RNA interference (RNAi) was originally described as a gene silencing mechanism triggered by the experimental introduction of double stranded (ds)RNA into the nematode C. elegans (Fire et al., 1998). The term RNAi is now used to refer to a diverse set of gene-regulatory mechanisms that share common features, including the involvement of a short 21-30 nucleotide (nt) long RNA and a protein cofactor of the Argonaute (RNase H-related) protein family. As an experimental tool, RNAi is of broad relevance to basic medical research in numerous fields, and RNAi therapeutics are now under development for several clinical applications. Furthermore, RNAi-related mechanisms function in conserved gene-regulatory pathways that are of basic and fundamental importance to human cellular and developmental biology. Remarkably, RNAi-related mechanisms in C. elegans keep inventory of all mRNAs and license gene expression in the germline, passing this information via the egg and sperm from one generation to the next. Distinct Argonaute pathways function in the transgenerational inheritance of small-RNA signals that constitute the CSR-1 self/protective (RNAa pathway) and the WAGO non-self/silencing (RNAe pathway). A third Argonaute pathway, the PRG-1/Piwi pathway scans germline mRNA for foreign sequences.
In Aim 1, we explore how these Argonaute pathways identify their targets and recruit downstream factors.
In Aim 2, we investigate how these Argonaute pathways interact to mediate genome-wide transcriptional surveillance. And finally, in Aim 3, we describe genetic screens that will allow us to identify new genes required for RNAi and the related RNAe and RNAa pathways. The ability to combine classical genetics with technology, including deep-sequencing, CRISPR-mediated genome editing, and proteomics, make C. elegans an ideal system for these studies. The mechanisms and protein families that mediate RNAi are highly conserved in animals and therefore insights from the proposed studies will be directly relevant to human biology and disease. These studies will shed light on an ancient gene-regulatory mechanism whose correlates in humans are likely to play important conserved roles in the protection of the human genome and the maintenance of stem cells.

Public Health Relevance

RNA interference (RNAi) is a highly conserved gene-silencing mechanism implicated in immunity, genome maintenance and developmental gene regulation in both plants and animals. The goal of this project is to investigate RNAi and related mechanisms so that we can better understand how they impact on development and human health. Insights from these studies may lead directly to new RNA-interference technologies for probing gene function in a variety of organisms including humans, and may ultimately lead to new diagnostics and therapeutics.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
5R37GM058800-18
Application #
9063553
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Bender, Michael T
Project Start
1999-01-01
Project End
2020-04-30
Budget Start
2016-05-01
Budget End
2017-04-30
Support Year
18
Fiscal Year
2016
Total Cost
Indirect Cost
Name
University of Massachusetts Medical School Worcester
Department
Other Basic Sciences
Type
Schools of Medicine
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
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
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
Shen, En-Zhi; Chen, Hao; Ozturk, Ahmet R et al. (2018) Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. Cell 172:937-951.e18
Gammon, Don B; Ishidate, Takao; Li, Lichao et al. (2017) The Antiviral RNA Interference Response Provides Resistance to Lethal Arbovirus Infection and Vertical Transmission in Caenorhabditis elegans. Curr Biol 27:795-806
Tang, Wen; Tu, Shikui; Lee, Heng-Chi et al. (2016) The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans. Cell 164:974-84
Elewa, Ahmed; Shirayama, Masaki; Kaymak, Ebru et al. (2015) POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA. Dev Cell 34:108-18
Gammon, Don B; Mello, Craig C (2015) RNA interference-mediated antiviral defense in insects. Curr Opin Insect Sci 8:111-120
Hainer, Sarah J; Gu, Weifeng; Carone, Benjamin R et al. (2015) Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF. Genes Dev 29:362-78
Conte Jr, Darryl; MacNeil, Lesley T; Walhout, Albertha J M et al. (2015) RNA Interference in Caenorhabditis elegans. Curr Protoc Mol Biol 109:26.3.1-30

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