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RNA ‐directed DNA methylation efficiency depends on trigger and target sequence identity
Author(s) -
Dalakouras Athanasios,
Dadami Elena,
Wassenegger Michèle,
Krczal Gabi,
Wassenegger Michael
Publication year - 2016
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13193
Subject(s) - biology , viroid , rna , transgene , small interfering rna , dna methylation , methylation , genetics , dna , gene , gene expression
Summary RNA ‐directed DNA methylation (Rd DM ) in plants has been extensively studied, but the RNA molecules guiding the Rd DM machinery to their targets are still to be characterized. It is unclear whether these molecules require full complementarity with their target. In this study, we have generated Nicotiana tabacum (Nt) plants carrying an infectious tomato apical stunt viroid ( TASV d) transgene (Nt‐ TASV d) and a non‐infectious potato spindle tuber viroid ( PSTV d) transgene (Nt‐ SB 2). The two viroid sequences exhibit 81% sequence identity. Nt‐ TASV d and Nt‐ SB 2 plants were genetically crossed. In the progeny plants (Nt‐ SB 2/ TASV d), deep sequencing of small RNA s ( sRNA s) showed that TASV d infection was associated with the accumulation of abundant small interfering RNA s (si RNA s) that mapped along the entire TASV d but only partially matched the SB 2 transgene. TASV d si RNA s efficiently targeted SB 2 RNA for degradation, but no transitivity was detectable. Bisulfite sequencing in the Nt‐ SB 2/ TASV d plants revealed that the TASV d transgene was targeted for dense cis ‐Rd DM along its entire sequence. In the same plants, the SB 2 transgene was targeted for trans ‐Rd DM . The SB 2 methylation pattern, however, was weak and heterogeneous, pointing to a positive correlation between trigger–target sequence identity and Rd DM efficiency. Importantly, trans ‐Rd DM on SB 2 was also detected at sites where no homologous si RNA s were detected. Our data indicate that Rd DM efficiency depends on the trigger–target sequence identity, and is not restricted to si RNA occupancy. These findings support recent data suggesting that RNA s with sizes longer than 24 nt (>24‐nt RNA s) trigger Rd DM .