Genes with novel cellular functions may evolve through exon shuffling, which can assemble novel protein architectures. Here, we show that DNA transposons provide a recurrent supply of materials to assemble protein-coding genes through exon shuffling. We find that transposase domains have been captured—primarily via alternative splicing—to form fusion proteins at least 94 times independently over the course of ~350 million years of tetrapod evolution. We find an excess of transposase DNA binding domains fused to host regulatory domains, especially the Krüppel-associated box (KRAB) domain, and identify four independently evolved KRAB-transposase fusion proteins repressing gene expression in a sequence-specific fashion. The bat-specific KRABINER fusion protein binds its cognate transposons genome-wide and controls a network of genes and cis-regulatory elements. These results illustrate how a transcription factor and its binding sites can emerge.

具有新细胞功能的基因可以通过外显子改组进化，这可以组装新的蛋白质结构。在这里，我们展示了 DNA 转座子提供了材料的循环供应，以通过外显子改组来组装蛋白质编码基因。我们发现转座酶域已经被捕获——主要是通过选择性剪接——在大约 3.5 亿年的四足动物进化过程中独立形成融合蛋白至少 94 次。我们发现过量的转座酶 DNA 结合域与宿主调节域融合，尤其是 Krüppel 相关框 (KRAB) 域，并确定了四种独立进化的 KRAB 转座酶融合蛋白，以序列特异性方式抑制基因表达。蝙蝠特异性 KRABINER 融合蛋白在全基因组范围内结合其同源转座子，并控制基因网络和顺式调控元件。这些结果说明了转录因子及其结合位点是如何出现的。