Abstract
Plant RNA silencing operates via RNA-directed DNA-methylation (RdDM) to repress transcription or by targeting mRNAs via posttranscriptional gene silencing (PTGS). These pathways rely on distinct Dicer-like (DCL) proteins that process double-stranded RNA (dsRNA) into small-interfering RNAs (siRNAs). Here, we explored the expression and subcellular localization of Arabidopsis thaliana DCL4. DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic protein, which also represents the ancestral form in plants. A longer DCL4 transcript isoform encoding a nuclear localization signal, DCL4NLS, is present in Arabidopsis, but DNA methylation normally suppresses its expression. Hypomethylation caused by mutation, developmental reprogramming, and biotic stress correlates with enhanced DCL4NLS expression, while hypermethylation of a DCL4 transgene causes a reduction in DCL4NLS expression. DCL4NLS functions in a noncanonical siRNA pathway, producing a unique set of 21-nucleotide-long “disiRNAs,” for DCL4NLS isoform-dependent siRNAs, through the nuclear RdDM dsRNA synthesis pathway. disiRNAs originate mostly from transposable elements (TEs) and TE-overlapping/proximal genes, load into the PTGS effector ARGONAUTE1 (AGO1), and display a subtle effect on transcript accumulation together with overlapping 24-nucleotide siRNAs. We propose that, via PTGS, disiRNAs could help to tighten the expression of epigenetically activated TEs and genes using the methylation-state-responsive DCL4NLS.
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Claims 13
Claim · model-written summary
DCL4 expression predominated as a transcription start site isoform encoding a cytoplasmic protein.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianae1 - Gene
- DCL4e0
- Outcome
- expression predominates as a transcription start site isoform encoding a cytoplasmic proteine0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic protein”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
The cytoplasmic DCL4 isoform represents the ancestral plant form.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- DCL4e1
- Outcome
- ancestral form in plantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“which also represents the ancestral form in plants”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
A longer DCL4NLS transcript isoform with a nuclear localization signal is present in Arabidopsis.
- Taxon
- ArabidopsisArabidopsise0
- Gene
- DCL4NLSe0
- Outcome
- a nuclear localization signale0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A longer DCL4 transcript isoform encoding a nuclear localization signal, DCL4NLS, is present in Arabidopsis”
Claim · model-written summary
DNA methylation normally suppresses DCL4NLS expression.
- Taxon
- ArabidopsisArabidopsise1
- Gene
- DCL4NLSe1
- Outcome
- expressione0
- Qualifier
- DNA methylatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“DNA methylation normally suppresses its expression”
e1“DCL4NLS, is present in Arabidopsis”
Claim · model-written summary
Hypomethylation caused by mutation correlated with enhanced DCL4NLS expression.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- Hypomethylation caused by mutatione0
- Gene
- DCL4NLSe0
- Outcome
- DCL4NLS expressione0
- Direction
- enhancede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Hypomethylation caused by mutation, developmental reprogramming, and biotic stress correlates with enhanced DCL4NLS expression”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
Hypomethylation caused by developmental reprogramming correlated with enhanced DCL4NLS expression.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- DCL4NLSe0
- Outcome
- DCL4NLS expressione0
- Direction
- enhancede0
- Qualifier
- developmental reprogramminge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Hypomethylation caused by mutation, developmental reprogramming, and biotic stress correlates with enhanced DCL4NLS expression”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
Hypomethylation caused by biotic stress correlated with enhanced DCL4NLS expression.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- biotic stresse0
- Gene
- DCL4NLSe0
- Outcome
- DCL4NLS expressione0
- Direction
- enhancede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Hypomethylation caused by mutation, developmental reprogramming, and biotic stress correlates with enhanced DCL4NLS expression”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
Hypermethylation of a DCL4 transgene reduced DCL4NLS expression.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- hypermethylation of a DCL4 transgenee0
- Gene
- DCL4NLSe0
- Outcome
- DCL4NLS expressione0
- Direction
- reductione0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“hypermethylation of a DCL4 transgene causes a reduction in DCL4NLS expression”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
DCL4NLS produced a unique set of 21-nucleotide disiRNAs through the nuclear RdDM dsRNA synthesis pathway.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- DCL4NLSe0
- Outcome
- a unique set of 21-nucleotide-long “disiRNAs,”e0
- Qualifier
- nuclear RdDM dsRNA synthesis pathwaye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“DCL4NLS functions in a noncanonical siRNA pathway, producing a unique set of 21-nucleotide-long “disiRNAs,” for DCL4NLS isoform-dependent siRNAs, through the nuclear RdDM dsRNA synthesis pathway.”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
disiRNAs originated mostly from transposable elements and nearby genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Outcome
- disiRNAs originate mostly from transposable elements (TEs) and TE-overlapping/proximal genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“disiRNAs originate mostly from transposable elements (TEs) and TE-overlapping/proximal genes”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
disiRNAs loaded into ARGONAUTE1.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae2
- Gene
- ARGONAUTE1e0
- Outcome
- load into the PTGS effector ARGONAUTE1 (AGO1)e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“load into the PTGS effector ARGONAUTE1 (AGO1)”
e1“disiRNAs originate mostly from transposable elements”
e2“Arabidopsis thaliana DCL4”
Claim · model-written summary
disiRNAs had a subtle effect on transcript accumulation together with overlapping 24-nucleotide siRNAs.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Outcome
- subtle effect on transcript accumulatione0
- Qualifier
- overlapping 24-nucleotide siRNAse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“display a subtle effect on transcript accumulation together with overlapping 24-nucleotide siRNAs”
e1“Arabidopsis thaliana DCL4”
Claim · model-written summary
The authors propose that disiRNAs may tighten expression of epigenetically activated transposable elements and genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- DCL4NLSe0
- Outcome
- expression of epigenetically activated TEs and genese0
- Qualifier
- could help to tightene0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“disiRNAs could help to tighten the expression of epigenetically activated TEs and genes using the methylation-state-responsive DCL4NLS”
e1“Arabidopsis thaliana DCL4”
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