Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.
Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, Spain.
Nat Plants. 2023 Mar;9(3):460-472. doi: 10.1038/s41477-023-01362-8. Epub 2023 Mar 6.
DNA methylation has been utilized for target gene silencing in plants. However, it is not well understood whether other silencing pathways can be also used to manipulate gene expression. Here we performed a gain-of-function screen for proteins that could silence a target gene when fused to an artificial zinc finger. We uncovered many proteins that suppressed gene expression through DNA methylation, histone H3K27me3 deposition, H3K4me3 demethylation, histone deacetylation, inhibition of RNA polymerase II transcription elongation or Ser-5 dephosphorylation. These proteins also silenced many other genes with different efficacies, and a machine learning model could accurately predict the efficacy of each silencer on the basis of various chromatin features of the target loci. Furthermore, some proteins were also able to target gene silencing when used in a dCas9-SunTag system. These results provide a more comprehensive understanding of epigenetic regulatory pathways in plants and provide an armament of tools for targeted gene manipulation.
DNA 甲基化已被用于植物中靶基因的沉默。然而，目前尚不清楚是否可以利用其他沉默途径来操纵基因表达。在这里，我们进行了一项功能获得筛选实验，以研究当与人工锌指融合时，哪些蛋白可以沉默靶基因。我们发现许多蛋白可以通过 DNA 甲基化、组蛋白 H3K27me3 沉积、H3K4me3 去甲基化、组蛋白去乙酰化、抑制 RNA 聚合酶 II 转录延伸或 Ser-5 去磷酸化来抑制基因表达。这些蛋白还可以不同的效率沉默许多其他基因，并且机器学习模型可以根据靶基因座的各种染色质特征准确预测每个沉默子的效率。此外，一些蛋白在使用 dCas9-SunTag 系统时也能够靶向基因沉默。这些结果为植物中表观遗传调控途径提供了更全面的理解，并为靶向基因操作提供了一套工具。
