Project title: Molecular mechanism of piRNA biogenesis. Project Summary: Non-coding RNAs have diverse functions in eukaryotic cells. Use of these non-coding RNAs in therapeutic approaches is a promising but rather unexplored direction in biomedical research. A few years ago, we discovered a new class of small non-coding RNAs, termed piwi-interacting RNAs (piRNAs), that are expressed in animal germlines. piRNAs, together with their protein partners, Piwi proteins, recognize and silence endogenous genomic parasites called transposable elements. The silencing of transposons is critical in germline cells and the failure of piRNA-mediated repression leads to sterility in both Drosophila and mice. The mechanism of biogenesis of piRNAs appears to be distinct from that of other classes of small non-coding RNAs, microRNA and siRNA. piRNAs are encoded in distinct genomic regions dubbed piRNA clusters that work as memory banks to store inactive copies of past transposon invaders. piRNA clusters produce long transcripts that are further processed to mature small RNA species. Our goal is to dissect piRNA biogenesis from their transcription to processing into mature piRNAs and to understand how these steps are regulated. We want to understand how transcripts that are destined for processing into piRNAs are selected and identify the enzymatic machinery responsible for processing. To meet these objectives we will dissect the molecular mechanism of piRNA biogenesis using D. melanogaster and insect cell lines. We will investigate the genomic and chromatin structure of piRNA clusters and map their promoter regions. These studies will identify regulatory elements necessary for piRNA expression and determine the role that chromatin plays in regulation of piRNA transcription. Next we will identify determinants in precursor transcripts that are required for piRNA biogenesis. We will determine if piRNA processing depends on distinct sequence elements inside the piRNA precursor transcripts. We will also search for a protein complex directly responsible for piRNA processing. Finally, we will study the intracellular localization of piRNA precursor transcripts and the role of nuage granules in piRNA biogenesis. Together, these experiments will comprehensively analyze all steps of piRNA biogenesis from transcription of precursor RNAs to processing into mature small RNAs. The failure of piRNA repression leads to sterility, and also might be important in aging and cancer progression. Thus, our findings will provide the basis for directing the piRNA pathway in order to make these non-coding RNAs useful tools in epigenetic research and in therapy.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Molecular Genetics A Study Section (MGA)
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Bender, Michael T
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California Institute of Technology
Schools of Arts and Sciences
United States
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Liu, Yiwei; Esyunina, Daria; Olovnikov, Ivan et al. (2018) Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. Cell Rep 24:453-462
Huang, Xiawei; Fejes Tóth, Katalin; Aravin, Alexei A (2017) piRNA Biogenesis in Drosophila melanogaster. Trends Genet 33:882-894
Ciabrelli, Filippo; Comoglio, Federico; Fellous, Simon et al. (2017) Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nat Genet 49:876-886
Hur, Junho K; Luo, Yicheng; Moon, Sungjin et al. (2016) Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila. Genes Dev 30:840-55
Chen, Yung-Chia Ariel; Stuwe, Evelyn; Luo, Yicheng et al. (2016) Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors. Mol Cell 63:97-109
Chen, Yung-Chia Ariel; Aravin, Alexei A (2015) Non-Coding RNAs in Transcriptional Regulation: The review for Current Molecular Biology Reports. Curr Mol Biol Rep 1:10-18
Webster, Alexandre; Li, Sisi; Hur, Junho K et al. (2015) Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper. Mol Cell 59:564-75
Le Thomas, Adrien; Stuwe, Evelyn; Li, Sisi et al. (2014) Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev 28:1667-80
Olovnikov, Ivan; Le Thomas, Adrien; Aravin, Alexei A (2014) A framework for piRNA cluster manipulation. Methods Mol Biol 1093:47-58
Le Thomas, Adrien; Marinov, Georgi K; Aravin, Alexei A (2014) A transgenerational process defines piRNA biogenesis in Drosophila virilis. Cell Rep 8:1617-1623

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