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Table 3 Reactions and their availability in the three models.

From: Is RNA-dependent RNA polymerase essential for transposon control?

Transposon life cycle
Description Reaction RdRP Antisense hairpin
VLP integration in genome + + +
production of mRNA + + +
production of other/antisense RNA + + +
transport of mRNA + + +
decay of mRNA + + +
production of VLP + + +
decay of VLP + + +
VLP integration failed implicitly present
Transcriptional gene silencing
Description Reaction RdRP Antisense hairpin
TE spontaneously silenced + + +
TE silenced by RITS + + +
TE activation + + +
production of dsRNA by RdRP + - -
dsRNA by sense-antisense base pairing - + +
transport of antisense RNA - + -
decay of other/antisense RNA + + +
production of siRNA + + +
decay of siRNA + + +
Post-transcriptional gene silencing
Description Reaction RdRP Antisense hairpin
production of dsRNA by RdRP + - -
production of dsRNA from primed mRNA + - -
dsRNA by sense-antisense base pairing - + -
dsRNA by hairpin formation - - +
degradation by RISC + + +
decay of mRNA + + +
decay of antisense RNA - + -
production of siRNA + + +
decay of siRNA + + +
  1. In the first column a short description of the reaction is given, in the second column the pseudo-reactions are given as a formula, followed by three columns indicating the presence (+) and absence (-) of each reaction in the different models. Note that we do not consider the decay of TEs, and as a consequence we study a system that is in a transient state, not an equilibrium. Symbol legend: T act active TE, T sil silent TE, V virus-like particle, M n nuclear mRNA, M c cytoplasmic mRNA, R n nuclear other/antisense RNA, R c cytoplasmic antisense RNA, D n nuclear dsRNA, D c cytoplasmic dsRNA, S n nuclear siRNA, S c cytoplasmic siRNA.