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

Yujuan Liu,Yujuan Liu,Yujuan Liu,Yujuan Liu,Yujuan Liu,Yujuan Liu,Yujuan Liu,Yujuan Liu,Yujuan Liu,Jie Shu,Jie Shu,Jie Shu,Jie Shu,Zhi Zhang,Zhi Zhang,Zhi Zhang,Zhi Zhang,Zhi Zhang,Zhi Zhang,Zhi Zhang,Zhi Zhang,Zhi Zhang,Ning Ding,Ning Ding,Ning Ding,Ning Ding,Jinyuan Liu,Jinyuan Liu,Jinyuan Liu,Jinyuan Liu,Jinyuan Liu,Jinyuan Liu,Jinyuan Liu,Jinyuan Liu,Jinyuan Liu,Jun Liu,Yuhai Cui,Yuhai Cui,Changhu Wang,Changhu Wang,Changhu Wang,Changhu Wang,Changhu Wang,Changhu Wang,Changhu Wang,Changhu Wang,Changhu Wang,Chen Chen,Chen Chen,Chen Chen

doi:10.1038/s41467-024-48940-8

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.

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