Autonomous transposons tune their sequences to ensure somatic suppression [polyA_HCT116]. Autonomous transposons tune their sequences to ensure somatic suppression [polyA_HCT116]

Transposable elements (TEs) are a major constituent of human genes, occupying approximately half of the intronic space. During pre-mRNA synthesis, intronŁic TEs are transcribed along with their host genes but rarely contribute to the final mRNA product as they are spliced out together with the intron and rapidly degraded. Paradoxically, TEs are an abundant source of RNA-processing signals through which they can create new introns (Huff et al. 2016), and functional (Cosby et al. 2021) or non-functional chimeric transcripts (Clayton et al. 2020). The rarity of these events impliesy the existence of a resilient splicing code that is able to suppress TE-exonization without compromising host pre-mRNA processing. Here we show that SAFB proteins play a unique dual role in defence against TEs by preventing retrotransposition of L1 elements as well as their exonization when they land into genes by coating their adenosine-rich RNA. The suppressive activity of SAFB extends to neuro-, muscle- and testis-specific giant protein-coding cassette exons of ANK3, MAP4 and CLIP1, nested genes as well as Tigger DNA transposons, which are all enriched with adenosine/purine-rich sequences that act as splicing-enhancers in SAFB depleted cells. In mice and flies, SAFB additionally suppresses LTR/ERV elements, which are active in mice and flies, but no longer in humans. Splicing events suppressed by SAFB in somatic cells are activated in the testis, coinciding with low SAFB expression in post-meiotic spermatids. Reminiscent of the division of labour between innate and adaptive immune systems that fight external pathogens, our results uncover SAFB proteins as an RNA-based, pattern-guided, non-adaptive defence system against TEs in the soma, complementing the RNA-based, adaptive Piwi-piRNA pathway of the germline. Overall design: Gene expression profiling of HCT116 cells subject to knockdown of two SAFB proteins (SAFB1 and SLTM) at the same time, and a control treatment. poly(A)+ RNAs were sequenced in three biological replicates per treatment (6 libraries in total).

转座因子（Transposable Elements, TEs）是人类基因组的主要组成成分，约占据一半的内含子区域。在前体mRNA（pre-mRNA）合成过程中，内含子内的TEs会随宿主基因一同转录，但通常不会进入最终的mRNA产物——因为它们会随内含子一同被剪接移除，并快速降解。矛盾的是，TEs是RNA加工信号的丰富来源，借此可形成新的内含子（Huff等，2016），以及功能性（Cosby等，2021）或非功能性嵌合转录本（Clayton等，2020）。
这类事件的罕见性暗示，存在一种稳健的剪接编码机制，能够在不影响宿主前体mRNA加工的前提下抑制TE外显子化。本研究证实，SAFB蛋白在抵御TEs中发挥独特的双重作用：通过包裹富含腺苷的RNA，既可以抑制L1元件的逆转录转座，也能阻止其插入宿主基因后发生的外显子化。
SAFB的抑制活性还波及ANK3、MAP4和CLIP1基因的神经、肌肉及睾丸特异性巨型编码蛋白盒式外显子、嵌套基因以及Tigger DNA转座子（Tigger DNA Transposons）；这些序列均富含腺苷/嘌呤序列，在SAFB敲低的细胞中，此类序列可作为剪接增强子发挥功能。
在小鼠和果蝇中，SAFB还可抑制LTR/ERV元件——这类元件在小鼠和果蝇中具有转录活性，但在人类中已无活性。SAFB在体细胞中抑制的剪接事件会在睾丸中被激活，这与减数分裂后精子细胞中SAFB的低表达水平相吻合。
这类似于对抗外源病原体的先天免疫与适应性免疫之间的分工，我们的研究结果揭示，SAFB蛋白是一种基于RNA、模式引导的非适应性防御系统，可在体细胞中抵御TEs，与生殖细胞中基于RNA的适应性Piwi-piRNA通路形成互补。
整体实验设计：对同时敲低两种SAFB蛋白（SAFB1和SLTM）的HCT116细胞进行基因表达谱分析，并设置对照组。各组设置3次生物学重复，共构建6个测序文库，对聚腺苷酸化RNA（poly(A)+ RNA）进行测序。