Tissue homogeneity requires inhibition of unequal gene silencing during development

Le, Hai H.; Looney, Monika; Strauss, Benjamin; Bloodgood, Michael; Jose, Antony M.

doi:10.1083/jcb.201601050

Cited by 11 publications

(26 citation statements)

References 67 publications

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“…While many genes do not require NRDE-3 for silencing, the bli-1 gene requires NRDE-3 for silencing by ingested dsRNA or neuronal dsRNA (13). Finally, a strict requirement for NRDE-3 but not for RRF-1 is seen for the silencing of repetitive DNA that occurs in an enhanced RNAi background upon growth at lower temperatures (30). These observations suggest that a mix of mechanisms could underlie RNAi in C. elegans.…”

Section: Introductionmentioning

confidence: 93%

“…This target is a multicopy transgene that generates trace amounts of dsRNA that can cause selfsilencing in enhanced RNAi backgrounds (e.g. adr-1(-); adr-2(-) in (55) and eri-1(-) or rrf-3(-) in (30)). Silencing by this target-derived dsRNA was modest ( Figure 1A, ~24 GFP+ nuclei in eri-1(-), p-value < 10 -3 when compared to ~30 GFP+ nuclei in eri-1(+)), consistent with earlier reports (11,30).…”

Section: Silencing By Neuronal Dsrna Can Be Distinct From Silencing Bmentioning

confidence: 99%

“…adr-1(-); adr-2(-) in (55) and eri-1(-) or rrf-3(-) in (30)). Silencing by this target-derived dsRNA was modest ( Figure 1A, ~24 GFP+ nuclei in eri-1(-), p-value < 10 -3 when compared to ~30 GFP+ nuclei in eri-1(+)), consistent with earlier reports (11,30). Similarly, silencing by gfp-dsRNA expressed in neurons (Prgef-1::gfp-dsRNA) was also modest ( Figure 1A, ~24 GFP+ nuclei, p-value < 10 -4 when compared to eri-1(+)), consistent with an earlier report (12).…”

Section: Silencing By Neuronal Dsrna Can Be Distinct From Silencing Bmentioning

confidence: 99%

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Gene silencing by double-stranded RNA fromC. elegansneurons reveals functional mosaicism of RNA interference

Ravikumar

Devanapally

Jose

2018

Preprint

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Graphical Abstract:Random sets of cells can either receive different amounts of double-stranded RNA from neurons or use different RdRPs -RRF-1 only versus RRF-1 or EGO-1 -to perform the same function. ABSTRACTDelivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the nematode C. elegans, dsRNA from multiple sources can trigger the amplification of silencing signals. Amplification occurs through the production of small RNAs by two RNA-dependent RNA polymerases (RdRPs) that are thought to be tissuespecific -EGO-1 in the germline and RRF-1 in somatic cells. Here we analyze instances of silencing in somatic cells that lack RRF-1. By varying dsRNA sources and target genes, we find that silencing in the absence of RRF-1 is most obvious when dsRNA from neurons is used to silence genes in intestinal cells. This silencing requires EGO-1, but the lineal identity of cells that can use EGO-1 varies. This variability could be because random sets of cells can either receive different amounts of dsRNA from the same source or use different RdRPs to perform the same function. As a result, all cells appear similarly functional despite underlying differences that vary from animal to animal. This functional mosaicism cautions against the use of a few molecules as proxies for predicting the behavior of a cell. 16: P14-P15).Transgenesis: C. elegans was transformed with plasmids and/or PCR products using microinjection (32) to generate extrachromosomal or integrated arrays. pHC337 was used to express an inverted repeat of gfp in neurons (11), which is expected to generate a hairpin RNA (gfp-dsRNA). Generation of the array that expresses unc-22-dsRNA in neurons (qtEx136) was described earlier (12). To rescue silencing defects in rde-1(jam1) and rrf-1(jam3) animals (Supplementary Figure S2), genomic DNA from wild-type animals (N2 gDNA) was used as a template to generate fused promoter/gene products through overlap extension PCR using Expand Long Template polymerase (Roche) and PCR products were purified using QIAquick PCR Purification Kit (Qiagen). The plasmid pHC448for DsRed2 expression in the pharynx or a PCR product, Prgef-1::DsRed2::unc-54 3'UTR, for DsRed2 expression in neurons was used as a co-injection marker (12). Additional details are provided in Supplementary Materials and Methods.Genome editing: Synthetic CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA) (IDT) or single guide RNAs (sgRNA) transcribed in vitro were combined with Cas9 protein

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Section: Introductionmentioning

confidence: 93%

Section: Silencing By Neuronal Dsrna Can Be Distinct From Silencing Bmentioning

confidence: 99%

Section: Silencing By Neuronal Dsrna Can Be Distinct From Silencing Bmentioning

confidence: 99%

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Gene silencing by double-stranded RNA fromC. elegansneurons reveals functional mosaicism of RNA interference

Ravikumar

Devanapally

Jose

2018

Preprint

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“…Once a tissue has been specified, however, its constituent cells must remain similar to each other, even as they continue to divide and, by chance, segregate their components unequally to their daughter cells. now identify a mechanism that helps maintain tissue homogeneity during C. elegans development (1). …”

mentioning

confidence: 99%

“…Jose and colleagues, led by undergraduate Hai Le, first investigated how the sur-5::gfp transgene is silenced, and found that dsRNA produced from the repetitive array is processed through the canonical RNAi pathway and the nuclear Argonaute protein NRDE-3 (1). The silencing was locus specific: the sur-5::gfp array could be silenced in intestinal cells that still showed expression from other repetitive transgenes or single-copy GFP inserts.…”

mentioning

confidence: 99%

A program to reduce inequality

Short¹

2016

Journal of Cell Biology

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ERI1: A case report of an autosomal recessive syndrome associated with developmental delay and distal limb abnormalities

Hoxha

Aliu

2022

American J of Med Genetics Pt A

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ERI1 is an evolutionary conserved 3′–5′ exonuclease with an important function in multiple RNA processing pathways. Although the molecular mechanisms in which ERI1 is involved have been studied extensively in model organisms, the pathology associated with ERI1 variants in humans has remained elusive because no case has been reported so far. Here, we present a case of a female patient with a homozygous nonsense variant in ERI1 gene. The patient exhibits mild intellectual disability, eyelid ptosis, and anomalies in her hands and feet (brachydactyly, clinodactyly, dysplastic/short nail of halluces, brachytelephalangy, short metacarpals, and toe syndactyly). This case report is the first of its kind and is invaluable for understanding ERI1 pathology in humans.

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Tissue homogeneity requires inhibition of unequal gene silencing during development

Cited by 11 publications

References 67 publications

Gene silencing by double-stranded RNA fromC. elegansneurons reveals functional mosaicism of RNA interference

Gene silencing by double-stranded RNA fromC. elegansneurons reveals functional mosaicism of RNA interference

A program to reduce inequality

ERI1: A case report of an autosomal recessive syndrome associated with developmental delay and distal limb abnormalities

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