Project III. Understanding the architecture, regulation, and function of piRNA-producing genes Phillip D. Zamore, P.I. Project Summary In flies, mammals, and worms, PIWI-interacting RNAs (piRNAs) silence transposons and repetitive elements, protecting the germline genome from DNA damage and mutation and ensuring that genetic information passes faithfully from generation to generation. They also have other, poorly understood functions. We propose to define the gene structure, genomic architecture, and regulation of the piRNA-producing genes in mice, flies, and worms. We will then use this information to investigate why some long RNAs make piRNAs while others do not. We will also explore how full-length piRNA precursor transcripts, often tens of kilobases long, are converted into mature piRNAs just 23?35 nt long. Finally, we will test a variety of hypotheses, generated from our data, as to how piRNAs function, particularly in mammals, where most piRNAs do not correspond to transposons. To pursue these aims, we will combine genetics, high-throughput sequencing, and classical biochemistry. We believe that by investigating a common set of questions about the piRNA pathway in three model animals, the conserved and divergent features we discover will yield a deeper understanding of this ancient pathway than could be achieved by working on a single species alone. Relevance Small RNAs called ?piRNAs? protect animal sperm and egg precursor cells from damage from selfish genetic elements called transposons or ?jumping genes.? Without piRNAs, animals from worms to mammals are sterile, yet we do not understand how piRNAs are made, and for many piRNAs, what they regulate. We hope to obtain a more complete and deeper understanding of this amazing process.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Research Program Projects (P01)
Project #
5P01HD078253-03
Application #
9233751
Study Section
Special Emphasis Panel (ZHD1-DSR-L)
Project Start
2017-03-01
Project End
2020-02-29
Budget Start
2017-03-01
Budget End
2018-02-28
Support Year
3
Fiscal Year
2017
Total Cost
$268,159
Indirect Cost
$108,064
Name
University of Massachusetts Medical School Worcester
Department
Genetics
Type
Domestic Higher Education
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
01655
Zhang, Donglei; Tu, Shikui; Stubna, Michael et al. (2018) The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes. Science 359:587-592
Yu, Bowen; Lin, Yu An; Parhad, Swapnil S et al. (2018) Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification. EMBO Rep 19:
Fu, Yu; Yang, Yujing; Zhang, Han et al. (2018) The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. Elife 7:
Gainetdinov, Ildar; Colpan, Cansu; Arif, Amena et al. (2018) A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals. Mol Cell 71:775-790.e5
Tang, Wen; Seth, Meetu; Tu, Shikui et al. (2018) A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans. Dev Cell 44:762-770.e3
Dokshin, Gregoriy A; Ghanta, Krishna S; Piscopo, Katherine M et al. (2018) Robust Genome Editing with Short Single-Stranded and Long, Partially Single-Stranded DNA Donors in Caenorhabditis elegans. Genetics 210:781-787
Fu, Yu; Wu, Pei-Hsuan; Beane, Timothy et al. (2018) Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers. BMC Genomics 19:531
Seth, Meetu; Shirayama, Masaki; Tang, Wen et al. (2018) The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans. Cell Rep 22:2254-2264
Ishidate, Takao; Ozturk, Ahmet R; Durning, Daniel J et al. (2018) ZNFX-1 Functions within Perinuclear Nuage to Balance Epigenetic Signals. Mol Cell 70:639-649.e6
Zhang, Gen; Tu, Shikui; Yu, Tianxiong et al. (2018) Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin. Cell Rep 24:3413-3422.e4

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