The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes

Abstract

At the end of mammalian sperm development, sperm cells expel most of their cytoplasm and dispose of the majority of their RNA. Yet, hundreds of RNA molecules remain in mature sperm. The biological significance of the vast majority of these molecules is unclear. To better understand the processes that generate sperm small RNAs and what roles they may have, we sequenced and characterized the small RNA content of sperm samples from two human fertile individuals. We detected 182 microRNAs, some of which are highly abundant. The most abundant microRNA in sperm is miR-1246 with predicted targets among spermspecific genes. The most abundant class of small noncoding RNAs in sperm are PIWI-interacting RNAs (piRNAs). Surprisingly, we found that human sperm cells contain piRNAs processed from pseudogenes. Clusters of piRNAs from human testes contain pseudogenes transcribed in the antisense strand and processed into small RNAs. Several human protein-coding genes contain antisense predicted targets of pseudogene-derived piRNAs in the male germline and these piRNAs are still found in mature sperm. Our study provides the most extensive data set and annotation of human sperm small RNAs to date and is a resource for further functional studies on the roles of sperm small RNAs. In addition, we propose that some of the pseudogene-derived human piRNAs may regulate expression of their parent gene in the male germline.

Comparative profiling of small RNAs of pig seminal plasma and ejaculated and epididymal sperm

“…The overall length distribution of small RNAs revealed that the dominant reads from pig seminal plasma, epididymal sperm and ejaculated sperm are 18-26 nucleotides (Fig. 1A), which is distinct from that observed in adult testes (Kowalczykiewicz et al 2014, Gebert et al 2015, where two peaks (18-25 nucleotides and 26-32 nucleotides) are observed, and in human sperm (24-31 nucleotides) (Pantano et al 2015). The majority of the 26-32 nucleotide small RNAs in the pig testes and the human sperm are piRNAs (Kowalczykiewicz et al 2014, Gebert et al 2015, Pantano et al 2015, which are actively involved in the retrotransposon silencing that protects the integrity of the genome.…”

“…Conversely, the current study revealed that the diversity of small RNAs across the three libraries is generally similar. In addition to mRNAs, the diversity of the population of the sperm RNAs has now been extended to several non-coding RNAs, including miRNAs, piRNAs (Amanai et al 2006, Krawetz et al 2011, Pantano et al 2015, endo-siRNAs , small RNAs derived from tRNA, rRNA, snRNA and snoRNA (Peng et al 2012) and lncRNA . The sperm miRNA has been reported most extensively and identified in all mammal species examined, including humans, mice, rats, rabbits, bulls, pigs and stallions (Amanai et al 2006, Cornwall 2009, Krawetz et al 2011, Das et al 2013, Stowe et al 2014, Kasimanickam & Kastelic 2016.…”

“…The complexity of non-coding RNA species has also been well characterized in the sperm (Krawetz et al 2011, Peng et al 2012, Jodar et al 2013, García-lópez et al 2015, Pantano et al 2015, and it is now commonly accepted that non-coding RNAs are critical for the process of embryogenesis (Liu et al 2012a, Chen et al 2016a,b, Yuan et al 2016. The miRNA family is the best Reproduction (2017) 153 [785][786][787][788][789][790][791][792][793][794][795][796] www.reproduction-online.org characterized of the small RNA species in sperm.…”

“…However, the role of some miRNAs in the development of early embryos remains controversial (Amanai et al 2006, Yuan et al 2015. piRNAs are the second best-known small RNA species in sperm (Krawetz et al 2011, Pantano et al 2015. It has been shown that the human sperm contains over tens of thousands of piRNAs with over 400 clusters and that piRNAs appear to be the most abundant class of small RNAs in mature human sperm and the most abundant sperm piRNAs targeting LINE1 transposons.…”

“…It has been shown that the human sperm contains over tens of thousands of piRNAs with over 400 clusters and that piRNAs appear to be the most abundant class of small RNAs in mature human sperm and the most abundant sperm piRNAs targeting LINE1 transposons. In addition, pseudogene-derived piRNAs complementary to protein-coding genes, which may regulate the expression of their parent gene in the male germ line, have been identified in the human sperm (Krawetz et al 2011, Pantano et al 2015. Moreover, Stoeckius and coworkers found that approximately half of all assayed endogenous piRNAs and siRNAs of 1-cell embryos in Caenorhabditis elegans are of sperm origin (Stoeckius et al 2014).…”