A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis

Wang, M.; Zhong, Z.; Gallego-Bartolome, J.; Li, Z.; Feng, S.; Kuo, P. H.; Kan, R. L.; Richey, J.; Jami-Alahmadi, Y.; Wohlschlegel, J.; Jacobsen, S. E.

doi:10.1101/2022.11.01.514775

bioRxiv · 10.1101/2022.11.01.514775

A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis

Wang, M.·Zhong, Z.·Gallego-Bartolome, J.·Li, Z.·Feng, S.·Kuo, P. H.·Kan, R. L.·Richey, J.·Jami-Alahmadi, Y.·Wohlschlegel, J.·Jacobsen, S. E.

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Abstract

DNA methylation has been utilized for target gene silencing in plants, however its 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 either through the establishment of DNA methylation, or via DNA methylation-independent processes including histone H3K27me3 deposition, H3K4me3 demethylation, H3K9, H3K14, H3K27, and H4K16 deacetylation, inhibition of RNA Polymerase II transcription elongation or Ser-5 dephosphorylation. The silencing fusion proteins also silenced many other genes with different efficacy, and a machine learning model could accurately predict the efficacy of each silencer based on various chromatin features of the target loci. These results provide a more comprehensive understanding of epigenetic regulatory pathways and provide an armament of tools for targeted manipulation of gene expression.

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Wang, M., Zhong, Z., Gallego-Bartolome, J., Li, Z., Feng, S., Kuo, P. H., Kan, R. L., Richey, J., Jami-Alahmadi, Y., Wohlschlegel, J., Jacobsen, S. E.. 2022-11-03. A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis. https://doi.org/10.1101/2022.11.01.514775

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