The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis

Abstract

DNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that CLASSY1-4 (CLSY1-4), four locus-specific regulators of DNA methylation that are differentially expressed during plant development, play major roles in controlling tissue-specific DNA methylation patterns. Depending on the tissue, the genetic requirements for specific CLSYs differ significantly and, on a global scale, certain clsy mutants are sufficient to largely shift the epigenetic landscape between tissues. Together, these findings not only reveal substantial epigenetic diversity between tissues, but assign these changes to specific CLSY proteins, revealing how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.

Ovule siRNAs methylate protein-coding genes in trans

“…CLSY3 is also the predominant family member expressed in 10 dpf seed and endosperm. Expression of CLSY3 is much higher than expression of CLSY4 in both ovule and endosperm, which is consistent with the stronger requirement for CLSY3 for siRNA production at siren loci in Arabidopsis (Zhou et al, 2021). In tissues lacking substantial siren siRNA accumulation, such as leaf and embryo, CLSY3 expression is low and CLSY1 is the predominant family member expressed.…”

“…In contrast, AT2G36700 shows strong NRPD1-dependent CHH and CHG methylation specifically in the region homologous to siren loci ( Supplemental Figure 6C ). RNAseq data demonstrates that AT2G36700 is upregulated 77-fold in nrpd1 ovules, 4.6 fold in clsy3 ovules, but is unchanged in nrpd1 or clsy3 leaves (Zhou et al, 2021), suggesting that siren-mediated trans -methylation represses transcription of PME genes in both Arabidopsis and B. rapa. Multiple non-syntenic siren loci targeting the same genes or gene families in Arabidopsis and B. rapa suggests convergent evolution of siren siRNA-mediated trans -methylation.…”

“…Loss of CLSY1, CLSY2, or SHH1 had no impact on siren siRNA accumulation. Zhou et al have also established that siRNA production in ovules is dependent on CLSY3 and CLSY4, which are highly expressed in ovules (Zhou et al, 2021).…”

“…Differential expression of Arabidopsis PME gene AT2G36700 in clsy mutant ovules was retrieved from (Zhou et al, 2021).…”

Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

“…Siren sRNAs in Brassica rapa and A. thaliana are expressed via the canonical RNA POLYMERASE IV (Pol IV)-RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) pathway from the same loci in maternal and seed tissues, relatively highly in ovules and seed coat, moderately in the endosperm, and lowly in embryos and mature seeds (64). We show that rice endosperm siren sRNAs, like those of Brassicaceous ovules (64,65) but unlike those of rice eggs and ovary (66), are associated with greater CHH methylation compared with the relatively lowly expressed nonsiren 24-nt sRNAs, suggestive of siren-mediated RdDM. However, our finding that imprinted siren sRNAs mediate as much or more trans RdDM than cis RdDM, despite frequent imprinted gene expression from the trans allele of genes which overlap siren loci, suggests either that siren-mediated RdDM is ineffective at gene silencing in rice endosperm or that imprinted genes overlapped by siren loci progress toward silencing of both alleles during rice endosperm development.…”