Transposable element products, functions, and regulatory networks in Arabidopsis thaliana. Transposable element products, functions, and regulatory networks in Arabidopsis thaliana

Transposable elements (TEs) are DNA sequences with the ability to propagate themselves within and across genomes. Their mobilization is catalyzed by self-encoded factors, yet these factors have been poorly investigated due to difficulties in defining TE genes in genomes. Here, we leveraged extensive long- and short-read transcriptome data, together with structural predictions, transcription factor binding site identification, and transcriptional network analyses, to construct a comprehensive atlas of TE transcripts and TE-encoded products in the model organism Arabidopsis thaliana. We uncovered hundreds of transcriptionally competent TEs, each potentially encoding multiple proteins either through distinct genes, alternative splicing, or post-translational processing. Structural-based protein analyses revealed dozens of hitherto unidentified domains of unknown function, enabling us to predict proteins with multimerization and DNA binding domains forming macromolecular complexes involved in transposition. Furthermore, we demonstrate that TE expression is highly intertwined with the transcriptional network of cellular genes, and identified transcription factors and cis-regulatory elements associated with their coordinated expression during development or in response to environmental cues. This comprehensive atlas of TE-genes and TE-proteins provides a valuable resource for studying the mechanisms involved in transposition and their consequences for genome and organismal function.

转座因子（Transposable elements, TEs）是一类能够在基因组内部以及跨基因组间自我复制传播的DNA序列。其转座移动过程由自身编码的因子介导，但由于在基因组中精准界定转座因子基因存在诸多困难，这类因子的研究长期以来进展有限。本研究依托大规模长读长与短读长转录组数据，结合结构预测、转录因子结合位点识别以及转录调控网络分析等手段，构建了模式生物拟南芥（Arabidopsis thaliana）中转座因子转录本及其编码产物的综合图谱。本研究共鉴定出数百个具有转录活性的转座因子，每个因子均可通过独立基因转录、可变剪接或翻译后加工等途径编码多种蛋白质。基于结构的蛋白质分析揭示了数十个此前未被鉴定的功能未知结构域，借此可预测到具备多聚化结构域与DNA结合结构域的蛋白质，这类蛋白质能够形成参与转座过程的大分子复合物。此外，本研究证实转座因子的表达与宿主细胞基因的转录调控网络存在高度紧密的关联，并鉴定出在发育过程或响应环境信号时与其协同表达相关的转录因子与顺式调控元件。这份转座因子基因与转座因子蛋白质的综合图谱，为研究转座作用机制及其对基因组与生物体功能的影响提供了极具价值的研究资源。