scholarly journals Mating can initiate stable RNA silencing that overcomes epigenetic recovery

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sindhuja Devanapally ◽  
Pravrutha Raman ◽  
Mary Chey ◽  
Samual Allgood ◽  
Farida Ettefa ◽  
...  
Keyword(s):  
Small Rna ◽  
Rna Silencing ◽  
Single Copy ◽  
Regulatory Sequences ◽  
Epigenetic Changes ◽  
Double Stranded Rna ◽  
Transient Change ◽  
C Elegans ◽  
Homologous Sequences ◽  
Germline Expression

AbstractStable epigenetic changes appear uncommon, suggesting that changes typically dissipate or are repaired. Changes that stably alter gene expression across generations presumably require particular conditions that are currently unknown. Here we report that a minimal combination of cis-regulatory sequences can support permanent RNA silencing of a single-copy transgene and its derivatives in C. elegans simply upon mating. Mating disrupts competing RNA-based mechanisms to initiate silencing that can last for >300 generations. This stable silencing requires components of the small RNA pathway and can silence homologous sequences in trans. While animals do not recover from mating-induced silencing, they often recover from and become resistant to trans silencing. Recovery is also observed in most cases when double-stranded RNA is used to silence the same coding sequence in different regulatory contexts that drive germline expression. Therefore, we propose that regulatory features can evolve to oppose permanent and potentially maladaptive responses to transient change.

scholarly journals The IDR-containing protein PID-2 affects Z granules and is required for piRNA-induced silencing in the embryo

2020 ◽  
Author(s):  
Maria Placentino ◽  
António Miguel de Jesus Domingues ◽  
Jan Schreier ◽  
Sabrina Dietz ◽  
Svenja Hellmann ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Caenorhabditis Elegans ◽  
Rna Polymerase ◽  
Small Rna ◽  
Rna Silencing ◽  
Rna Dependent Rna Polymerase ◽  
Prolyl Aminopeptidase ◽  
C Elegans

AbstractIn Caenorhabditis elegans, the piRNA (21U RNA) pathway is required to establish proper gene regulation and an immortal germline. To achieve this, PRG-1-bound 21U RNAs trigger silencing mechanisms mediated by RNA-dependent RNA polymerase (RdRP)-synthetized 22G RNAs. This silencing can become PRG-1-independent, and heritable over many generations. This state is named RNAe. It is unknown how and when RNAe is established, and how it is maintained. We show that maternally provided 21U RNAs can be sufficient to trigger RNAe in embryos. Additionally, we identify the IDR-containing protein PID-2, as a factor required to establish and maintain RNAe. PID-2 interacts with two novel, partially redundant, eTudor domain proteins, PID-4 and PID-5. Additionally, PID-5 has a domain related to the X-prolyl aminopeptidase protein APP-1, and binds APP-1, implicating N-terminal proteolysis in RNAe. All three proteins are required for germline immortality, localize to perinuclear foci, affect Z granules, and are required for balancing of 22G RNA populations. Overall, our study identifies three new proteins with crucial functions in the C. elegans small RNA silencing network.

scholarly journals Each cell needs long double-stranded RNA for silencing by feeding RNAi in C. elegans

2016 ◽  
Author(s):  
Pravrutha Raman ◽  
Soriayah M Zaghab ◽  
Edward C Traver ◽  
Antony M Jose
Keyword(s):  
Rna Interference ◽  
Single Copy ◽  
Animal Cells ◽  
Tissue Specific ◽  
Double Stranded Rna ◽  
C Elegans ◽  
Dsrna Binding ◽  
Dsrna Binding Protein ◽  
Systemic Rnai ◽  
Derivatives Of

ABSTRACTLong double-stranded RNA (dsRNA) can silence genes of matching sequence upon ingestion in many invertebrates and is therefore being developed as a pesticide. Such feeding RNA interference (RNAi) is best understood in the worm C. elegans, where it is thought that derivatives of ingested dsRNA, including short dsRNAs, move between cells and cause systemic silencing. Movement of short dsRNAs has been inferred using tissue-specific rescue of the long dsRNA-binding protein RDE-4 by expressing it from repetitive transgenes. We found that the use of repetitive transgenes for the tissue-specific rescue of a gene could inhibit RNAi within that tissue and could result in misexpression of the gene in other tissues. Both inhibition and misexpression were not detectable when a single-copy transgene was used for tissue-specific rescue. In animals with single-copy rescue of RDE-4, RNAi was restricted to the tissue with RDE-4 expression. Thus, unlike previous observations using repetitive transgenes, these results suggest that binding of long dsRNA by RDE-4 in each silenced cell is required for systemic RNAi. Taken together with the requirement for long dsRNA to trigger RNAi in insects, these results suggest that the entry of long dsRNA is a necessary first step for feeding RNAi in animal cells.

scholarly journals Intercellular transport of RNA can limit heritable epigenetic changes

2021 ◽  
Author(s):  
Nathan Shugarts ◽  
Andrew L. Yi ◽  
Winnie M. Chan ◽  
Julia A. Marré ◽  
Aishwarya Sathya ◽  
...  
Keyword(s):  
Gene Expression ◽  
Substrate Specificity ◽  
Extracellular Space ◽  
Epigenetic Changes ◽  
Germline Gene ◽  
Intercellular Transport ◽  
Rna Regulation ◽  
Double Stranded Rna ◽  
C Elegans ◽  
Regulatory Information

AbstractRNAs in circulation carry sequence-specific regulatory information between cells in animal, plant, and host-pathogen systems. Double-stranded RNA (dsRNA) delivered into the extracellular space of the nematode C. elegans accumulates within the germline and reaches progeny. Here we provide evidence for spatial, temporal, and substrate specificity in the transport of dsRNA from parental circulation to progeny. Temporary loss of dsRNA transport resulted in the persistent accumulation of mRNA from a germline gene. The expression of this gene varied among siblings and even between gonad arms within one animal. Perturbing RNA regulation of the gene created new epigenetic states that lasted for many generations. Thus, one role for the transport of dsRNA into the germline in every generation is to limit heritable changes in gene expression.One Sentence SummaryRNA from parental circulation reduces heritable changes in gene expression.

scholarly journals Engineering rules that minimize germline silencing of transgenes in simple extrachromosomal arrays in C. elegans

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohammed D. Aljohani ◽  
Sonia El Mouridi ◽  
Monika Priyadarshini ◽  
Amhed M. Vargas-Velazquez ◽  
Christian Frøkjær-Jensen
Keyword(s):  
Fluorescent Proteins ◽  
Single Copy ◽  
Regulatory Elements ◽  
Transgene Silencing ◽  
Small Interfering Rnas ◽  
Web Based ◽  
C Elegans ◽  
Genomic Location ◽  
Germline Expression ◽  
Extensive Collection

AbstractTransgenes are prone to progressive silencing due to their structure, copy number, and genomic location. In C. elegans, repressive mechanisms are particularly strong in the germline with almost fully penetrant transgene silencing in simple extrachromosomal arrays and frequent silencing of single-copy transgene insertions. A class of non-coding DNA, Periodic An/Tn Clusters (PATCs) can prevent transgene-silencing in repressive chromatin or from small interfering RNAs (piRNAs). Here, we describe design rules (codon-optimization, intron and PATC inclusion, elevated temperature (25 °C), and vector backbone removal) for efficient germline expression from arrays in wildtype animals. We generate web-based tools to analyze PATCs and reagents for the convenient assembly of PATC-rich transgenes. An extensive collection of silencing resistant fluorescent proteins (e.g., gfp, mCherry, and tagBFP) can be used for dissecting germline regulatory elements and a set of enhanced enzymes (Mos1 transposase, Cas9, Cre, and Flp recombinases) enable efficient genetic engineering in C. elegans.

scholarly journals RNA-silencing induces target gene relocalization toward a specialized nuage domain

2021 ◽  
Author(s):  
Yuchen Yang ◽  
David Grunwald ◽  
James R. Priess ◽  
Craig C. Mello
Keyword(s):  
Small Rna ◽  
Rna Silencing ◽  
Target Gene ◽  
Developmentally Regulated ◽  
Rna Sequences ◽  
P Granules ◽  
C Elegans ◽  
Heterochromatin Silencing ◽  
Rna Pathways ◽  
Target Rna

Argonaute small RNA pathways maintain genome integrity and fertility by enforcing the transgenerational silencing of transposons as well as many developmentally regulated germline genes 1. To propagate silencing, Argonaute pathways coordinate heterochromatin silencing with cycles of small RNA amplification 2. In animal germlines, mRNA surveillance is thought to occur within cytoplasmic perinuclear domains called nuage 3. In C. elegans 20-50 nuage droplets called P granules surround each pachytene germline nucleus. P granules are known to host many of the Argonaute small RNA systems that carry out transcriptome surveillance, but what if any specific roles P granules might play in Argonaute silencing have remained mysterious. Here we show that RNAi triggers the expansion of a unique P granule, which accumulates large amounts of the target RNA. As transcriptional silencing ensues, both alleles of the target gene relocate near the inner nuclear membrane (INM) directly adjacent this enlarged P granule. Similarly, during piRNA-mediated silencing, both alleles of a target gene reside adjacent to a P granule containing target RNA sequences. In an Argonaute mutant defective in piRNA silencing, the target RNA is released from nuage, and the target alleles dissociate from each other and from the INM. Our findings suggest that transcriptome-surveillance tasks are sub-divided between nuage domains that become specialized to coordinate small RNA silencing signals to their heterochromatin targets.

scholarly journals Induction of Promoter DNA Methylation Upon High-Pressure Spraying of Double-Stranded RNA in Plants

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 789
Author(s):  
Athanasios Dalakouras ◽  
Ioannis Ganopoulos
Keyword(s):  
High Pressure ◽  
De Novo ◽  
Epigenetic Changes ◽  
Double Stranded Rna ◽  
Rna Molecules ◽  
Promoter Sequences ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
First Time ◽  
De Novo Methylation

Exogenous application of RNA molecules is a potent method to trigger RNA interference (RNAi) in plants in a transgene-free manner. So far, all exogenous RNAi (exo-RNAi) applications have aimed to trigger mRNA degradation of a given target. However, the issue of concomitant epigenetic changes was never addressed. Here, we report for the first time that high-pressure spraying of dsRNAs can trigger de novo methylation of promoter sequences in plants.

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