Abstract
The biological relevance of non-protein coding RNAs in the regulation of critical plant processes has been firmly established in recent years. This has been mostly achieved with the discovery and functional characterization of small non-coding RNAs, such as small interfering RNAs and microRNAs (miRNAs). However, recent next-generation sequencing techniques have widened our view of the non-coding RNA world, which now includes long non-coding RNAs (lncRNAs). Small and lncRNAs seem to diverge in their biogenesis and mode of action, but growing evidence highlights their relevance in developmental processes and in responses to particular environmental conditions. Light can affect MIRNA gene transcription, miRNA biogenesis, and RNA-induced silencing complex (RISC) activity, thus controlling not only miRNA accumulation but also their biological function. In addition, miRNAs can mediate several light-regulated processes. In the lncRNA world, few reports are available, but they already indicate a role in the regulation of photomorphogenesis, cotyledon greening, and photoperiod-regulated flowering. In this review, we will discuss how light controls MIRNA gene expression and the accumulation of their mature forms, with a particular emphasis on those miRNAs that respond to different light qualities and are conserved among species. We will also address the role of small non-coding RNAs, particularly miRNAs, and lncRNAs in the regulation of light-dependent pathways. We will mainly focus on the recent progress done in understanding the interconnection between these non-coding RNAs and photomorphogenesis, circadian clock function, and photoperiod-dependent flowering.
Highlights
INTRODUCTIONPlant pri-miRNAs fold into stem-loop structures and are processed by a complex containing DICER-LIKE1 (DCL1), HYPONASTIC LEAVES1 (HYL1), and SERRATE (SE), which will first release the stemloop (pre-miRNA) structure, and cleave it giving rise to a mature miRNA:miRNA∗ duplex, normally 20–22 nucleotides (nt) long, with the rarer cases of 23–25 nt, with 2-nt 3 overhangs (Voinnet, 2009; Borges and Martienssen, 2015; Yu et al, 2017)
We present a summary of the different miRNAs that respond to two or more light treatments. 1miRNA families reported to be regulated by light in at least two papers have been included. miRNA families are ordered according to the number of papers reporting their light regulation. 2W, white light; FR, far-red light; R, red light; B, blue light; L/D, light/dark; LD/SD, long days/short days. 3Ath, Arabidopsis thaliana; Gma, Glycine max; Mdo, Malus x domestica; Osa, Oryza sativa; Ppy, Pyrus pyrifolia (Chinese sand pear); Ptr, Populus tremula; Stu, Solanum tuberosum; Tae, Triticum aestivum; Zma, Zea mays
Further research is still necessary to uncover the molecular mechanisms that account for this regulation. Both small and long non-coding RNAs (lncRNAs) have been associated with specific biological processes that can occur at particular developmental stages, often in very precise locations within certain organs and tissues
Summary
Plant pri-miRNAs fold into stem-loop structures and are processed by a complex containing DICER-LIKE1 (DCL1), HYPONASTIC LEAVES1 (HYL1), and SERRATE (SE), which will first release the stemloop (pre-miRNA) structure, and cleave it giving rise to a mature miRNA:miRNA∗ duplex, normally 20–22 nucleotides (nt) long, with the rarer cases of 23–25 nt, with 2-nt 3 overhangs (Voinnet, 2009; Borges and Martienssen, 2015; Yu et al, 2017) This duplex is methylated at its 3 ends by the methyltransferase HUA ENHANCER1 (HEN1) and this methylation is necessary to stabilize miRNAs (Yu et al, 2005). We will discuss light regulation of miRNA expression, biogenesis, processing, and function, as well as their role in light-related processes, such as photomorphogenesis and photoperiod-dependent flowering. Due to the interconnection between light and the circadian clock, we will discuss the available reports on circadian-regulated ncRNAs
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