scholarly journals Abolished miR158 activity leads to 21-nucleotide tertiary phasiRNA biogenesis that targets NHX2 in Arabidopsis thaliana

2021 ◽  
Author(s):  
Abhinandan Mani Tripathi ◽  
Rajneesh Singh ◽  
Akanksha Singh ◽  
Ashwani Kumar Verma ◽  
Parneeta Mishra ◽  
...  

ABSTRACTSmall RNAs including microRNAs (miRNAs) are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Some small RNAs, mostly 22-nucleotide long trigger biogenesis of secondary small interfering RNAs (siRNAs). Those siRNAs having distinctive phased configuration are known as phased siRNAs (phasiRNAs) and act either in cis or trans enhancing silencing cascade. Here, we report natural variants of MIR158 having deletions or insertions led to negligible or reduced expression of miR158. The deletion/insertion events affected processing of primary transcript of miR158 to precursor and to mature miR158. We show that miR158 targets a pseudo-pentatricopeptide gene and its abolished activity led to 21-nucleotide tertiary phasiRNA generation from its target. The biogenesis of these phasiRNAS is triggered by TAS2 derived two siRNAs. Accordingly, small RNA analyses of these natural variants, mutants and over-expression lines of MIR158 or its target exhibited enhanced or reduced phasiRNA biogenesis. Finally, we functionally validated the highest expressed tertiary phasiRNA that targets NHX2 thereby regulating transpiration and stomatal conductance. Overall, we deciphered a new module of small RNA network, miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2, suggesting an additional layer of gene regulation and larger role of pseudogene in plants.

Parasitology ◽  
2019 ◽  
Vol 147 (8) ◽  
pp. 855-864
Author(s):  
Collette Britton ◽  
Roz Laing ◽  
Eileen Devaney

AbstractSmall RNAs are important regulators of gene expression. They were first identified in Caenorhabditis elegans, but it is now apparent that the main small RNA silencing pathways are functionally conserved across diverse organisms. Availability of genome data for an increasing number of parasitic nematodes has enabled bioinformatic identification of small RNA sequences. Expression of these in different lifecycle stages is revealed by small RNA sequencing and microarray analysis. In this review we describe what is known of the three main small RNA classes in parasitic nematodes – microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs) and small interfering RNAs (siRNAs) – and their proposed functions. miRNAs regulate development in C. elegans and the temporal expression of parasitic nematode miRNAs suggest modulation of target gene levels as parasites develop within the host. miRNAs are also present in extracellular vesicles released by nematodes in vitro, and in plasma from infected hosts, suggesting potential regulation of host gene expression. Roles of piRNAs and siRNAs in suppressing target genes, including transposable elements, are also reviewed. Recent successes in RNAi-mediated gene silencing, and application of small RNA inhibitors and mimics will continue to advance understanding of small RNA functions within the parasite and at the host–parasite interface.


Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. 93-93
Author(s):  
Youmna Kfoury ◽  
Anthony Anselmo ◽  
Jefferson Seidl ◽  
Ani Papazian ◽  
Francois Mercier ◽  
...  

Abstract Background The bone marrow microenvironment (BMEV) regulates the highly regenerative hematopoietic system. However, there are a limited number of BMEV-derived molecules with a definitive role in maintaining hematopoietic stem and progenitor cells (HSPCs). Extracellular vesicles (EVs) encapsulate bioactive molecules, and may modify the physiology of their target cells. In hematopoiesis, EVs derived from culture-expanded mesenchymal cells can rescue irradiation damage, expand human umbilical cord blood cells and support HSPCs in vitro . However, in vivo evidence of EV function is lacking. We therefore sought to investigate the role of EVs in the interaction between the BMEV and the hematopoietic system and took advantage of existing mice bearing genetic reporters of key mesenchymal cell types. Results While analyzing the bone marrow (BM) of different mesenchymal cell-GFP reporter mice, we unexpectedly found CD45+ GFP+ cells. These were confirmed as single cells with intracellular GFP as demonstrated by imaging flow cytometry and confocal microscopy (Fig. 1A). Moreover, their hematopoietic identity was confirmed by their ability to form myeloid colonies in methylcellulose. Transplanted CD45.1 BM into Osteocalcin-Topaz (Ocn-Topaz) and Collagen1-GFP (Col1-GFP) mice that label osteoblasts, as well as Nestin-GFP (Nes-GFP) that labels mesenchymal stem cells demonstrated that donor cells are comparably labeled with GFP in Ocn-Topaz and Col1-GFP (2.2%) but at a much lower frequency (0.05%) in Nes-GFP. We therefore decided to proceed with the Ocn-Topaz model to investigate the role of osteoblast derived EVs in hematopoietic communication. Within the lineage negative compartment, the frequency of GFP+ cells increased with maturation. The highest frequency found in GMPs (0.06% of live cells were GFP+), followed by CMPs (0.01%), MEPs (0.002%) and LKS (0.004%) (Fig. 1B). Of particular interest, Lin- GFP+ cells formed ~5 fold more colonies as compared to their GFP- counterparts. However, transplantation assays demonstrated that the GFP+ cells possessed a decreased ability for long term reconstitution. Given the molecular weight of GFP, we hypothesized that EVs were the basis for transfer. Transmission electron microscopy coupled with immunogold staining revealed microvesicular structures of ~100 nm in size that contained GFP and that were labeled with the exosome marker TSG101 (Fig. 1C). Western blotting and flow cytometry detected labeling with exosome markers CD81 and CD9. Heparin sulfate proteoglycans (HSPGs) have been implicated in the biogenesis and uptake of EVs. Osteoblast-specific disruption of HSPGs by the knock out of the glycosyl transferase EXT1 resulted in a (40%) drop in the frequency of GFP+ cells in the GMP compartment. These findings demonstrate the EV-dependent transfer of GFP from osteoblasts to BM hematopoietic cells, and confirm GFP as a marker for the isolation and characterization of EV target cells. Exosomes from the BM of Ocn-Topaz mice in addition to GFP+ and GFP- GMPs were isolated for small RNA sequencing. In parallel, GMP populations were collected for mRNA sequencing. Global analysis of small RNA libraries from EVs and GMPs demonstrated that piRNAs was the most abundant species in both EVs (30%) and GMPs (18%). Surprisingly, EVs had low miRNA content (1.4%) compared to GMPs (9.2%) (Fig. 1D). When comparing GFP+ GMPs to GFP- ones, 6 miRNAs (mir-143, mir-122, mir-423-5p, mir-451, mir-206, mir-146b*) showed at least 100% increase in the GFP+GMPs. Predicted targets of mir-143, mir-206, mir-146 emerged as enriched sets when comparing gene expression of GFP+ and GFP- GMPs. In contrast, tRNAs was the most enriched species in EVs (10.5%) when compared to GMPs (2.5%) (Fig. 1D) and interestingly, GFP+ GMPs had higher content of tRNA when compared to GFP- (3.3% vs 1.7%) respectively. Given the role of tRNAs in translation and the emerging role of tRNA fragments (tRFs) in translation regulation and stress signaling, it was of interest to see translation and ribosome genesis among the top enriched gene sets when comparing GFP+ and GFP- GMPs. In conclusion, we present evidence for the in vivo transfer of bioactive EVs from osteoblasts to BM progenitor populations, and that this transfer alters hematopoietic cell function and gene expression. Moreover, we identify piRNAs and tRNAs as the most enriched species of small RNAs within BM derived EVs. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.


Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 371 ◽  
Author(s):  
Zeng ◽  
Gupta ◽  
Jiang ◽  
Yang ◽  
Gong ◽  
...  

Small RNAs (sRNAs), a class of regulatory non-coding RNAs around 20~30-nt long, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), are critical regulators of gene expression. Recently, accumulating evidence indicates that sRNAs can be transferred not only within cells and tissues of individual organisms, but also across different eukaryotic species, serving as a bond connecting the animal, plant, and microbial worlds. In this review, we summarize the results from recent studies on cross-kingdom sRNA communication. We not only review the horizontal transfer of sRNAs among animals, plants and microbes, but also discuss the mechanism of RNA interference (RNAi) signal transmission via cross-kingdom sRNAs. We also compare the advantages of host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS) technology and look forward to their applicable prospects in controlling fungal diseases.


2021 ◽  
Vol 22 (20) ◽  
pp. 11166
Author(s):  
Songqian Huang ◽  
Kazutoshi Yoshitake ◽  
Shuichi Asakawa

PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.


Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Qin Feng ◽  
Yan Li ◽  
Zhi-Xue Zhao ◽  
Wen-Ming Wang

AbstractSmall RNAs (sRNAs) are mainly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs) according to their origin. miRNAs originate from single-stranded RNA precursors, whereas siRNAs originate from double-stranded RNA precursors that are synthesized by RNA-dependent RNA polymerases. Both of single-stranded and double-stranded RNA precursors are processed into sRNAs by Dicer-like proteins. Then, the sRNAs are loaded into ARGONAUTE proteins, forming RNA-induced silencing complexes (RISCs). The RISCs repress the expression of target genes with sequences complementary to the sRNAs through the cleavage of transcripts, the inhibition of translation or DNA methylation. Here, we summarize the recent progress of sRNA pathway in the interactions of rice with various parasitic organisms, including fungi, viruses, bacteria, as well as insects. Besides, we also discuss the hormone signal in sRNA pathway, and the emerging roles of circular RNAs and long non-coding RNAs in rice immunity. Obviously, small RNA pathway may act as a part of rice innate immunity to coordinate with growth and development.


ExRNA ◽  
2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Fangfang Jin ◽  
Zhigang Guo

Abstract The discovery of small non-coding RNAs, such as miRNA and piRNA, has dramatically changed our understanding of the role RNA plays in organisms. Recent studies show that a novel small non-coding RNA generated from cleavage of tRNA or pre-tRNA, called tRNA-derived small RNA (tsRNA), serves as a new regulator of gene expression. tsRNA has been determined participate in regulating some specific physiological and pathological processes. Although knowledge regarding the biological roles of miRNA and piRNA is expanding, whether tsRNAs play similar roles remains poorly understood. Here, we review the current knowledge regarding the mechanisms of action and biological functions of tsRNAs in intracellular, extracellular and intergenerational inheritance, and highlight the potential application of tsRNAs in human diseases, and present the current problems and future research directions.


2020 ◽  
Author(s):  
Joanna Houghton ◽  
Angela Rodgers ◽  
Graham Rose ◽  
Kristine B. Arnvig

ABSTRACTAlmost 140 years after the identification of Mycobacterium tuberculosis as the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of post-transcriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of the M. tuberculosis sRNA, F6, and show it to be dependent on SigF for expression and significantly induced during in vitro starvation and in a mouse model of infection. However, we found no evidence of attenuation of a ΔF6 strain within the first 20 weeks of infection. A further exploration of F6 using in vitro models of infection suggests a role for F6 as a highly specific regulator of the heat shock repressor, HrcA. Our results point towards a role for F6 during periods of low metabolic activity similar to cold shock and associated with nutrient starvation such as that found in human granulomas in later stages of infection.


2008 ◽  
Vol 389 (4) ◽  
pp. 323-331 ◽  
Author(s):  
David Umlauf ◽  
Peter Fraser ◽  
Takashi Nagano

Abstract Transcriptome studies have uncovered a plethora of non-coding RNAs (ncRNA) in mammals. Most originate within intergenic regions of the genome and recent evidence indicates that some are involved in many different pathways that ultimately act on genome architecture and gene expression. In this review, we discuss the role of well-characterized long ncRNAs in gene regulation pointing to their similarities, but also their differences. We will attempt to highlight a paradoxical situation in which transcription is needed to repress entire chromosomal domains possibly through the action of ncRNAs that create nuclear environments refractory to transcription.


2021 ◽  
Author(s):  
Juan Manuel Crescente ◽  
Diego Zavallo ◽  
Mariana del Vas ◽  
Sebastian Asurmendi ◽  
Marcelo Helguera ◽  
...  

Abstract Plant microRNAs (miRNAs) are a class of small non-coding RNAs that are 20–24 nucleotides length and can repress gene expression at post-transcriptional levels by target degradation or translational repression. There is increasing evidence that some microRNAs can be derived from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs) in plants. We used public small RNA, degradome libraries and the common wheat (Triticum aestivum) genome to screen miRNAs production and target sites. We also created a comprehensive wheat MITE database using known and identifying novel elements. We found high homology between MITEs and 14% of all the miRNAs production sites in wheat. Furthermore, we show that MITE-derived miRNAs have preference for target degradation sites with MITE insertions in 3' UTR regions in wheat.


2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Yongli Qiao ◽  
Rui Xia ◽  
Jixian Zhai ◽  
Yingnan Hou ◽  
Li Feng ◽  
...  

Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves trans-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host–pathogen interactions. We highlight secondary small interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of small RNAs trafficking at the host–pathogen interface are discussed. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.


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