Small RNAs in epigenetic inheritance: from mechanisms to trait transmission

Abstract

Inherited information is transmitted to progeny primarily by the genome through the gametes. However, in recent years, epigenetic inheritance has been demonstrated in several organisms, including animals. Although it is clear that certain post-translational histone modifications, DNA methylation, and noncoding RNAs regulate epigenetic inheritance, the molecular mechanisms responsible for epigenetic inheritance are incompletely understood. This review focuses on the role of small RNAs in transmitting epigenetic information across generations in animals. Examples of documented cases of transgenerational epigenetic inheritance are discussed, from the silencing of transgenes to the inheritance of complex traits, such as fertility, stress responses, infections, and behavior. Experimental evidence supporting the idea that small RNAs are epigenetic molecules capable of transmitting traits across generations is highlighted, focusing on the mechanisms by which small RNAs achieve such a function. Just as the role of small RNAs in epigenetic processes is redefining the concept of inheritance, so too our understanding of the molecular pathways and mechanisms that govern epigenetic inheritance in animals is radically changing.

Keywords: RNA interference; epigenetics; gene regulation; gene silencing; miRNAs; piRNAs; small RNAs; transgenerational epigenetic inheritance.

Fig. 1

Schematic of the inheritance of C. elegans RNAi. The exposure to dsRNAs targeting a fluorescent GFP sequence leads to the inactivation of the GFP reporter (green and gray worms). The GFP reporter remains silenced even in subsequent generations that are not exposed to dsRNAs. The production of primary siRNAs generated by Dicer (DCR‐1) and its cofactor RDE‐4 are loaded into the Argonaute RDE‐1. The catalytic activity of RDE‐1 serves to remove one of the strands of the double‐stranded siRNA. The targeting of the complementary sequence by RDE‐1 leads to the recruitment of the endonuclease RDE‐8 and subsequently to the pUGylation of the cleaved mRNAs. pUGylated mRNAs become the substrate for the RdRP, which generates secondary single‐stranded 5′ triphosphorylated small RNAs called 22G‐RNAs. The 22G‐RNAs are loaded into downstream WAGO proteins, the effector Argonautes that trigger post‐transcriptional and transcriptional silencing. Such silencing persists for multiple generations and correlates with the presence of inherited 22G‐RNAs and pUGylated mRNAs. The nuclear Argonaute HRDE‐1 also triggers heritable histone PTMs.

Fig. 2

Schematic of the different endogenous germline small RNA pathways and their inheritance in C. elegans. Most of the Argonaute proteins localize to germ granules, phase‐separated condensates surrounding the nuclear membrane in the germline of C. elegans. Three different condensates characterize germ granules (P granules, Z granules, and mutator foci). The P granules contain most of the WAGOs, PIWI, and CSR‐1 proteins. The Z granules contain factors involved in heritable RNAi. The mutator foci include most of the enzymes required for the biogenesis of 22G‐RNAs triggered by dsRNAs or piRNAs. The 22G‐RNAs derived from active germline genes are produced by the RdRP EGO‐1 and are loaded into the Argonaute CSR‐1. These CSR‐1 22G‐RNAs can protect germline mRNAs from piRNA silencing and promote the degradation of the complementary mRNAs in the cytosol through the CSR‐1 catalytic activity. CSR‐1 can also bind nascent transcripts and prevent HRDE‐1 nuclear silencing. Most of the germline 22G‐RNAs and pUGylated mRNAs are transmitted to the embryos inside the germ granules. Somatic 22G‐RNAs and dsRNAs are transmitted to the germline through the dsRNA receptor SID‐1 or possibly through EVs carrying yolk protein from the intestine to the oocytes.

Fig. 3

Paternal inheritance of miRNAs in the mouse. Metabolic changes or different types of stress alter the small RNA cargoes loaded into mature mouse sperm. Diet‐induced tRNA fragmentation results in high production of tRFs loaded into mature sperm through epididymosomes vesicles. These vesicles might also transport miRNAs induced by stress. The microinjection of miRNAs extracted from mature sperm produced by animals subjected to stresses recapitulates the stress‐induced phenotypes in subsequent generations. It is unclear whether the miRNA cargoes loaded into mature sperm can effectively regulate embryonic mRNAs after fertilization.