Fig. 1

Genome-wide release of silencing in a new pol2a-12 mutant allele. a L5-GUS transgene activity detected by X-Gluc histochemical staining in 3-week-old L5 plants and anx2/pol2a-12 mutants. b Representative pictures of 16-day-old L5 and anx2 plants. Scale bar: 1 cm. c (top) Gene model for POL2A showing point mutations. The new nomenclature of pol2a mutant alleles used in this study is detailed in Table S1. The til1-4/pol2a-4 mutant allele contains two point mutations in the POL2A gene: one in exon 12 and a second one in intron 14. abo4-1/pol2a-8 is a G to A mutation at position 4171 changing Gly 522 to Asp. The same mutation was identified in anx3/pol2a-13. esd7-1/pol2a-10 is a G to A mutation at position 8074 changing Gly 992 to Arg. anx4/pol2a-14 is a C to T transition at position 5023 changing Leu 579 to Phe. (bottom) POL2A protein model showing point mutations and their corresponding amino acid changes (positions are indicated relative to the start ATG). Functional domains are indicated according to the conserved domain database from NCBI. DNA PolB ε: DNA polymerase type-B epsilon subfamily catalytic domain. Exo: DNA polymerase family B 3′ to 5′ exonuclease domain. DUF1714: domain of unknown function. d Transcript accumulation at four silent loci detected by RT-qPCR, normalized to the ACTIN2 gene with pol2a-8 set to 1. Asterisks mark statistically significant differences (unpaired two-sided Student’s t test, P < 0.05). Error bars represent standard error of the mean across three biological replicates. e Number of PCGs and TEs detected as differentially expressed in pol2a-12. f Proportion of TE superfamilies of all TEs in the Arabidopsis genome and of TEs upregulated in pol2a-12. g Changes in transcript accumulation in pol2a-12 relative to L5 control plants represented along chromosome 3 by log₂ ratios of average reads per kilobase per million mapped reads (RPKM) over non-overlapping 100 kb bins (black, left y-axis). Total TE density is the proportion of TE annotations per 100 kb bins, indicating the pericentromeric region (gray, right y-axis)