The spatial and temporal dynamics of nuclear RNAi-targeted retrotransposon transcripts in <i>Caenorhabditis elegans</i>

Ni, Julie Zhouli; Kalinava, Natallia; Mendoza, Sofia Galindo; Gu, Sam Guoping

doi:10.1242/dev.167346

Cited by 11 publications

(7 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our work links deregulation of the nuclear 22G-RNA pathways to ectopic H3K9 and H3K27 methylation at endogenous genes. Both histone marks can be artificially induced on active genes targeted by exogenous dsRNA (8,31,80), and several H3K9 methyltransferases have been connected to WAGO-induced silencing (30,72,80,81). However, it was not possible to reliably correlate nuclear Argonaute function in inhibiting endogenous genes with H3K9 methylation (34,35).…”

Section: Discussionmentioning

confidence: 99%

Interplay between small RNA pathways shapes chromatin landscapes in C. elegans

Gushchanskaia

Esse

et al. 2019

Nucleic Acids Research

View full text Add to dashboard Cite

The nematode Caenorhabditis elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both ‘silencing’ siRNAs bound by Worm-specific Argonautes (WAGO) and ‘activating’ siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here, we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partially rescued null mutant strain (WM193), this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements and an increased number of small RNAs that match enhancers in both drh-3 and csr-1 mutants. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to sites with increased silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.

show abstract

Section: Discussionmentioning

confidence: 99%

Interplay between small RNA pathways shapes chromatin landscapes in C. elegans

Gushchanskaia

Esse

et al. 2019

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…A phylogenetic analysis based on the amino acid sequence of reverse transcriptase indicated that Cer1 - Cer6 retrotransposons fall in the same family domain as the gypsy/Ty3 groups that are adjacent to the family domain that includes HERV-K. Although most of the retrotransposons are silenced by ADARs (adenosine deaminases acting on double-stranded RNA) and nuclear RNAi to protect endogenous genome structure, a few C. elegans retrotransposons have been reported to be actively expressed ( 21 , 22 ). Cer1 produces capsids that assemble virus-like particles (VLPs) in C. elegans germ cells ( 23 ).…”

Section: Discussionmentioning

confidence: 99%

Human Endogenous Retrovirus K (HERV-K) can drive gene expression as a promoter in Caenorhabditis elegans

et al. 2020

View full text Add to dashboard Cite

Endogenous retroviruses (ERVs) are retrotransposons present in various metazoan genomes and have been implicated in metazoan evolution as well as in nematodes and humans. The long terminal repeat (LTR) retrotransposons contain several regulatory sequences including promoters and enhancers that regulate endogenous gene expression and thereby control organismal development and response to environmental change. ERVs including the LTR retrotransposons constitute 8% of the human genome and less than 0.6% of the Caenorhabditis elegans ( C. elegans ) genome, a nematode genetic model system. To investigate the evolutionarily conserved mechanism behind the transcriptional activity of retrotransposons, we generated a transgenic worm model driving green fluorescent protein (GFP) expression using Human endogenous retroviruses (HERV)-K LTR as a promoter. The promoter activity of HERV-K LTR was robust and fluorescence was observed in various tissues throughout the developmental process. Interestingly, persistent GFP expression was specifically detected in the adult vulva muscle. Using deletion constructs, we found that the region from positions 675 to 868 containing the TATA box was necessary for promoter activity driving gene expression in the vulva. Interestingly, we found that the promoter activity of the LTR was dependent on che-1 transcription factor, a sensory neuron driver, and lin-15b , a negative regulator of RNAi and germline gene expression. These results suggest evolutionary conservation of the LTR retrotransposon activity in transcriptional regulation as well as the possibility of che-1 function in non-neuronal tissues.

show abstract

“…Our work links deregulation of the nuclear 22G-RNA pathways to ectopic H3K9 and H3K27 methylation at endogenous genes. Both histone marks can be artificially induced on active genes targeted by exogenous dsRNA (8,31,70), and several H3K9 methyltransferases have been connected to WAGO-induced silencing (30,(70)(71)(72). However, it was not possible to reliably correlate nuclear Argonautes' function in inhibiting endogenous genes with H3K9 methylation (34,35).…”

Section: Discussionmentioning

confidence: 99%

The interplay between small RNA pathways shapes chromatin landscapes inC. elegans

Gushchanskaia

Esse

et al. 2018

Preprint

View full text Add to dashboard Cite

The nematode C. elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both "silencing" siRNAs bound by Worm-specific Argonautes (WAGO) and "activating" siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here we show that, in the drh-3(ne4253) mutant deficient in RdRPproduced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partial loss-of-function mutant this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements in both drh-3 and csr-1 partial loss-of-function mutants and describe small RNAs matching enhancers. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to increase in silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.

show abstract

The spatial and temporal dynamics of nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans

Cited by 11 publications

References 77 publications

Interplay between small RNA pathways shapes chromatin landscapes in C. elegans

Interplay between small RNA pathways shapes chromatin landscapes in C. elegans

Human Endogenous Retrovirus K (HERV-K) can drive gene expression as a promoter in Caenorhabditis elegans

The interplay between small RNA pathways shapes chromatin landscapes inC. elegans

Contact Info

Product

Resources

About