@article {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/105114,
    title ="RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility",
    author = "Chen, Peiwei and Luo, Yicheng",
    
    
    
    
    month = "August",
    year = "2020",
    
    
    
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200826-094353695",
    note = "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nPosted August 25, 2020. \n\nWe are grateful to Xin Chen, Peter Andersen, William Theurkauf, Trudi Schüpbach, Paul Lasko, Elena Pasyukova and three Drosophila Stock Centers (Bloomington, Vienna, Kyoto) for fly stocks. \n\nWe thank Katalin Fejes Toth and members of Aravin lab for discussion and comments. We appreciate the help of Maria Ninova and Fan Gao (Bioinformatics Resource Center, Caltech) with bioinformatics analysis, the help of Grace Shin and Maayan Schwarzkopf with HCR experiments, the help of Giada Spigolon and Andres Collazo (Biological Imaging Facility, Caltech) with microscopy, and the help of Igor Antoshechkin (Millard and Muriel Jacobs Genetics and Genomics Laboratory, Caltech) with sequencing. This work was supported by grants from the National Institutes of Health (R01 GM097363) and by the HHMI Faculty Scholar Award to A.A.A. \n\nData and code availability: Sequencing data will be uploaded to NCBI SRA. \n\nThe authors declare no competing interests.",
    revision_no = "8",
    abstract = "piRNAs are small non-coding RNAs that guide the silencing of transposons and other targets in animal gonads. In Drosophila female germline, many piRNA source loci dubbed \"piRNA clusters\" lack hallmarks of active genes and exploit an alternative path for transcription, which relies on the Rhino-Deadlock-Cutoff (RDC) complex. It remains to date unknown how piRNA cluster transcription is regulated in the male germline. We found that components of RDC complex are expressed in male germ cells during early spermatogenesis, from germline stem cells (GSCs) to early spermatocytes. RDC is essential for expression of dual-strand piRNA clusters and transposon silencing in testis; however, it is dispensable for expression of Y-linked Suppressor of Stellate piRNAs and therefore Stellate silencing. Despite intact Stellate repression, rhi mutant males exhibited compromised fertility accompanied by germline DNA damage and GSC loss. Thus, piRNA-guided repression is essential for normal spermatogenesis beyond Stellate silencing. While RDC associates with multiple piRNA clusters in GSCs and early spermatogonia, its localization changes in later stages as RDC concentrates on a single X-linked locus, AT-chX. Dynamic RDC localization is paralleled by changes in piRNA cluster expression, indicating that RDC executes a fluid piRNA program during different stages of spermatogenesis.",
}
@article {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/105115,
    title ="piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline",
    author = "Chen, Peiwei and Kotov, Alexei A.",
    
    
    
    
    month = "August",
    year = "2020",
    
    
    
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200826-100150960",
    note = "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nPosted August 25, 2020. \n\nWe are grateful to William Theurkauf, Trudi Schüpbach, Julius Brennecke and Bloomington Drosophila Stock Center for fly stocks. We thank Katalin Fejes Toth and members of Aravin lab for discussion and comments. We appreciate the help of Maria Ninova and Fan Gao (Bioinformatics Resource Center, Caltech) with bioinformatics analysis, the help of Grace Shin and Maayan Schwarzkopf with HCR experiments, the help of Giada Spigolon and Andres Collazo (Biological Imaging Facility, Caltech) with microscopy, and the help of Igor Antoshechkin (Millard and Muriel Jacobs Genetics and Genomics Laboratory, Caltech) with sequencing. This work was supported by grants from the National Institutes of Health (R01 GM097363) and by the HHMI Faculty Scholar Award to A.A.A. \n\nThe authors declare no competing interests.\n\nData and code availability: Sequencing data will be uploaded to NCBI SRA.",
    revision_no = "9",
    abstract = "Small non-coding piRNAs act as sequence-specific guides to repress complementary targets in Metazoa. Prior studies in Drosophila ovaries have demonstrated the function of piRNA pathway in transposon silencing and therefore genome defense. However, the ability of piRNA program to respond to different transposon landscape and the role of piRNAs in regulating host gene expression remain poorly understood. Here, we comprehensively analyzed piRNA expression and defined the repertoire of their targets in Drosophila melanogaster testes. Comparison of piRNA programs between sexes revealed sexual dimorphism in piRNA programs that parallel sex-specific transposon expression. Using a novel bioinformatic pipeline, we identified new piRNA clusters and established complex satellites as dual-strand piRNA clusters. While sharing most piRNA clusters, two sexes employ them differentially to combat sex-specific transposon landscape. We found several host genes targeted by piRNAs in testis, including CG12717/pita, a SUMO protease gene. piRNAs encoded on Y chromosome silence pita, but not its paralog, to exert sex- and paralog-specific gene regulation. Interestingly, pita is targeted by endogenous siRNAs in a sibling species, Drosophila mauritiana, suggesting distinct but related silencing strategies invented in recent evolution to regulate a conserved protein-encoding gene.",
}
@article {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/104390,
    title ="Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex",
    author = "Huang, Xiawei and Hu, Hongmiao",
    
    
    
    
    month = "July",
    year = "2020",
    
    
    
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200715-143612345",
    note = "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nPosted July 14, 2020. \n\nWe thank members of the Aravin lab for discussion and comments. We thank the BL19U1 beamlines staff at the Shanghai Synchrotron Radiation Facility for assistance during data collection. We thank Igor Antoshechkin (Caltech) for help with sequencing. This work was supported by grants from the National Institutes of Health (R01 GM097363) and by the HHMI Faculty Scholar Award to A.A.A. and the National Natural Science Foundation of China (31870755) and the Guangdong Innovation Research Team Fund (2016ZT06S172) to S.L. \n\nData availability: Small RNA-seq data are available on the GEO database, GSE153156. X-ray structures have been deposited in the RCSB Protein Data Bank with the accession codes: 7CFB for the eTud1 apo structure, 7CFC for the eTud1-Ago3 complex structure and 7CFD for the eTud2-AubR15me2 structure.",
    revision_no = "15",
    abstract = "Piwi proteins use guide piRNAs to repress selfish genomic elements, protecting the genomic integrity of gametes and ensuring the fertility of animal species. Efficient transposon repression depends on amplification of piRNA guides in the ping-pong cycle, which in Drosophila entails tight cooperation between two Piwi proteins, Aub and Ago3. Here we show that post-translational modification, symmetric dimethylarginine (sDMA), of Aub is essential for piRNA biogenesis, transposon silencing and fertility. Methylation is triggered by loading of a piRNA guide into Aub, which exposes its unstructured N-terminal region to the PRMT5 methylosome complex. Thus, sDMA modification is a signal that Aub is loaded with piRNA guide. Amplification of piRNA in the ping-pong cycle requires assembly of a tertiary complex scaffolded by Krimper, which simultaneously binds the N-terminal regions of Aub and Ago3. To promote generation of new piRNA, Krimp uses its two Tudor domains to bind Aub and Ago3 in opposite modification and piRNA-loading states. Our results reveal that post-translational modifications in unstructured regions of Piwi proteins and their binding by Tudor domains that are capable of discriminating between modification states is essential for piRNA biogenesis and silencing.",
}