Detection of SARS-CoV-2 Derived Small RNAs and Changes in Circulating Small RNAs Associated with COVID-19

Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of this mechanism for SARS-CoV-2-directed immune responses remains elusive. Herein, we used high throughput sequencing to profile the plasma of active and convalescent COVID-19 patients for the presence of small circulating RNAs. The existence of SARS-CoV-2 derived small RNAs in plasma samples of mild and severe COVID-19 cases is described. Clusters of high siRNA abundance were discovered, homologous to the nsp2 3’-end and nsp4 virus sequence. Four virus-derived small RNA sequences have the size of human miRNAs, and a target search revealed candidate genes associated with ageusia and long COVID symptoms. These virus-derived small RNAs were detectable also after recovery from the disease. The additional analysis of circulating human miRNAs revealed differentially abundant miRNAs, discriminating mild from severe cases. A total of 29 miRNAs were reduced or absent in severe cases. Several of these are associated with JAK-STAT response and cytokine storm.

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Sequence-Specific Post-Transcriptional Gene Silencing by Double-Stranded RNA

Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine ◽

10.1007/3-540-29623-9_5911 ◽

2006 ◽

pp. 1744-1744

Keyword(s):

Gene Silencing ◽

Transcriptional Gene Silencing ◽

Double Stranded Rna ◽

Post Transcriptional Gene Silencing

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Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants

Cells ◽

10.3390/cells10051187 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1187

Author(s):

Michael Wassenegger ◽

Athanasios Dalakouras

Keyword(s):

Dna Methylation ◽

Rna Interference ◽

Gene Silencing ◽

Plant Cells ◽

Transcriptional Gene Silencing ◽

Rnai Machinery ◽

Double Stranded Rna ◽

Post Transcriptional Gene Silencing ◽

Cumulative Amount

Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.

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An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

10.1101/2021.03.05.432875 ◽

2021 ◽

Author(s):

Ganna Reshetnyak ◽

Jonathan M. Jacobs ◽

Florence Auguy ◽

Coline Sciallano ◽

Lisa Claude ◽

...

Keyword(s):

Gene Silencing ◽

Stress Responses ◽

Small Rnas ◽

Early Stage ◽

Kinase Domain ◽

Transcriptional Gene Silencing ◽

Small Interfering Rnas ◽

Post Transcriptional Gene Silencing ◽

Virulent Strains ◽

Microbe Interactions

ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.

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Cucumber mosaic virus Infection Transiently Breaks dsRNA-Induced Transgenic Immunity to Potato virus Y in Tobacco

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2003.16.10.936 ◽

2003 ◽

Vol 16 (10) ◽

pp. 936-944 ◽

Cited By ~ 30

Author(s):

Neena Mitter ◽

Emy Sulistyowati ◽

Ralf G. Dietzgen

Keyword(s):

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Potato Virus ◽

Potato Virus Y ◽

Defense Mechanism ◽

Transcriptional Gene Silencing ◽

Mrna Levels ◽

Post Transcriptional Gene Silencing ◽

The Stability ◽

High Level

Post-transcriptional gene silencing (PTGS), an intrinsic plant defense mechanism, can be efficiently triggered by double stranded (ds)RNA-producing transgenes and can provide high level virus resistance by specific targeting of cognate viral RNA. The discovery of virus-encoded suppressors of PTGS led to concerns about the stability of such resistance. Here, we show that Cucumber mosaic virus (CMV) is able to suppress dsRNA-induced PTGS and the associated Potato virus Y (PVY) immunity in tobacco. CMV suppression supported only a transient PVY accumulation and did not prevent recovery of the transgenic plants from PVY infection. CMV inoculation resulted in strongly increased transgene mRNA levels due to suppression of PTGS, but accumulation of PVY-specific small interfering (si)RNA was unaffected. However, PVY accumulation in previously immune plants resulted in increased PVY siRNA levels and transgene mRNA was no longer detected, despite the presence of CMV. Transgene mRNA returned to high levels once PVY was no longer detected in CMV-infected plants. Recovered and chronically CMV-infected tissues were immune to further PVY infection.

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Nanoparticle delivery systems for siRNA-based therapeutics

Journal of Materials Chemistry B ◽

10.1039/c6tb01462c ◽

2016 ◽

Vol 4 (41) ◽

pp. 6620-6639 ◽

Cited By ~ 25

Author(s):

Jinming Li ◽

Shanshan Xue ◽

Zong-Wan Mao

Keyword(s):

Rna Interference ◽

Gene Silencing ◽

Delivery Systems ◽

Regulatory Process ◽

Transcriptional Gene Silencing ◽

Double Stranded Rna ◽

Nanoparticle Delivery ◽

Naturally Occurring ◽

Post Transcriptional Gene Silencing

RNA interference (RNAi) is a naturally occurring endogenous regulatory process in which the short double-stranded RNA causes sequence-specific post-transcriptional gene silencing.

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Virus and Viroid-Derived Small RNAs as Modulators of Host Gene Expression: Molecular Insights Into Pathogenesis

Frontiers in Microbiology ◽

10.3389/fmicb.2020.614231 ◽

2021 ◽

Vol 11 ◽

Author(s):

S. V. Ramesh ◽

Sneha Yogindran ◽

Prabu Gnanasekaran ◽

Supriya Chakraborty ◽

Stephan Winter ◽

...

Keyword(s):

Gene Silencing ◽

Small Rnas ◽

Rna Silencing ◽

Transcriptional Gene Silencing ◽

Genomic Rnas ◽

Post Transcriptional Gene Silencing ◽

Viroid Infection ◽

Wide Range ◽

Associated Symptoms ◽

Sequence Complementarity

Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.

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The long hand of the small RNAs reaches into several levels of gene regulation

Biochemistry and Cell Biology ◽

10.1139/o04-046 ◽

2004 ◽

Vol 82 (4) ◽

pp. 472-481 ◽

Cited By ~ 3

Author(s):

Tony Nolan ◽

Carlo Cogoni

Keyword(s):

Gene Silencing ◽

Small Rnas ◽

Developmental Regulation ◽

Transcriptional Gene Silencing ◽

Rna Molecules ◽

New Class ◽

Post Transcriptional Gene Silencing ◽

Wide Range ◽

Cellular Defence ◽

Genomic Organisation

Small RNA molecules such as siRNAs and miRNAs represent a new class of molecules that have been implicated in a wide range of diverse gene silencing phenomena. It is now becoming clear that these two similar molecules share several common features in both their biogenesis and their mechanism of action. Thus, the siRNA and miRNA pathways may have evolved from a common ancestral mechanism that has diverged to play important roles in developmental regulation, genomic organisation, and cellular defence against foreign nucleic acids.Key words: miRNA, siRNA, post-transcriptional gene silencing, RNAi, heterochromatin.

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Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains

10.1101/2021.08.25.457601 ◽

2021 ◽

Author(s):

Vivek H Sundar ◽

Chenna Swetha ◽

Debjani Basu ◽

Kannan Pachamuthu ◽

Tania Chakraborty ◽

...

Keyword(s):

Small Rnas ◽

Transcriptional Activity ◽

Constitutive Heterochromatin ◽

Division Of Labour ◽

Transcriptional Gene Silencing ◽

Protein Coding ◽

Heterochromatin Formation ◽

Protein Coding Genes ◽

Post Transcriptional Gene Silencing ◽

Architectural Feature

Heterochromatin is the predominant architectural feature of genomes that ensures genomic stability across eukaryotes. It mostly functions in restricting expression of repeats, mobile elements such as transposons and other regions. The establishment, maintenance and spreading of heterochromatin requires several factors including chromatin modifiers. However, how exactly heterochromatin formation is avoided in protein-coding domains is poorly understood. Here we show that a plant specific paralogue of RNA polymerase (pol) II, named pol IV, is involved in avoidance of facultative heterochromatic marks in protein coding genes, in addition to silencing the repeats and transposons forming constitutive heterochromatin. In its absence, H3K27 trimethylation mark intrudes the protein coding genes, more profoundly in genes embedded with repeats. In a subset of genes that lack the compensatory silencing, spurious transcriptional activity results in small(s)RNA production leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with larger genome with distributed heterochromatin when compared to Arabidopsis. Our results indicate the surprising division of labour among plant-specific polymerases, not just in establishing effective silencing via small RNAs and epigenetics, but also in influencing chromatin boundaries.

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