Is RNA-dependent RNA polymerase essential for transposon control?

BMC Systems Biology

Table 3 Reactions and their availability in the three models.

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		+	+	+

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.

ISSN: 1752-0509