A conserved Pol II elongator SPT6L mediates Pol V transcription to regulate RNA-directed DNA methylation in Arabidopsis

Yujuan Liu, Jie Shu, Zhi Zhang, Ning Ding, Jinyuan Liu, Jun Liu, Yuhai Cui, Changhu Wang () and Chen Chen ()
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Yujuan Liu: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou
Jie Shu: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou
Zhi Zhang: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou
Ning Ding: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou
Jinyuan Liu: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou
Jun Liu: Guangzhou
Yuhai Cui: London Research and Development Centre
Changhu Wang: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou
Chen Chen: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract In plants, the plant-specific RNA polymerase V (Pol V) transcripts non-coding RNAs and provides a docking platform for the association of accessory proteins in the RNA-directed DNA methylation (RdDM) pathway. Various components have been uncovered that are involved in the process of DNA methylation, but it is still not clear how the transcription of Pol V is regulated. Here, we report that the conserved RNA polymerase II (Pol II) elongator, SPT6L, binds to thousands of intergenic regions in a Pol II-independent manner. The intergenic enrichment of SPT6L, interestingly, co-occupies with the largest subunit of Pol V (NRPE1) and mutation of SPT6L leads to the reduction of DNA methylation but not Pol V enrichment. Furthermore, the association of SPT6L at Pol V loci is dependent on the Pol V associated factor, SPT5L, rather than the presence of Pol V, and the interaction between SPT6L and NRPE1 is compromised in spt5l. Finally, Pol V RIP-seq reveals that SPT6L is required to maintain the amount and length of Pol V transcripts. Our findings thus uncover the critical role of a Pol II conserved elongator in Pol V mediated DNA methylation and transcription, and shed light on the mutual regulation between Pol V and II in plants.

Date: 2024
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DOI: 10.1038/s41467-024-48940-8

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