Structural Diversity Repertoire of Gene Silencing Small Interfering RNAs

2011 ◽  
pp. 121102072334007
Author(s):  
Chan Il Chang ◽  
Helena Andrade Kim ◽  
Pooja Dua ◽  
Soyoun Kim ◽  
Chiang J. Li ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Structural Diversity ◽  
Small Interfering Rnas

scholarly journals Structural Diversity Repertoire of Gene Silencing Small Interfering RNAs

2011 ◽  
Vol 21 (3) ◽  
pp. 125-131 ◽  
Author(s):  
Chan Il Chang ◽  
Helena Andrade Kim ◽  
Pooja Dua ◽  
Soyoun Kim ◽  
Chiang J. Li ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Structural Diversity ◽  
Small Interfering Rnas

scholarly journals Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoyu Yang ◽  
Chenjiang You ◽  
Xufeng Wang ◽  
Lei Gao ◽  
Beixin Mo ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Gene Silencing ◽  
High Frequency ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Small Interfering Rnas ◽  
Widespread Occurrence ◽  
Membrane Bound ◽  
Different Tissues

Abstract Background Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular localization has not yet been well studied, thus limiting our mechanistic understanding of sRNA action. Results We investigate the cytoplasmic partitioning of sRNAs and their targets globally in maize (Zea mays, inbred line “B73”) and rice (Oryza sativa, cv. “Nipponbare”) by high-throughput sequencing of polysome-associated sRNAs and 3′ cleavage fragments, and find that both miRNAs and a subset of 21-nucleotide (nt)/22-nt siRNAs are enriched on membrane-bound polysomes (MBPs) relative to total polysomes (TPs) across different tissues. Most of the siRNAs are generated from transposable elements (TEs), and retrotransposons positively contributed to MBP overaccumulation of 22-nt TE-derived siRNAs (TE-siRNAs) as opposed to DNA transposons. Widespread occurrence of miRNA-mediated target cleavage is observed on MBPs, and a large proportion of these cleavage events are MBP-unique. Reproductive 21PHAS (21-nt phasiRNA-generating) and 24PHAS (24-nt phasiRNA-generating) precursors, which were commonly considered as noncoding RNAs, are bound by polysomes, and high-frequency cleavage of 21PHAS precursors by miR2118 and 24PHAS precursors by miR2275 is further detected on MBPs. Reproductive 21-nt phasiRNAs are enriched on MBPs as opposed to TPs, whereas 24-nt phasiRNAs are nearly completely devoid of polysome occupancy. Conclusions MBP overaccumulation is a conserved pattern for cytoplasmic partitioning of sRNAs, and endoplasmic reticulum (ER)-bound ribosomes function as an independent regulatory layer for miRNA-induced gene silencing and reproductive phasiRNA biosynthesis in maize and rice.

Suppression of endogenous gene silencing by bidirectional cytoplasmic RNA decay in Arabidopsis

Science ◽  
2015 ◽  
Vol 348 (6230) ◽  
pp. 120-123 ◽  
Author(s):  
Xinyan Zhang ◽  
Ying Zhu ◽  
Xiaodan Liu ◽  
Xinyu Hong ◽  
Yang Xu ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Plant Immunity ◽  
Rna Decay ◽  
Foreign Gene ◽  
Small Interfering Rnas ◽  
Developmental Defects ◽  
Posttranscriptional Gene Silencing ◽  
Endogenous Gene ◽  
Cytoplasmic Rna ◽  
Cognate Gene

Plant immunity against foreign gene invasion takes advantage of posttranscriptional gene silencing (PTGS). How plants elaborately avert inappropriate PTGS of endogenous coding genes remains unclear. We demonstrate in Arabidopsis that both 5′-3′ and 3′-5′ cytoplasmic RNA decay pathways act as repressors of transgene and endogenous PTGS. Disruption of bidirectional cytoplasmic RNA decay leads to pleiotropic developmental defects and drastic transcriptomic alterations, which are substantially rescued by PTGS mutants. Upon dysfunction of bidirectional RNA decay, a large number of 21- to 22-nucleotide endogenous small interfering RNAs are produced from coding transcripts, including multiple microRNA targets, which could interfere with their cognate gene expression and functions. This study highlights the risk of unwanted PTGS and identifies cytoplasmic RNA decay pathways as safeguards of plant transcriptome and development.

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

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.

Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Yongli Qiao ◽  
Rui Xia ◽  
Jixian Zhai ◽  
Yingnan Hou ◽  
Li Feng ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Small Rna ◽  
Small Rnas ◽  
Plant Immunity ◽  
Receptor Gene ◽  
Current Status ◽  
Annual Review ◽  
Publication Date ◽  
Small Interfering Rnas ◽  
Host Pathogen

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.

Impacts of CD40- and CD86-Silenced Antigen-Specific B Cells on the Control of Allergies

2019 ◽  
Vol 33 (5) ◽  
pp. 513-523
Author(s):  
Motohiko Suzuki ◽  
Tamami Matsumoto ◽  
Kiichi Toyoda ◽  
Yoshihisa Nakamura ◽  
Shingo Murakami
Keyword(s):  
B Cells ◽  
Gene Silencing ◽  
Immunoglobulin E ◽  
Japanese Cedar ◽  
Keyhole Limpet Hemocyanin ◽  
Specific Ige ◽  
Small Interfering Rnas ◽  
Nasal Tissue ◽  
Allergic Symptoms ◽  
Cedar Pollen

Background We previously reported that CD40-silenced B cells inhibited allergic responses and symptoms. However, more potent therapies are needed. To our knowledge, the effects of CD86-silenced B cells and synergic effects of gene silencing in B cells by 2 small interfering RNAs (siRNAs) on allergic disease control have not been reported. Objective To investigate the effects of CD86-silenced B cells and synergic effects of gene silencing in B cells on allergic responses and symptoms. Methods Mice were treated with CD40- and/or CD86-silenced B cells transfected with siRNAs and pulsed with ovalbumin (OVA). And the effects of these B cells were estimated. Results CD86-silenced OVA-pulsed B cells significantly inhibited OVA-induced allergies. Treatment with CD40-/CD86-silenced OVA-pulsed B cells led to a significantly fewer sneezes and nasal rubbing movements, as well as lower OVA-specific immunoglobulin E (IgE) levels, than that with CD40-silenced or CD86-silenced OVA-pulsed B cells alone. These inhibitory effects were observed prior to sensitization as well as after the establishment of allergic rhinitis. CD40-/CD86-silenced OVA-pulsed B cells did not inhibit keyhole limpet hemocyanin-induced allergies. CD40-/CD86-silenced OVA-pulsed B cells also significantly inhibited allergic symptoms and OVA-specific IgE level in sera compared with CD40-/CD86-silenced OVA-pulsed dendritic cells (DCs). In addition, CD19+CD40− B cells significantly increased in the nasal tissue after intravenous administration of these cells. Furthermore, CD40-/CD86-silenced B cells inhibited allergic symptoms caused by Cry j 1, a major aeroallergen of Japanese cedar pollen, and Cry j 1-specific IgE in sera. Conclusion This study showed, for the first time, that siRNA-induced CD86-silenced B cells significantly inhibited allergic responses and symptoms antigen-specifically, and that siRNA-induced CD40-/CD86-silenced antigen-specific B cells are a more useful antigen-specific therapy than CD40- or CD86-silenced B cells alone for the control of allergies. Furthermore, it was shown that CD40-/CD86-silenced B cells have stronger inhibition of IgE production and allergic symptoms than CD40-/CD86-silenced DCs.

Gene Silencing Mediated by Small Interfering RNAs in Mammalian Cells

2003 ◽  
Vol 10 (3) ◽  
pp. 245-256 ◽  
Author(s):  
Michaela Scherr ◽  
Michael Morgan ◽  
Matthias Eder
Keyword(s):  
Gene Silencing ◽  
Mammalian Cells ◽  
Small Interfering Rnas
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