PRJNA263691: Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition

Summary: Methylation patterns of plants are unique as, in addition to the methylation at CG dinucleotides that occurs in mammals, methylation also occurs at non‐CG sites. Genes are methylated at CG sites, but transposable elements (TE s) are methylated at both CG and non‐CG sites. The role of non‐CG methylation in transcriptional silencing of TE s is being extensively studied at this time, but only very rare transpositions have been reported when non‐CG methylation machineries have been compromised. To understand the role of non‐CG methylation in TE suppression and in plant development, we characterized rice mutants with changes in the chromomethylase gene, OsCMT 3a. oscmt3a mutants exhibited a dramatic decrease in CHG methylation, changes in the expression of some genes and TE s, and pleiotropic developmental abnormalities. Genome resequencing identified eight TE families mobilized in oscmt3a during normal propagation. These TE s included tissue culture‐activated copia retrotransposons Tos17 and Tos19 (Lullaby ), a pericentromeric clustered high‐copy‐number non‐autonomous gypsy retrotransposon Dasheng , two copia retrotransposons Osr4 and Osr13 , a hAT ‐tip100 transposon DaiZ , a MITE transposon mP ing , and a LINE element LINE 1‐6_OS . We confirmed the transposition of these TE s by polymerase chain reaction (PCR ) and/or Southern blot analysis, and showed that transposition was dependent on the oscmt3a mutation. These results demonstrated that OsCMT 3a‐mediated non‐CG DNA methylation plays a critical role in development and in the suppression of a wide spectrum of TE s. These in planta mobile TE s are important for studying the interaction between TE s and the host genome, and for rice functional genomics.

Overall Design: RNA-seq to study the role of a rice chromomethylase gene OsCMT3a on the transcriptional regulation of cellular gene and transposable elements.