SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana.

Sureshkumar, Sridevi; Bandaranayake, Champa; Lv, Junqing; Dent, Craig I; Bhagat, Prakash Kumar; Mukherjee, Sourav; Sarwade, Rucha; Atri, Chhaya; York, Harrison M; Tamizhselvan, Prashanth; Shamaya, Nawar; Folini, Giulia; Bergey, Benjamin G; Yadav, Avilash Singh; Kumar, Subhasree; Grummisch, Oliver S; Saini, Prince; Yadav, Ram K; Arumugam, Senthil; Rosonina, Emanuel; Sadanandom, Ari; Liu, Hongtao; Balasubramanian, Sureshkumar

Abstract

Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreich's ataxia in humans. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown. Using a plant model with a temperature-sensitive phenotype, we have previously shown that expanded repeats can induce small RNAs, which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway. Here, using a genetic suppressor screen and yeast two-hybrid assays, we identified novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP GENE CLASS 1 (FUG1)-an uncharacterized SUMO protease with no known role in gene silencing-is required for epigenetic silencing caused by expanded repeats. In addition, we demonstrate that FUG1 physically interacts with ALFIN-LIKE 3 (AL3)-a histone reader that is known to bind to active histone mark H3K4me . Loss of function of AL3 abolishes epigenetic silencing caused by expanded repeats. AL3 physically interacts with the chromodomain protein LIKE HETEROCHROMATIN 1 (LHP1)-known to be associated with the spread of the repressive histone mark H3K27me to cause repeat expansion-induced epigenetic silencing. Loss of any of these components suppresses repeat expansion-associated phenotypes coupled with an increase in IIL1 expression with the reversal of gene silencing and associated change in epigenetic marks. Our findings suggest that the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing and highlight the importance of post-translational modifiers and histone readers in epigenetic silencing. [Abstract copyright: © 2024. The Author(s), under exclusive licence to Springer Nature Limited.]

Citation

Sureshkumar, S., Bandaranayake, C., Lv, J., Dent, C. I., Bhagat, P. K., Mukherjee, S., …Balasubramanian, S. (2024). SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana. Nature Plants, 10, 749-759. https://doi.org/10.1038/s41477-024-01672-5

• Journal Article Type: Letter
• Acceptance Date: Mar 15, 2024
• Online Publication Date: Apr 19, 2024
• Publication Date: 2024-05
• Deposit Date: May 23, 2024
• Journal: Nature plants
• Print ISSN: 2055-026X
• Publisher: Nature Research
• Peer Reviewed: Peer Reviewed
• Volume: 10
• Pages: 749-759
• DOI: https://doi.org/10.1038/s41477-024-01672-5
• Public URL: https://durham-repository.worktribe.com/output/2433297