Frontiers in plant science · 2026
Ac killer 1 establishes two epigenetically distinct regions associated with stable silencing of the maize Ac transposon.
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Wang Dafang, Wang Sicong, Horowitz Lilly, Zhao Meixia, Ishraq Zuhair, Huang Charlotte, Scelfo Michelle, Singh Tejbir, Singh Ryan, Kim Sihun
Аннотация
INTRODUCTION: We previously identified the silenced maize line p1-ww-id1, which carries Ac killer 1 (Ack1), a naturally occurring inverted-repeat allele generated by alternative transposition. Ack1 produces Ac-homologous small RNAs associated with reduced Ac activity, but how these small RNAs relate to Ac silencing across development remains unclear.
METHODS: We examined Ack1-associated silencing across four developmental stages representing embryonic, juvenile vegetative, adult vegetative, and reproductive tissues. Ac transcript abundance, region-specific small RNAs, and DNA methylation were analyzed, and Ack1 was introduced into a mop1 mutant background to test the contribution of the canonical 24-nt RNA-directed DNA methylation (RdDM) pathway.
RESULTS: Across all four developmental stages, the Ac subterminal/promoter region accumulated predominantly 24-nt small RNAs, whereas the Ac-transcribed region accumulated predominantly 21-22 nt small RNAs. Both regions gained CG, CHG, and CHH methylation despite their distinct small RNA compositions. Ac transcript abundance was reduced across the developmental series, with significant repression in embryonic, juvenile, and adult vegetative tissues. In V8 leaf 10, loss of MOP1 depleted subterminal/promoter 24-nt small RNAs and reduced DNA methylation in this region. In contrast, the Ac-transcribed region accumulated more 21-22-nt small RNAs and showed increased DNA methylation, while Ac remained transcriptionally repressed.
DISCUSSION: These findings reveal two epigenetically distinct regions of Ac characterized by different predominant small RNA populations and contrasting responses to disruption of canonical RdDM. The results support a model in which a naturally occurring inverted-repeat allele organizes region-specific epigenetic states across an active transposon while transcriptional repression persists.
METHODS: We examined Ack1-associated silencing across four developmental stages representing embryonic, juvenile vegetative, adult vegetative, and reproductive tissues. Ac transcript abundance, region-specific small RNAs, and DNA methylation were analyzed, and Ack1 was introduced into a mop1 mutant background to test the contribution of the canonical 24-nt RNA-directed DNA methylation (RdDM) pathway.
RESULTS: Across all four developmental stages, the Ac subterminal/promoter region accumulated predominantly 24-nt small RNAs, whereas the Ac-transcribed region accumulated predominantly 21-22 nt small RNAs. Both regions gained CG, CHG, and CHH methylation despite their distinct small RNA compositions. Ac transcript abundance was reduced across the developmental series, with significant repression in embryonic, juvenile, and adult vegetative tissues. In V8 leaf 10, loss of MOP1 depleted subterminal/promoter 24-nt small RNAs and reduced DNA methylation in this region. In contrast, the Ac-transcribed region accumulated more 21-22-nt small RNAs and showed increased DNA methylation, while Ac remained transcriptionally repressed.
DISCUSSION: These findings reveal two epigenetically distinct regions of Ac characterized by different predominant small RNA populations and contrasting responses to disruption of canonical RdDM. The results support a model in which a naturally occurring inverted-repeat allele organizes region-specific epigenetic states across an active transposon while transcriptional repression persists.