录后和表观遗传调控。
