Paramutation in maize: RNA mediated trans-generational gene silencing

Abstract

Paramutation involves trans-interactions between alleles or homologous sequences that establish distinct gene expression states that are heritable for generations. It was first described in maize by Alexander Brink in the 1950s, with his studies of the red1 (r1) locus. Since that time, paramutation-like phenomena have been reported in other maize genes, other plants, fungi, and animals. Paramutation can occur between endogenous genes, two transgenes or an endogenous gene, and transgene. Recent results indicate that paramutation involves RNA-mediated heritable chromatin changes and a number of genes implicated in RNAi pathways. However, not all aspects of paramutation can be explained by known mechanisms of RNAi-mediated transcriptional silencing.

Figure 1. Model for paramutation at the b1 locus in maize

(A) Description of the two alleles and model for long distance cis regulation of b1 transcription. The two epialleles involved in paramutation, B-I (darkly pigmented) and B′ (lightly pigmented) exhibit different b1 transcription levels. The seven tandem repeats (depicted as black arrows) required to induce paramutation in maize are located ∼100 kb upstream of the transcription start site (TSS) of the b1 coding region. These tandem repeats also contain enhancer activity and interaction between the tandem repeats and the TSS is proposed to mediate high b1 transcription by a multi-loop structure in B-I (I) in contrast to a simple loop structure in B′ (II). a) B-I and B′ tandem repeats are bi-directionally transcribed at similar rates, with the majority of transcription by Pol II (Pol IV/V-like enzymes may also play a role, see text). b) transcripts derived from the tandem repeats are used to generate dsRNA either by pairing of opposite strands or through the activity of MOP1 (RDR), which may function in a reinforcement loop to maintain and amplify dsRNA. c) accumulation of short interfering siRNAs depends on the activity of MOP1, RMR6, MOP2/RMR7, RMR1 and hypothesized proteins (indicated by an asterisk) such as DCL3* and HEN1*. d) siRNA-guided chromatin based modification may involve the activity of RMR6, MOP2/RMR7, RMR1, DRD1*, DRM2* and AGO4*, and other RdDM related components. Experimental data indicate the alleles have two contrasting chromatin states with B-I (e) in an active conformation (green box) and B′ (f) in a silent conformation (red box). One model to explain how B-I can remain active in spite of producing siRNAs is that its chromatin structure is immune to silencing, potentially because RNA silencing complexes cannot assemble or the B-I repeats are not localized in the same subnuclear compartment as B′. (B) Model for paramutation and RNA-mediated trans-interactions between alleles. (1) B-I can spontaneously turn into B′ at a relatively high frequency (1-10%), indicating that while heritable, the B-I state is unstable. B′* symbolizes a B′ allele that was B-I in the previous generation. B′ and B′* are indistinguishable in terms of their paramutation activity and B′ (B′*) is extremely stable; no changes from B′ to B-I have ever been observed in wild type backgrounds. (2) When B-I and B′ are crossed paramutation always occurs; B-I is always changed into B′* (asterisk indicates that the newly generated B′ state was B-I in the previous generation). The genes required for paramutation are indicated and repeat siRNAs are assumed to be generated using a pathway similar to that diagramed in Panel A. Experimental evidence strongly suggests RNA plays a key role in mediating these trans-interactions. However, RNA may not be sufficient. One possibility is that B-I is efficiently silenced in the presence of B′ through chromatin associated pairing with the B′ repeats that allows the RNA silencing complexes to assemble on B-I and establish a B′* state.