PLoS Biol. 1(3): 420-428 (Dec 2003)
Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification.
Zachary Lippman, Bruce May, Cristy Yordan, Tatjana Singer, Rob Martienssen

Heritable, but reversible, changes in transposable element activity were first observed in maize by Barbara McClintock in the 1950s. More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi). Using a genetic approach, we have investigated the role of these modifications in the epigenetic regulation and inheritance of six Arabidopsis transposons. Silencing of most of the transposons is relieved in DNA methyltransferase (met1), chromatin remodeling ATPase (ddm1), and histone modification (sil1) mutants. In contrast, only a small subset of the transposons require the H3mK9 methyltransferase KRYPTONITE, the RNAi gene ARGONAUTE1, and the CXG methyltransferase CHROMOMETHYLASE3. In crosses to wild-type plants, epigenetic inheritance of active transposons varied from mutant to mutant, indicating these genes differ in their ability to silence transposons. According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing. Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation.

Silencing of Active Transposons via siRNA

Active retrotransposons are epigenetically inherited from the methyltransferase mutants met1 and cmt3. An attractive mechanism accounting for this inheritance is that loss of DNA methylation cannot be restored by maintenance methyltransferase (Tariq et al. 2003). However, the loss of DNA methylation in sil1 is comparable to cmt3 and met1, and yet active transposons are readily silenced in sil1/+ backcrosses. One difference between these mutants is that met1 does not accumulate siRNA corresponding to AtSN1 or AtMu1, resembling in this respect the silencing mutants ago4 and sde4 (Hamilton et al. 2002; Zilberman et al. 2003). siRNA accumulates normally in sil1. Loss of siRNA is not due to silencing of these transposons, as AtMu1 is activated in sil1, ddm1, and met1. In contrast, ATGP1 siRNA levels are unaffected and ATGP1 is silenced in met1/+. Further, the only elements that retained H3mK9 in met1 (ATLANTYS2-1, ATLINE1-4, and ATGP1) exhibited at least some resilencing in met1+.

Thus, MET1 may require siRNA for silencing de novo. CMT3 may also require siRNA: ATLINE1-4 was not silenced when cmt3 was backcrossed to WT, but PAI2 and SUP genes activated in cmt3 could be silenced by complementation with CMT3 transgenes (Bartee et al. 2001; Lindroth et al. 2001). Complementation was in the presence of an inverted repeat, which could provide siRNA in trans. We have not been able to detect siRNA from ATLINE1-4. If siRNA guides silencing by MET1, it would have to act in cis, as it is provided from the WT parent in met1/+ backcrossed plants. siRNA contributed in trans might eventually reestablish silencing in subsequent generations, resembling the presetting and cycling of transposon activity in maize. Such long-term consequences of silencing deserve further investigation.