Skip to main content

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.