A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans.

Julie Zhouli Ni,Alex Huang,Natallia Kalinava,Thi Trinh,Esteban Chen,Sam Guoping Gu

doi:10.1186/s13072-016-0052-x

Julie Zhouli Ni, Alex Huang + Show 4 more

Open Access

https://doi.org/10.1186/s13072-016-0052-x

Copy DOI

Abstract

BackgroundEnvironmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human. The capacity and mechanism of such phenomena are poorly understood. In C. elegans, siRNA mediates transgenerational gene silencing through the germline nuclear RNAi pathway. This pathway is also required to maintain the germline immortality when C. elegans is under heat stress. However, the underlying molecular mechanism is unknown. In this study, we investigated the impact of heat stress on chromatin, transcription, and siRNAs at the whole-genome level, and whether any of the heat-induced effects is transgenerationally heritable in either the wild-type or the germline nuclear RNAi mutant animals.ResultsWe performed 12-generation temperature-shift experiments using the wild-type C. elegans and a mutant strain that lacks the germline-specific nuclear Argonaute protein HRDE-1/WAGO-9. By examining the mRNA, small RNA, RNA polymerase II, and H3K9 trimethylation profiles at the whole-genome level, we revealed an epigenetic role of HRDE-1 in repressing heat stress-induced transcriptional activation of over 280 genes. Many of these genes are in or near LTR (long-terminal repeat) retrotransposons. Strikingly, for some of these genes, the heat stress-induced transcriptional activation in the hrde-1 mutant intensifies in the late generations under the heat stress and is heritable for at least two generations after the mutant animals are shifted back to lower temperature. hrde-1 mutation also leads to siRNA expression changes of many genes. This effect on siRNA is dependent on both the temperature and generation.ConclusionsOur study demonstrated that a large number of the endogenous targets of the germline nuclear RNAi pathway in C. elegans are sensitive to heat-induced transcriptional activation. This effect at certain genomic loci including LTR retrotransposons is transgenerational. Germline nuclear RNAi antagonizes this temperature effect at the transcriptional level and therefore may play a key role in heat stress response in C. elegans.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0052-x) contains supplementary material, which is available to authorized users.

Highlights

Environmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human
By using the published HRDE-1-coIP small RNA dataset [10], we found that nuclear RNAi-repressed heat-inducible genes (NHGs) tend to have abundant HRDE-1-bound small interfering RNA (siRNA) (Fig. 2c), strongly suggesting that they are targeted by the germline nuclear RNA interference (RNAi) pathway
We investigated the impact of heat stress on mRNA expression, transcription, H3K9me3, and siRNAs at the whole-genome level in the wild-type C. elegans and a mutant strain that lacks the germline-specific nuclear AGO protein HRDE-1/WAGO-9

Summary

Introduction

Environmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human. Similar to plants and S. pombe, secondary siRNAs in C. elegans, either triggered by exogenous dsRNA or endogenous silencing RNA (e.g., piRNAs), can guide nuclear Argonaute proteins, together with other protein factors, to target genes for heterochromatin formation, marked by H3K9 trimethylation (H3K9me3), and transcriptional silencing [8,9,10,11,12] Despite these similarities, several features of nuclear RNAi in C. elegans make this pathway a unique model system to explore novel mechanisms of RNA-mediated chromatin silencing and its roles in developmental regulation. HRDE-1/WAGO-9 is one of several worm-specific AGO proteins [15] and is essential for the heritable H3K9me response and heritable gene silencing triggered by exogenous dsRNA, piRNA, or transgene [10, 12,13,14] These findings have established nuclear RNAi in C. elegans as an important model system to study RNA-mediated chromatin regulation and transgenerational epigenetic inheritance. These findings have established nuclear RNAi in C. elegans as an important model system to study RNA-mediated chromatin regulation and transgenerational epigenetic inheritance. (The name HRDE-1 is used in the rest of this article to reflect the heritable RNAi-deficient phenotype of the mutant.)

Methods

Results

Discussion

Conclusion