Project II. piRNA pathway organization and precursor processing William Theurkauf, P. I. Project Summary PIWI interacting RNAs (piRNAs) have a conserved function in transcriptional and post- transcriptional transposon silencing in the germline, which is dedicated to transmitting the inherited genome. Here we focus on identifying conserved organizational principles and molecular mechanisms driving transposon control by the piRNA pathway. Transposon control by piRNAs is best understood in Drosophila, where the primary piRNAs that initiate silencing are derived from large heterochromatic ?clusters? composed of nested transposon fragments. Cluster transcripts appear to be processed into mature piRNAs in nuage, which is an electron dense structure closely associated with the cytoplasmic surface of germline nuclei. In flies, heterochromatic clusters at the nuclear periphery appear to organize the perinuclear nuage, forming a compartment that spans the nuclear envelope. This compartment appears to increase the efficiency and specificity of piRNA production, with is critical to germline development. Studies under Aim1 will define this novel germline specific compartment in flies, mouse and worm. How cluster transcripts are differentiated from mRNAs and processed into mature piRNAs is a critical to the specificity of the system, but remains poorly understood. A complex of Drosophila nuclear proteins suppresses cluster transcript splicing, stalled splicing appears to trigger transposon silencing siRNA production in the pathogenic yeast Cryptocccus, and several putative splicing factors are required for fertility in mouse and humans. These observations suggest that stalled splicing has a conserved role in differentiating piRNA precursors from pre-mRNAs. Studies under Aim 2 will broadly define precursor flow though the piRNA pathway, and test the novel hypothesis that regulated splicing differentiates transposons from protein coding. Relevance Transposons and transposon remnants comprise approximately half of the human genome and represent a potentially explosive source of genome instability. Mobilization of these elements can induce insertions, deletions and rearrangements that cause disease, sterility, and developmental defects. The goals of the proposed studies are to define conserved organizational principles and molecular mechanisms that directly impact human reproductive heath.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Research Program Projects (P01)
Project #
5P01HD078253-04
Application #
9449375
Study Section
Special Emphasis Panel (ZHD1)
Project Start
Project End
Budget Start
2018-03-01
Budget End
2019-02-28
Support Year
4
Fiscal Year
2018
Total Cost
Indirect Cost
Name
University of Massachusetts Medical School Worcester
Department
Type
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
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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