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 Small Interfering RNAs That Trigger Posttranscriptional Gene Silencing Are Not Required for the Histone H3 Lys9 Methylation Necessary for Transgenic Tandem Repeat Stabilization in Neurospora crassa

2005 ◽  
Vol 25 (9) ◽  
pp. 3793-3801 ◽  
Author(s):  
Agustin Chicas ◽  
Emma C. Forrest ◽  
Silvia Sepich ◽  
Carlo Cogoni ◽  
Giuseppe Macino
Keyword(s):  
Gene Silencing ◽  
Neurospora Crassa ◽  
Chromatin Immunoprecipitation ◽  
Histone H3 ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Posttranscriptional Gene Silencing ◽  
Endogenous Gene ◽  
Homologous Genes ◽  
Interfering Rna

ABSTRACT In Neurospora crassa, the introduction of a transgene can lead to small interfering RNA (siRNA)-mediated posttranscriptional gene silencing (PTGS) of homologous genes. siRNAs can also guide locus-specific methylation of Lys9 of histone H3 (Lys9H3) in Schizosaccharomyces pombe. Here we tested the hypothesis that transgenically derived siRNAs may contemporaneously both activate the PTGS mechanism and induce chromatin modifications at the transgene and the homologous endogenous gene. We carried out chromatin immunoprecipitation using a previously characterized albino-1 (al-1) silenced strain but detected no alterations in the pattern of histone modifications at the endogenous al-1 locus, suggesting that siRNAs produced from the transgenic locus do not trigger modifications in trans of those histones tested. Instead, we found that the transgenic locus was hypermethylated at Lys9H3 in our silenced strain and remained hypermethylated in the quelling defective mutants (qde), further demonstrating that the PTGS machinery is dispensable for Lys9H3 methylation. However, we found that a mutant in the histone Lys9H3 methyltransferase dim-5 was unable to maintain PTGS, with transgenic copies being rapidly lost, resulting in reversion of the silenced phenotype. These results indicate that the defect in PTGS of the Δdim-5 strain is due to the inability to maintain the transgene in tandem, suggesting a role for DIM-5 in stabilizing such repeated sequences. We conclude that in Neurospora, siRNAs produced from the transgenic locus are used in the RNA-induced silencing complex-mediated PTGS pathway and do not communicate with an RNAi-induced initiation of transcriptional gene silencing complex to effect chromatin-based silencing.

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.

scholarly journals Homology-dependent Gene Silencing inParamecium

1998 ◽  
Vol 9 (4) ◽  
pp. 931-943 ◽  
Author(s):  
Françoise Ruiz ◽  
Laurence Vayssié ◽  
Catherine Klotz ◽  
Linda Sperling ◽  
Luisa Madeddu
Keyword(s):  
Gene Silencing ◽  
Matrix Protein ◽  
Gene Families ◽  
Single Copy ◽  
Multigene Families ◽  
Coding Region ◽  
Posttranscriptional Gene Silencing ◽  
Endogenous Gene ◽  
Copy Gene ◽  
Mutant Phenotypes

Microinjection at high copy number of plasmids containing only the coding region of a gene into the Paramecium somatic macronucleus led to a marked reduction in the expression of the corresponding endogenous gene(s). The silencing effect, which is stably maintained throughout vegetative growth, has been observed for allParamecium genes examined so far: a single-copy gene (ND7), as well as members of multigene families (centrin genes and trichocyst matrix protein genes) in which all closely related paralogous genes appeared to be affected. This phenomenon may be related to posttranscriptional gene silencing in transgenic plants and quelling in Neurospora and allows the efficient creation of specific mutant phenotypes thus providing a potentially powerful tool to study gene function in Paramecium. For the two multigene families that encode proteins that coassemble to build up complex subcellular structures the analysis presented herein provides the first experimental evidence that the members of these gene families are not functionally redundant.

scholarly journals H3K9me3 is Required for Inheritance of Small RNAs that Target a Unique Subset of Newly Evolved Genes

2018 ◽  
Author(s):  
Itamar Lev ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Small Rnas ◽  
Foreign Gene ◽  
Small Interfering Rnas ◽  
Endogenous Gene ◽  
C Elegans ◽  
Histone 3 ◽  
Repressive Chromatin ◽  
Genome Wide

AbstractIn Caenorhabditis elegans, RNA interference (RNAi) responses can transmit across generations via small RNAs. RNAi inheritance is associated with Histone-3-Lysine-9 tri-methylation (H3K9me3) of the targeted genes. In other organisms, maintenance of silencing requires a feed-forward loop between H3K9me3 and small RNAs. Here we show that in C. elegans not only is H3K9me3 unnecessary for inheritance, the modification’s function depends on the identity of the RNAi-targeted gene. We found an asymmetry in the requirement for H3K9me3 and the main worm H3K9me3 methyltransferases, SET-25 and SET-32. Both methyltransferases promote heritable silencing of the foreign gene gfp, but are dispensable for silencing of the endogenous gene oma-1. Genome-wide examination of heritable endogenous small interfering RNAs (endo-siRNAs) revealed that the SET-25-dependent heritable endo-siRNAs target newly acquired and highly H3K9me3 marked genes. Thus, “repressive” chromatin marks could be important specifically for heritable silencing of genes which are flagged as “foreign”, such as gfp.

scholarly journals Posttranscriptional gene silencing in nuclei

2010 ◽  
Vol 108 (1) ◽  
pp. 409-414 ◽  
Author(s):  
Paul Hoffer ◽  
Sergey Ivashuta ◽  
Olga Pontes ◽  
Alexa Vitins ◽  
Craig Pikaard ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Target Genes ◽  
Rna Degradation ◽  
Small Interfering Rnas ◽  
Double Stranded Rna ◽  
Posttranscriptional Gene Silencing ◽  
Subcellular Compartmentation ◽  
Specific Degradation ◽  
Precursor Mrna ◽  
Specific Sequences

In plants, small interfering RNAs (siRNAs) with sequence homology to transcribed regions of genes can guide the sequence-specific degradation of corresponding mRNAs, leading to posttranscriptional gene silencing (PTGS). The current consensus is that siRNA-mediated PTGS occurs primarily in the cytoplasm where target mRNAs are localized and translated into proteins. However, expression of an inverted-repeat double-stranded RNA corresponding to the soybeanFAD2-1Adesaturase intron is sufficient to silenceFAD2-1, implicating nuclear precursor mRNA (pre-mRNA) rather than cytosolic mRNA as the target of PTGS. SilencingFAD2-1using intronic or 3′-UTR sequences does not affect transcription rates of the target genes but results in the strong reduction of target transcript levels in the nucleus. Moreover, siRNAs corresponding to pre-mRNA–specific sequences accumulate in the nucleus. In Arabidopsis, we find that two enzymes involved in PTGS, Dicer-like 4 and RNA-dependent RNA polymerase 6, are localized in the nucleus. Collectively, these results demonstrate that siRNA-directed RNA degradation can take place in the nucleus, suggesting the need for a more complex view of the subcellular compartmentation of PTGS in plants.

scholarly journals The Coat Protein of Turnip Crinkle Virus Suppresses Posttranscriptional Gene Silencing at an Early Initiation Step

2003 ◽  
Vol 77 (1) ◽  
pp. 511-522 ◽  
Author(s):  
Feng Qu ◽  
Tao Ren ◽  
T. Jack Morris
Keyword(s):  
Coat Protein ◽  
Gene Silencing ◽  
Rna Silencing ◽  
Rna Degradation ◽  
Plant Viruses ◽  
Early Initiation ◽  
Turnip Crinkle Virus ◽  
Small Interfering Rnas ◽  
Posttranscriptional Gene Silencing ◽  
Initiation Step

ABSTRACT Posttranscriptional gene silencing (PTGS), or RNA silencing, is a sequence-specific RNA degradation process that targets foreign RNA, including viral and transposon RNA for destruction. Several RNA plant viruses have been shown to encode suppressors of PTGS in order to survive this host defense. We report here that the coat protein (CP) of Turnip crinkle virus (TCV) strongly suppresses PTGS. The Agrobacterium infiltration system was used to demonstrate that TCV CP suppressed the local PTGS as strongly as several previously reported virus-coded suppressors and that the action of TCV CP eliminated the small interfering RNAs associated with PTGS. We have also shown that the TCV CP must be present at the time of silencing initiation to be an effective suppressor. TCV CP was able to suppress PTGS induced by sense, antisense, and double-stranded RNAs, and it prevented systemic silencing. These data suggest that TCV CP functions to suppress RNA silencing at an early initiation step, likely by interfering the function of the Dicer-like RNase in plants.

scholarly journals H3K9me3 is required for inheritance of small RNAs that target a unique subset of newly evolved genes

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Itamar Lev ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Small Rnas ◽  
Editorial Note ◽  
Foreign Gene ◽  
Editorial Process ◽  
Small Interfering Rnas ◽  
Endogenous Gene ◽  
C Elegans ◽  
Histone 3 ◽  
Repressive Chromatin ◽  
Genome Wide

In Caenorhabditis elegans, RNA interference (RNAi) responses can transmit across generations via small RNAs. RNAi inheritance is associated with Histone-3-Lysine-9 tri-methylation (H3K9me3) of the targeted genes. In other organisms, maintenance of silencing requires a feed-forward loop between H3K9me3 and small RNAs. Here, we show that in C. elegans not only is H3K9me3 unnecessary for inheritance, the modification’s function depends on the identity of the RNAi-targeted gene. We found an asymmetry in the requirement for H3K9me3 and the main worm H3K9me3 methyltransferases, SET-25 and SET-32. Both methyltransferases promote heritable silencing of the foreign gene gfp, but are dispensable for silencing of the endogenous gene oma-1. Genome-wide examination of heritable endogenous small interfering RNAs (endo-siRNAs) revealed that endo-siRNAs that depend on SET-25 and SET-32 target newly acquired and highly H3K9me3 marked genes. Thus, ‘repressive’ chromatin marks could be important specifically for heritable silencing of genes which are flagged as ‘foreign’, such as gfp.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (<xref ref-type="decision-letter" rid="SA1">see decision letter</xref>).

scholarly journals The epigenetic factor FVE orchestrates cytoplasmic SGS3-DRB4-DCL4 activities to promote transgene silencing in Arabidopsis

2021 ◽  
Vol 7 (32) ◽  
pp. eabf3898
Author(s):  
Di Sun ◽  
Yanjun Li ◽  
Zeyang Ma ◽  
Xingxing Yan ◽  
Niankui Li ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Small Interfering Rnas ◽  
Loss Of Function ◽  
Double Stranded Rna ◽  
Posttranscriptional Gene Silencing ◽  
Epigenetic Factor ◽  
Dsrna Binding ◽  
Dsrna Binding Protein

Posttranscriptional gene silencing (PTGS) is a regulatory mechanism to suppress undesired transcripts. Here, we identified Flowering locus VE (FVE), a well-known epigenetic component, as a new player in cytoplasmic PTGS. Loss-of-function fve mutations substantially reduced the accumulation of transgene-derived small interfering RNAs (siRNAs). FVE interacts with suppressor of gene silencing 3 (SGS3), a master component in PTGS. FVE promotes SGS3 homodimerization that is essential for its function. FVE can bind to single-stranded RNA and double-stranded RNA (dsRNA) with moderate affinities, while its truncated form FVE-8 has a significantly increased binding affinity to dsRNA. These affinities affect the association and channeling of SGS3-RNA to downstream dsRNA binding protein 4 (DRB4)/Dicer-like protein 2/4 (DCL2/4) complexes. Hence, FVE, but not FVE-8, biochemically enhances the DRB4/DCL2/4 activity in vitro. We surmise that FVE promotes production of transgene-derived siRNAs through concertedly tuning SGS3-DRB4/DCL2/4 functions. Thus, this study revealed a noncanonical role of FVE in PTGS.

scholarly journals Defective Interfering RNA Hinders the Activity of a Tombusvirus-Encoded Posttranscriptional Gene Silencing Suppressor

2005 ◽  
Vol 79 (1) ◽  
pp. 450-457 ◽  
Author(s):  
Zoltán Havelda ◽  
Csaba Hornyik ◽  
Anna Válóczi ◽  
József Burgyán
Keyword(s):  
Gene Silencing ◽  
Viral Infections ◽  
Rna Viruses ◽  
Helper Virus ◽  
Small Interfering Rnas ◽  
Posttranscriptional Gene Silencing ◽  
Virus Rna ◽  
Defective Interfering Rna ◽  
Interfering Rna

ABSTRACT Defective interfering (DI) RNAs are subviral replicons originating from the viral genome and are associated with many plant RNA viruses and nearly all animal RNA viruses. The presence of DI RNAs in tombusvirus-infected plants reduces the accumulation of helper virus RNA and results in the development of attenuated symptoms similar to those caused by tombusviruses defective in p19, the posttranscriptional gene silencing (PTGS) suppressor. In situ analysis of infected plants containing DI RNAs revealed that the extent of virus infection was spatially restricted as was found for p19-defective tombusvirus. Previously, p19 was shown to suppress PTGS by sequestering the small interfering RNAs (siRNAs), which act as the specificity determinant for PTGS. Our results demonstrate that DI RNAs dramatically elevate the level of virus-specific siRNAs in viral infections, resulting in the saturation of p19 and the accumulation of unbound siRNAs. Moreover, we showed that, at low temperature, where PTGS is inhibited, DI RNAs are not able to efficiently interfere with virus accumulation and protect the plants. These data show that the activation of PTGS plays a pivotal role in DI RNA-mediated interference. Our data also support a role for 21-nucleotide siRNAs in PTGS signaling.

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