Expanding the plant non-coding RNA world

Abstract

in mouse revealed "a new continent in the RNA world", through the novel observation showing that ~73% of genomic regions are used for transcription of non-coding RNAs (Carninci et al. 2005;Katayama et al. 2005). The emergence of next-generation sequencing technologies encouraged this trend to identify a variety of non-coding RNAs. These big successes by non-coding RNA research have generated new RNA biology; now we know that RNA molecules are not only working as the intermediates between DNAs and proteins, but as key players of posttranscriptional and epigenetic regulation of gene expression. This is obviously true in plants, as many experimental reports have indicated the importance of non-coding RNAbased gene regulation in plant development, environmental responses, and biotic and/or abiotic stress responses.In this special issue of JPR Symposium "Expanding the plant non-coding RNA world", our current understanding of biogenesis, metabolisms, and function of plant non-coding RNA is reviewed and discussed with updated review articles, an original paper, and a technical note. First, we tried to provide detailed molecular views of small RNA biogenesis in plants. The siRNA and microRNA (miRNA), classes of small RNA with 18-25 nucleotides (nt) in length, pursue their function as the guides to target specific mRNAs for gene silencing, after incorporation into an RNA-induced silencing complex (RISC). These small RNAs are generated through multiple steps of RNA metabolic regulation; (1) formation of inter-or intramolecular double-stranded RNA (dsRNA) precursors, (2) biogenesis of small RNA duplexes through catalyzing dsRNA by dsRNA-specific endoribonucleases, Dicer-like (DCL) proteins, (3) loading of small RNA duplex onto ARGONAUTE (AGO) proteins, and (4) elimination of miRNA* or passenger siRNA strand, which are complementary strands for guide strand RNAs in small RNA duplex, by unwinding of Ribonucleic acid (RNA) is one of the biopolymers essential for organisms. In the "classical" view of molecular biology, functional RNA species have been categorized into three major groups, such as messenger RNAs (mRNAs), template molecules to biosynthesize proteins, ribosomal RNAs (rRNAs), components of huge molecular machinery ribosome for protein biosynthesis, and transfer RNAs (tRNAs), molecular couriers of amino acids to the ribosome. Function of these RNAs brought the perspective of so-called "central dogma", in which RNA molecules are considered as the mediators of genomic information written within DNA molecules for protein biosynthesis to achieve required cell activity.However, our view of RNA function has been greatly revised with the advent of the post genome era. One notable study was the discovery of small non-coding RNAs, called small interference RNAs (siRNAs), that function in post-transcriptional gene silencing (Fire et al. 1998). Later, the phenomenon known as co-suppression in plants and quelling in fungi, in which transgenes suppress the accumulation of endogenous transcripts based on the homology between tran...

Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice

“…The molecular mechanism of heterosis is still unclear through extensive studies on genome, transcriptome and epigenetics ( Larièpe et al, 2012 ; Shen et al, 2014 ; Shao et al, 2019 ; Wang and Wang, 2022 ; Zhang, 2022 ). In recent years, several ncRNAs and their corresponding regulatory networks have been proved to play important roles in plant growth and development ( Ohtani, 2017 ; Yuan et al, 2018 ; Luan et al, 2019 ; Wang et al, 2020 ; Zhai et al, 2020 ; Chand Jha et al, 2021 ; Qiao et al, 2021 ). However, there are few studies on the role of ncRNA in plant heterosis so far, which have been conducted in maize and cabbage ( Crisp et al, 2020 ; Hou et al, 2020 ; Li et al, 2021 ).…”

“…With the rapid rise of modern genomics techniques, noncoding RNA or nonprotein-coding RNAs (ncRNA or npcRNA), once called genomic “dark matter,” has been discovered ( Morris and Mattick, 2014 ; Yu et al, 2019 ). By targeting to corresponding DNA, RNA and proteins, ncRNAs participate in a variety of biological processes and molecular mechanisms in plants ( Ohtani, 2017 ; Chand Jha et al, 2021 ). In rice, many experimental reports have indicated the importance of ncRNAs in growth, development, environmental response ( Yuan et al, 2018 ; Luan et al, 2019 ; Wang et al, 2020 ; Zhai et al, 2020 ; Qiao et al, 2021 ).…”

Identification and differential analysis of noncoding RNAs in response to drought in Phyllostachys aureosulcata f. spectabilis

“…Many experimental reports have shown that ncRNAs and their target genes play important roles in plant development, environmental responses, and biotic and abiotic stress responses (Ohtani, 2017).…”

“…ncRNAs are mainly classified into long noncoding RNAs (lncRNAs), which are longer than 200 nt, and small noncoding RNAs (sRNAs), which are smaller than 200 nt ( Gelaw and Sanan-Mishra, 2021 ). Many experimental reports have shown that ncRNAs and their target genes play important roles in plant development, environmental responses, and biotic and abiotic stress responses ( Ohtani, 2017 ).…”

Identification and analysis of short-term and long-term salt-associated lncRNAs in the leaf of Avicennia marina

“…However, only approximately 2% of the transcribed genome possesses protein-coding ability, and most of the transcripts are non-coding RNAs (ncRNAs) [ 1 , 2 ]. The ncRNAs are involved in a series of biological processes and pathways in organisms by acting on corresponding targets, such as DNA, RNA, and proteins [ 3 , 4 ]. Long non-coding RNAs (lncRNAs) are freshly discovered functional ncRNAs that are longer than 200 nt in length, possessing little or no coding possibility, exerting extensive regulatory effects through a variety of mechanisms [ 5 – 7 ].…”