The international cooperation between University of Chicago and NCKU reveals piRNA targeting rules in C. elegans

Prof. Wei-Sheng Wu and his master student Wei-Che Huang joined Prof. Heng-Chi Lee’s research team in University of Chicago to identify piRNA targeting rules in C. elegans. This research is recently published in Science.

Summary of the research:

piRNAs play a critical role in silencing transposons to promote genome integrity in animals. However, it has been difficult to probe the functions of the many piRNAs that do not map to transposons because the piRNA targeting rules remain undefined. Here we show that piRNA targeting in C. elegans prefers perfect pairing at a piRNA seed region but otherwise can tolerate a few mismatches. Our findings suggest the broad targeting capacity of piRNAs underlies the germline silencing of transgenes in C. elegans. Indeed, transgenes engineered to avoid piRNA recognition are stably expressed. Interestingly, many endogenous germline-expressed genes also contain predicted piRNA targeting sites, and our data suggest that periodic An/Tn clusters (PATCs) are an intrinsic signal that provides resistance to piRNA silencing. Together, our study reveals the piRNA targeting logic and highlights a unique strategy that C. elegans uses to distinguish endogenous nucleic acids from foreign nucleic acids.

Impact of the research:

Our study provides an interesting explanation of why many animals produce tens of thousands of piRNAs, as such diversity allows piRNAs to recognize various foreign nucleic acids. Indeed, we show piRNA-mediated silencing is the underlying mechanism of the notorious germline transgene silencing phenomenon. We used our piRNA targeting rule to predict piRNA-targeting sites on several silencing-prone transgenes, including GFP, mCherry and Cas9. Remarkably, by introducing silent mutations that disrupt these predicted piRNA targeting sites, we showed that these silencing-prone transgenes can now be stably expressed in the germline. Our piRNA targeting algorithm offers a practical approach to avoid germline silencing that has confounded C. elegans researchers for over two decades and therefore will be highly valuable for scientists of various fields using this important model organism.

In summary, this study reveals the piRNA targeting logic, which suggests that diverse C. elegans piRNAs can recognize both self and non-self RNAs. In addition, we showed that endogenous genes are resistant to piRNA silencing. Finally, we revealed a licensing mechanism that protects endogenous genes from piRNA silencing. Our work provides direct implications to the function of diverse piRNAs in other animals and suggests a similar licensing mechanism could exist as well.

About the international cooperation

Prof. Wei-Sheng Wu did his sabbatical research in University of Chicago from July 2016 to Feb. 2017. He met Prof. Heng-Chi Lee at 2017 Chinese New Year gathering held by UChicago Taiwanese Student Association. Since then, they immediately talked about possible research cooperation. After Prof. Wu came back to NCKU in Feb. 2017, he and his master student (Wei-Che Huang) started to implement a webtool (called piScan) for identifying piRNA target sites in the input RNA sequence using the piRNA targeting rules found by Prof. Lee’s group. Using piScan, Prof. Wu’s team performed data analysis on Prof. Lee’s data. Since the analyzing results were used by Prof. Lee in his story, Prof. Wu and his student became the co-authors of Prof. Lee’s Science paper.