Fact Sheet 3: Small RNAs and other non-coding RNAs

Adrián Contreras Garrido

Small RNAs (sRNAs) are a category of non-coding RNAs characterized for its short sequence (<200 nucleotide length) that are widespread in various eukaryotes [1]. Because of its arbitrary categorization by length, they form a heterogeneous group of short transcripts that is better understood when subcategorized in different groups. This subcategorization is accomplished by their specific role and their biogenesis [2].

 Although the first role assigned to this sRNAs was in the post transcriptional gene silencing (PTGS), it has been shown that sRNAs participate also in genome stability, heterochromatin formation, developmental gene regulation, transposon regulation and in the epigenetic silencing of repetitive regions and other genomic regions [3]. Overall, we can say that sRNAs (and other non-coding RNAs) establish a layer of regulation of coding and non-coding genomic regions of the eukaryotic cell [4]. sRNAs are unable to perform their biological role by themselves and they need to associate with proteins to perform their task [5]. Inside this protein-RNA complexes, sRNAs usually functions as targeting machinery of the complex, guiding the complex to its loci of action (which usually is the biogenesis loci of a particular sRNA but there are exceptions like the phasiRNAs [6].

In this chapter we will focus in the major subgroup of sRNAs, the small interference RNAs (siRNAs) because of its role in epigenetics by the establishment of the de novo DNA methylation in plants [7]. Although it was first discovered in tobacco, the molecular mechanism has been well characterized in Arabidopsis thaliana [8]. We will describe at the molecular level the canonical and non-canonical [9] RNA directed DNA methylation pathways (RdDM) that exists in A. thaliana and its biological implications: The RdDM pathway has been implicated in transposon silencing, pathogen defense, stress responses, reproduction, and interallelic and intercellular communication [8]. We will also summarize the current knowledge that we have in this pathway in other plant organisms, specially maize [10] and how generalized it is.

Last, we will go briefly through other non-coding, epigenetic related, RNAs, specially those who are proposed as a link between environmental stimuli and changes in gene expression [11]. Among them, long non coding RNAs (lncRNAs)  can function as cis and trans-regulators of gene expression, mainly through the recruitment of chromatin remodeling complexes to loci they scaffold in but also by mimicking miRNAs such as the lncRNA INDUCED BY PHOSPHATE STARVATION 1 (IPS1) [12].

Our knowledge of the existence of biologically relevant ncRNAs  has been increasing since the implementation of the Next generation sequence (NGS) techniques but there are still several areas poorly understood about ncRNAs. We know its role in Eukaryotic organisms as gene expression regulators working in conjunction with protein complexes and guiding them to their specific target loci. Their relevance in stress responses and in the developmental stages of plants, yet it is poorly understood how this ncRNAs are selectively produced from their own loci and their regulation pathways.

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