Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans

Kalinava, Natallia; Ni, Julie Zhouli; Peterman, Kimberly; Chen, Esteban; Gu, Sam Guoping

doi:10.1186/s13072-017-0114-8

Cited by 70 publications

(147 citation statements)

References 56 publications

Supporting

Mentioning

126

Contrasting

Order By: Relevance

“…Our results agree with previous studies suggesting that germ granules are necessary for maintaining small RNA homeostasis and assignment to different argonautes 21,22 . The HRDE-1 argonaute was shown in numerous studies to be absolutely essential for dsRNA-induced RNAi inheritance [9][10][11]14,48,49 . As we found strong RNAi inheritance in germ granule mutants despite severe defects in HRDE-1-associated small RNAs, we hypothesized that when the germ granules are defective, RNAi might be inherited via alternative routes.…”

Section: Resultsmentioning

confidence: 99%

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

Lev

Toker

et al. 2019

Preprint

View full text Add to dashboard Cite

In C. elegans nematodes, components of liquid-like germ granules were shown to be required for transgenerational small RNA inheritance. Surprisingly, we show here that mutants with defective germ granules (pptr-1, meg-3/4, pgl-1) can nevertheless inherit potent small RNA-based silencing responses, but some of the mutants lose this ability after many generations of homozygosity. Animals mutated in pptr-1, which is required for stabilization of P granules in the early embryo, display extremely strong heritable RNAi responses, which last for tens of generations, long after the responses in wild type animals peter out. The phenotype of mutants defective in the core germ granules proteins MEG-3 and MEG-4, depends on the genotype of the ancestors: Mutants that derive from maternal lineages that had functional MEG-3 and MEG-4 proteins exhibit enhanced RNAi inheritance for multiple generations. While functional ancestral meg-3/4 alleles correct, and even potentiates the ability of mutant descendants to inherit RNAi, defects in germ granules functions can be memorized as well; Wild type descendants that derive from lineages of mutants show impaired RNAi inheritance for many (>16) generations, although their germ granules are intact. Importantly, while P granules are maternally deposited, wild type progeny derived from meg-3/4 male mutants also show reduced RNAi inheritance. Unlike germ granules, small RNAs are inherited also from the sperm.Moreover, we find that the transgenerational effects that depend on the ancestral germ granules require the argonaute protein HRDE-1, which carries heritable small RNAs in the germline. Indeed, small RNA sequencing reveals imbalanced levels of many endogenous small RNAs in germ granules mutants. Strikingly, we find that hrde-1;meg-3/4 triple mutants inherit RNAi, although hrde-1 was previously thought to be essential for heritable silencing. We propose that germ granules sort and shape the RNA pool, and that small RNA inheritance memorizes this activity for multiple generations.

show abstract

Section: Resultsmentioning

confidence: 99%

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

Lev

Toker

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…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). Our results connect an increase in H3K9me3 to reduced transcription of CSR-1 target genes when CSR-1 is limited ( Figure 6A).…”

Section: Discussionmentioning

confidence: 72%

“…Both are capable of inducing H3K9me3 at genes complementary to exogenous dsRNA or at transgenes downstream of piRNAs (6,8,(28)(29)(30)(31)(32)(33). However, the interconnection between 22G-RNA production, H3K9 methylation and transcriptional silencing at the endogenous WAGO targets remains unclear (34,35).…”

Section: Whether They Also Regulate Chromatin Compaction Is An Open Qmentioning

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

“…additional chromatin PTMs), which are present on the oma-1 gene, but not the spr-5 gene after RNAi, may act with H3K9me3 to localize HERI-1 to oma-1 chromatin. Second, animals lacking the putative H3K9me3 methyltransferase SET-32/HRDE-3 (in which HERI-1 fails to localize to chromatin) are defective, not enhanced, for RNAi inheritance (Ashe et al 2012;Spracklin et al 2017 MET-2 and SET-25, lack biochemically detectable levels of H3K9me2/3 and yet do not show obvious defects in RNAi inheritance (at least in some assays) (Towbin et al 2012;Kalinava et al 2017) . Indeed, depletion of one of these enzymes (MET-2) actually enhances RNAi inheritance (at least in some assays) (Lev et al 2017) .…”

Section: How Does Heri-1 Inhibit Nuclear Rnai?mentioning

confidence: 99%

HERI-1 is a Chromodomain Protein that Negatively Regulates Transgenerational Epigenetic Inheritance

Perales

Pagano

Wan

et al. 2018

Preprint

View full text Add to dashboard Cite

Abstract:Transgenerational epigenetic inheritance (TEI) is the inheritance of epigenetic information for two or more generations. In most cases, TEI is limited to 2-3 generations. This short-term nature of TEI could be set by innate biochemical limitations to TEI or by genetically encoded systems that actively limit TEI.dsRNA-mediated gene silencing (RNAi) can be inherited in C. elegans (termed RNAi inheritance or RNA-directed TEI). To identify systems that might actively limit RNA-directed TEI, we conducted a forward genetic screen for factors whose mutation enhanced RNAi inheritance. This screen identified the gene h eritable e nhancer of R NA i ( heri-1 ), whose mutation causes RNAi inheritance to last longer (>20 generations) than normal. heri-1 encodes a protein with a chromodomain and a kinase-homology domain that is expressed in germ cells and localizes to nuclei. In C. elegans , a nuclear branch of the RNAi pathway (nuclear RNAi or NRDE pathway) is required for RNAi inheritance. We find that this NRDE pathway is hyper-responsive to RNAi in heri-1 mutant animals, suggesting that a normal function of HERI-1 is to limit nuclear RNAi and that limiting nuclear RNAi may be the mechanism by which HERI-1 limits RNAi inheritance. Interestingly, we find that HERI-1 binds to genes targeted by RNAi, suggesting that HERI-1 may have a direct role in limiting nuclear RNAi and, therefore, RNAi inheritance. Surprisingly, recruitment of the negative regulator HERI-1 to genes depends upon that same NRDE factors that drive co-transcriptional gene silencing during RNAi inheritance. We therefore speculate that the generational perdurance of RNAi inheritance is set by competing pro-and anti-silencing outputs of the NRDE nuclear RNAi machinery. 2All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

show abstract

Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans

Cited by 70 publications

References 56 publications

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

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

HERI-1 is a Chromodomain Protein that Negatively Regulates Transgenerational Epigenetic Inheritance

Contact Info

Product

Resources

About