About this Research Topic
Small RNAs are 18-24 nucleotide non-coding RNAs and are key regulators of gene expression in eukaryotes at the transcriptional level. The two major classes of small RNAs are microRNAs (miRNA) and small interfering RNA (siRNAs), classified based on their origin and biogenesis. miRNA genes are transcribed by RNA polymerase II and are further processed by DICER-LIKE 1 into a miRNA/miRNA* duplex. One of the strands is subsequently loaded onto AGO1 as part of RISC to carry out either post-transcriptional gene silencing or translational inhibition. siRNAs, on the other hand, are synthesized from dsRNA and are further classified according to their origin and processing enzymes into heterochromatic siRNAs, natural antisense siRNAs, and phased siRNAs or transacting siRNA secondary siRNAs. hc-siRNAs are 24nt in length, transcribed by a plant-specific PolIV at the site of RdDM, and make dsRNA by RDR2, which is then processed via DCL3. They are recognized by AGO4 and interact with scaffold RNAs transcribed at the target loci by RNA polymerase V to carry out DNA methylation. nat-siRNAs are derived from annealed pair regions of natural antisense transcripts. The phasiRNAs are derived from cleaved target templates of a miRNA that are in phase relative to the miRNA cleavage site. They generally act in trans to regulate other genes via mRNA cleavage. Thus, though the major biological function of all small RNAs is in gene regulation, mostly by mRNA cleavage, however, their origin and biogenesis differ.
A plethora of information is available with respect to the biogenesis and biological role of small RNAs in plants. Although a major part of existing knowledge in the area has been generated from angiosperms, recent development in NGS technologies has helped researchers to gain insight into other plant groups including lower plants. However, there is still a lack of knowledge about the origin of small RNAs and how they arise. The main focus of plant small RNA research so far remains on the identification and the interaction of small RNAs and their targets. Research on the regulatory mechanisms of small RNAs and their evolution in different lineages or under different climatic conditions is mostly lacking. To achieve a greater understanding of these issues, there is a need for research focused on: i) identifying different cis and trans elements involved in different classes of small RNA expression in different plants lineages or under different climatic conditions, ii) the evolution of different components of small RNA mediated gene regulation including RdDM pathways in different plant groups including lower plants, and iii) identifying new small RNAs from understudied plant lineages.
The main focus of this Research Topic is to better understand the evolution of different components of plant small RNA machinery in different plant lineages including lower plants. The scope of the Research Topic includes studies related to the evolutionary relationship of such components amongst different plant groups and the fitness advantages they provide under particular environmental conditions; identification of novel small RNAs from unexplored and important plant groups which may be used for crop improvement under various abiotic or biotic stress conditions; new insight into the origin, biogenesis, and regulatory mechanisms of small RNA in plant species including lower groups of plants; environmental factors affecting small RNA expression as well as their processing machinery, etc. Examples of specific themes include:
• The origin of small RNA genes, small RNA biogenesis, and functions
• Evolutionary relationships of small RNA components
• New insight into the regulatory mechanisms of small RNAs
• Small RNAs in lower plant groups
• Role of small RNAs in future crop improvement programs
Keywords: small RNA, plants, environmental change, evolution
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