sgs1: a neomorphic nac52 allele impairing post‐transcriptional gene silencing through SGS3 downregulation

Abstract

Post-transcriptional gene silencing (PTGS) is a defense mechanism that targets invading nucleic acids from endogenous (transposons) or exogenous (pathogens, transgenes) sources. Genetic screens based on the reactivation of silenced transgenes have long been used to identify cellular components and regulators of PTGS. Here we show that the first isolated PTGS-deficient mutant, sgs1, is impaired in the transcription factor NAC52. This mutant exhibits striking similarities to a mutant impaired in the H3K4me3 demethylase JMJ14 isolated from the same genetic screen. These similarities include increased transgene promoter DNA methylation, reduced H3K4me3 and H3K36me3 levels, reduced PolII occupancy and reduced transgene mRNA accumulation. It is likely that increased DNA methylation is the cause of reduced transcription because the effect of jmj14 and sgs1 on transgene transcription is suppressed by drm2, a mutation that compromises de novo DNA methylation, suggesting that the JMJ14-NAC52 module promotes transgene transcription by preventing DNA methylation. Remarkably, sgs1 has a stronger effect than jmj14 and nac52 null alleles on PTGS systems requiring siRNA amplification, and this is due to reduced SGS3 mRNA levels in sgs1. Given that the sgs1 mutation changes a conserved amino acid of the NAC proteins involved in homodimerization, we propose that sgs1 corresponds to a neomorphic nac52 allele encoding a mutant protein that lacks wild-type NAC52 activity but promotes SGS3 downregulation. Together, these results indicate that impairment of PTGS in sgs1 is due to its dual effect on transgene transcription and SGS3 transcription, thus compromising siRNA amplification.

Exploiting Genomic Features to Improve the Prediction of Transcription Factor-Binding Sites in Plants

“…We have also to point out NAC50 and NAC52, for which TF-pooled models are substantially less performing than the TF-specific ones. NAC50 and NAC52 bind the DNA on sites exhibiting a particular palindromic motif and might recruit a demethylase that will cause the silencing of the targeted genes (S. Zhang et al, 2015;Butel et al, 2017;van Rooijen et al, 2020). However, for NAC50 and NAC52 we could still demonstrate a positive association with the histone variant H2A.Z, representing a hallmark of cis-regulatory regions (Sequeira-Mendes et al, 2014).…”

De novo SNP calling reveals the genetic differentiation and morphological divergence in genus Amaranthus

“…AH021320 , AH021553 , and AH001353 were homologous to brassinosteroid‐insensitive 1 ( bri1 ; AT4G39400 ), an enhancer of FLC , consequently leading to late flowering (Domagalska et al., 2007). AH021139 was homologous to sgs1 ( AT3G10490 ), which encoded a transcription factor of NAC52 and regulated flowering time through DNA methylation (Butel et al., 2017). AH001354 was homologous to FLOWERING TIME CONTROL LOCUS A ( FCA ; AT4G16280 ), a fca1 mutant expressed late flowering in Arabidopsis (Macknight et al., 1997).…”

De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus

“…AH021320, AH021553 and AH001353 were homologous to brassinosteroid - insentitive 1 ( bri1; AT4G39400 ), an enhancer of FLC , consequently leading to late flowering (Domagalska et al, 2007). AH021139 was homologous to sgs1 ( AT3G10490 ), which encoded a transcription factor of NAC52 and regulated flowering time through DNA methylation (Butel et al, 2017). AH001354 was homologous to FLOWERING TIME CONTROL LOCUS A ( FCA; AT4G16280 ); a fca1 mutant was revealed late flowering in Arabidopsis (Macknight et al, 1997).…”

“…(AT3G10490), which encoded a transcription factor of NAC52 and regulated flowering time through DNA methylation (Butel et al, 2017). AH001354 was homologous to FLOWERING TIME CONTROL LOCUS A (FCA; AT4G16280); a fca1 mutant was revealed late flowering in Arabidopsis (Macknight et al, 1997).…”