Non-coding RNAs (ncRNAs) include small RNAs and long non-coding RNAs. They do not encode protein; however, they could be involved in the post-transcriptional regulation of genes. Among the classes of small ncRNAs, PIWI-interacting RNAs (piRNAs) are germ cell-specific and longer than other types of small RNAs, such as endogenous small interfering RNAs (siRNAs) and micro RNAs (miRNAs). Most piRNAs in mammalian testes are derived from long non-coding RNAs, which are fragmented into pre-piRNAs, and the pre-piRNAs loaded onto PIWI proteins at a 1:1 ratio undergo further trimming and 2’-O-methylation at the 3’end, which generates mature piRNAs (Sun et al., 2022). The primary function of mature piRNAs is to silence transposable elements (TEs) across bilateral animals.
In mammalian testes, germ cells express a low amount of piRNAs during the pre-pachytene stages of germ cell development. In contrast, germ cells express highly abundant piRNAs during the pachytene stage of germ cell development. Because over 80 percent of pachytene piRNAs in adult mammalian testes lack obvious targets, earlier studies proposed that pachytene piRNAs regulate mRNAs or stabilize PIWI proteins essential for spermatogenesis (Vourekas et al., 2012; Gou et al., 2014; Zhang et al., 2015; Goh et al., 2015; Wu et al., 2020; Choi et al., 2021). However, the exact function of pachytene piRNAs and the mechanism promoting rapid evolution and divergence of piRNAs and piRNA-producing loci still remains to be clearly understood.
In our new paper, “Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity” (Sun et al., 2023), we revealed three fundamental evolutionary forces driving the rapid evolution of piRNA loci across amniotes. The first force is a high local mutation rate of structural variations (SVs), the second force is a positive selection to suppress young and actively mobilizing TEs (all identified TEs belong to retrotransposons) after meiosis, and the third force is a negative selection to eliminate deleterious SV hotspots. To reveal the above findings, we performed comprehensive comparative studies of amniotes, including six different chicken breeds (Red Jungle Fowl, Athens Canadian Random Bred chickens, White Leghorn Cornell Special C chickens, Araucana chickens, Lvyang Black-bone chickens, and Tibetan chickens), ducks (Pekin ducks), mice, and humans. Our new paper collectively indicates that genetic instability at the pachytene piRNA loci also protects germ-line genome integrity against TE mobilization by driving the formation of rapidly-evolving piRNA sequences.
This work engages not only chickens from all over the world, but also people from all over the world, especially beginner students. We have researchers from 10 universities and one company listed in the authorship, but we actually have more global and interdisciplinary engagement. Of the seven authors from my lab, most of them are visiting students, undergrads, or master’s students from various majors. For example, Duolin Wang was a visiting undergrad from the joint program between Tsinghua University and Peking Union Medical College, China, who is now a physician scientist at Peking Union Medical College Hospital. Gayathri Murthy was a visiting undergrad from Sri Ramaswamy Memorial (SRM) Institute of Science & Technology, India, who is now a PhD student in our toxicology program. Qian Mu, who was a master’s student majoring in mechanical engineering and knew nothing about bench work, is now a PhD student majoring in biomedical engineering at UMass Amherst. Compared to the costly research on mice and humans, chickens are more friendly and approachable to beginner scientists. I am glad to see how our lab members’ research experiences with chickens have shaped their career paths, and we are committed to develop more alternative model organisms, such as green anoles, to engage beginners.