Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.

中文翻译：

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KRAB-KAP1 抑制复合物的结构和功能映射

转座因子是一个遗传库，新基因和调控元件可以从中出现。然而，转座因子的表达可能是致病的，因此受到严格控制。含有 KRAB 结构域的锌指蛋白 (KRAB-ZFPs) 募集共抑制因子 KRAB 相关蛋白 1 (KAP1/TRIM28) 来调节许多转座因子，但 KRAB-ZFPs 和 KAP1 如何相互作用仍不清楚。在这里，我们报告了与人类 KRAB-ZFP ZNF93 的 KRAB 结构域复合的 KAP1 三联基序 (TRIM) 的晶体结构。KAP1-KRAB 结合界面中的结构导向突变消除了表观遗传转录沉默测定中的抑制活性。在表达具有消除 KRAB 结合的突变的 KAP1 变体的细胞中，H3K9me3 在数千个基因座上的沉积在全基因组范围内丢失。我们的工作确定并在功能上验证了 KRAB-KAP1 分子界面，这对于脊椎动物的中央转录控制轴至关重要。此外，基于结构的 KAP1 募集效率预测将能够优化 CRISPRi 中使用的 KRAB。