title: A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans.
abstract: BACKGROUND
  Environmental 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Our 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.
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA.
authors.forename: Julie Zhouli
authors.initials: JZ
authors.lastname: Ni
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA.
authors.forename: Natallia
authors.initials: N
authors.lastname: Kalinava
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA.
authors.forename: Esteban
authors.initials: E
authors.lastname: Chen
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Huang
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA.
authors.forename: Thi
authors.initials: T
authors.lastname: Trinh
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA ; Nelson Labs A125, 604 Allison Road, Piscataway, NJ 08854 USA.
authors.forename: Sam Guoping
authors.initials: SG
authors.lastname: Gu
keywords: ChIP-seq; Germline; Heat stress; Heterochromatin; LTR retrotransposon; Mortal germline phenotype (Mrt); Nuclear Argonaute protein HRDE-1/WAGO-9; Nuclear RNAi; RNA-seq; Retrotransposon silencing; Transcriptional silencing