Abstract
Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle mechanism. Viroids interact with host processes in complex ways, emerging as one of the most productive tools for studying the functions of lncRNAs. Defective (D) RNAs, another category of lnc RNAs, are found in a variety of plant RNA viruses, most of which are noncoding. These are derived from and are replicated by the helper virus. D RNA-virus interactions evolve into mutually beneficial combinations, enhancing virus fitness via competitive advantages of moderated symptoms. Yet the satellite RNAs are single-stranded and include either large linear protein-coding ss RNAs, small linear ss RNAs, or small circular ss RNAs (virusoids). The satellite RNAs lack sequence homology to the helper virus, but unlike viroids need a helper virus to replicate and encapsidate. They can attenuate symptoms via RNA silencing and enhancement of host defense, but some can be lethal as RNA silencing suppressor antagonists. Moreover, selected viruses produce lncRNAs by incomplete degradation of genomic RNAs. They do not replicate but may impact viral infection, gene regulation, and cellular functions. Finally, the host plant lncRNAs can also contribute during plant-virus interactions, inducing plant defense and the regulation of gene expression, often in conjunction with micro and/or circRNAs.
Highlights
The genes encoding long non-coding RNAs (lncRNAs) occur in very large numbers in the human genome (58,648 genes) and their regulative roles are implicated at all levels of gene expression, influencing multiple cellular activities
We focus on lncRNAs related to plant RNA viruses, both to those that do not
We focus on lncRNAs related to plant RNA viruses, both to those that do not originate from virus genomes and those of viral origin (defectiveoriginate from virus genomes and those of viral origin (Figure 1)
Summary
Over several decades numerous classes of noncoding RNAs (ncRNAs) have been identified in all organismal kingdoms. An example of regulation of flowering is lncRNA COLDAIR, which is or for controlling diseases, and in turn play roles in flowering, morphogenesis, reproduction, crop yield downregulated by cold treatment, recruits a protein PRC2 which suppresses the expression of or stress response. LncRNAs can regulate histone modifications at the chromatin level, via interacting with or acting described in the case of repressive complex PRC2 [7] or COMPASS-like complex [8], which are as scaffolds for methylation and acetylation complexes. We focus on lncRNAs related to plant RNA viruses, both to those that do not originate from virus genomes (viroids and satellite RNAs) and those of viral origin (defectiveoriginate from virus genomes (viroids and satellite RNAs) and those of viral origin (defective-interfering interfering DI RNAs or subviral RNAs) (Figure 1). HV—Helper virus, RdRp—RNA dependent RNA polymerase, CP—Coat protein
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