Sperm RNA Payload: Implications for Intergenerational Epigenetic Inheritance

Abstract

There is mounting evidence that ancestral life experiences and environment can influence phenotypes in descendants. The parental environment regulates offspring phenotypes potentially via modulating epigenetic marks in the gametes. Here, we review examples of across-generational inheritance of paternal environmental effects and the current understanding of the role of small RNAs in such inheritance. We discuss recent advances in revealing the small RNA payload of sperm and how environmental conditions modulate sperm small RNAs. Further, we discuss the potential mechanism of inheritance of paternal environmental effects by focusing on sperm small RNA-mediated regulation of early embryonic gene expression and its role in influencing offspring phenotypes.

Keywords: epigenetics; inheritance; small RNAs; sperm.

Figure 1

sRNA sequencing approaches: (Different colors represent RNA types harboring specific modification or chemical structures.) (A) Ligation-based protocols require 5′ phosphate and 3′ hydroxyl groups for adaptor ligation. In addition, many reverse transcriptase (RT) enzymes cannot read through the hard-stop modifications on highly modified RNA molecules and fall off prematurely. Therefore, small RNAs that are endowed with the above characteristics are not efficiently sequenced. (B) To allow sequencing of highly modified RNA molecules, in ARM-seq, RNA is pretreated with AlkB demethylase to remove specific methyl modifications that interfere with RT. (C) In addition to using AlkB treatment, PANDORA-seq also uses pretreatment of RNA with T4 Polynucleotide Kinase (PNK) to allow efficient 5′ and 3′ end adaptor ligation. (D) DM-tRNA-seq utilizes a combination of AlkB demethylase and a thermostable template-switching reverse transcriptase-TGIRT to overcomes 3′ structure and modification-induced RT stop. (E) OTTR utilizes a retroelement reverse transcriptase that allows the addition of 5′ and 3′ adaptors in a single tube during cDNA synthesis by serial template switching.

Figure 2

Model for intergenerational inheritance via sperm RNAs: (A) Epididymis shapes the small RNA payload of mature sperm. Small RNAs are delivered from the epididymis epithelial cells to sperm via extracellular vesicles known as epididymosomes represented by orange and green dots to depict different types of vesicles. (B) Mature sperm in mice are chiefly comprised of rsRNAs, tRFs, miRNAs, and piRNAs. Various studies demonstrate that levels of sperm small RNAs are altered in response to paternal environmental conditions. (C) Different epigenetic marks, including DNA methylation, histone modifications, and small RNAs, can function synergistically to regulate intergenerational epigenetic inheritance and influence offspring phenotypes. (D) In males, intergenerational inheritance involves the transmission of paternal environmental effects from F0 to F1. In some instances, paternal environmental effects can be transmitted to F2 and later generations, constituting transgenerational inheritance.