Poster number 23 submitted by Yi-Hui Wang
Investigating transcriptional program of C. elegans piRNA expression
Yi-Hui Wang (Department of Biological Chemistry and Pharmacology), Hannah L. Hertz (Department of Biological Chemistry and Pharmacology), Benjamin Pastore (Department of Biological Chemistry and Pharmacology; The Center for RNA Biology), Wen Tang (Department of Biological Chemistry and Pharmacology; The Center for RNA Biology)
PIWI-interacting RNAs (piRNAs) are a class of germline small non-coding RNA that are required for silencing the transposable elements. The piRNAs biogenesis involves processing of long transcript precursors into mature piRNAs that are 21-35 nucleotides (nts) in length. In C. elegans, piRNA precursors are capped small RNAs (csRNAs) (Gu et al., 2012). After 5’ and 3’ processing, the mature piRNAs uniformly start with 5’ Uracil and are 21 nts in length, thus referred to as 21U-RNAs. Most 21U-RNAs are produced from the two large piRNA clusters in chromosome IV, which encode over 15,000 unique piRNA sequences. The upstream of these piRNAs gene contains a conserve 8 nts motif, named Ruby motif, which is associated with transcription factors, including TOFU-5, TOFU-4, SNPC-4, and PRDE-1 (Ruby et al.,2006; Weng et al., 2019). To comprehensively define the transcriptional program of piRNA genes, we used a proximity-based labeling approach in combination with mass spectrometry to identify the proteins associated with piRNA clusters (Hertz et al., 2022). Our proteomics data revealed several promising candidates for piRNA biogenesis. We show that a novel transcription factor colocalizes with the piRNA cluster and its depletion causes the diffusion of PRDE-1 from the piRNA cluster, suggesting it acts upstream or co-dependently of PRDE-1. Moreover, upon loss of the transcription factor, the expression levels of 21U-RNA and csRNAs are significantly reduced. Our ongoing research will elucidate the function of this novel transcription factor and provide insights into transcription and processing of piRNAs.
1. Gu, W., Lee, H. C., Chaves, D., Youngman, E. M., Pazour, G. J., Conte Jr, D., & Mello, C. C. (2012). CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell, 151(7), 1488-1500
2. Ruby, J. G., Jan, C., Player, C., Axtell, M. J., Lee, W., Nusbaum, C., ... & Bartel, D. P. (2006). Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 127(6), 1193-1207.
3. Weng, C., Kosalka, J., Berkyurek, A. C., Stempor, P., Feng, X., Mao, H., ... & Miska, E. A. (2019). The USTC co-opts an ancient machinery to drive piRNA transcription in C. elegans. Genes & development, 33(1-2), 90-102.
4. Hertz, H. L., Price, I. F., & Tang, W. (2022). Visualization and Purification of Caenorhabditis elegans Germ Granule Proteins Using Proximity Labeling. Bio-protocol, 12(8), e4386-e4386.
Keywords: piRNA biogenesis, Transcription factor, Ruby motif