Epigenetics represents an exciting new frontier of biomedical research. A central yet essentially unexplored question in epigenetics is how epigenetic regulators are directed to specific loci in the genome to exert their function. It is known that a few transcriptional factors can recruit certain epigenetic factors to the promoters of target genes. However, this mechanism so far can only account for a handful of genes, and a tiny fraction of the genome. The latest Drosophila work in my lab suggest that PIWI-interacting RNAs (piRNAs) play a major and direct role in guiding epigenetic factors to many sites in the genome. Particularly, piRNA form complexes with PIWI proteins and directly bind to piRNA-complementary sites in the genome to regulate their epigenetic state. Furthermore, we have shown that PIWI directly recruits a key epigenetic factor called Heterochromatin Protein 1a to these sites. Based on these results, we propose a "Piwi-piRNA guidance hypothesis", in which the Piwi-piRNA complex serves as a sequence- recognition machinery that recruits epigenetic effectors to specific genomic sites to execute epigenetic regulation. Here we propose to use combined genetic and genomic approaches to systematically test this hypothesis and to determine the contribution of the PIWI-piRNA- mediated mechanism to the genome at 10-basepair resolution. Specifically, we propose to: (1) Create the first functional epigenome map to determine the specific epigenetic effect of PIWI towards different regions of the genome;(2) develop a genome-wide epigenetic assay to examine the sufficiency and direct role of PIWI in regulating the transcriptional state of chromatin;and (3) take a four-pronged approach to directly test the role of piRNAs in guiding epigenetic factors to their sites. The proposed study should reveal a fascinating dimension of epigenetic regulation and generate a potentially transformative impact to the broad fields of epigenetics, genetics, molecular, developmental, and stem cell biology.

Public Health Relevance

This proposal aims to systematically test and further develop a new epigenetic programming theory that can potentially transform our understanding of gene regulation. Because epigenetic programming is essential for normal development with broad implications in diverse types of diseases, the proposed research, if achieved, should provide a new and fundamental guiding principle to medicine, from cancer prevention and treatment to the cure of degenerative diseases.

National Institute of Health (NIH)
National Cancer Institute (NCI)
NIH Director’s Pioneer Award (NDPA) (DP1)
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Special Emphasis Panel (ZGM1-NDPA-B (01))
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Mietz, Judy
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Yale University
Anatomy/Cell Biology
Schools of Medicine
New Haven
United States
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Ross, Robert J; Weiner, Molly M; Lin, Haifan (2014) PIWI proteins and PIWI-interacting RNAs in the soma. Nature 505:353-9
Watanabe, Toshiaki; Lin, Haifan (2014) Posttranscriptional regulation of gene expression by Piwi proteins and piRNAs. Mol Cell 56:18-27
Yin, Hang; Lin, Haifan (2014) Chromatin immunoprecipitation assay of Piwi in Drosophila. Methods Mol Biol 1093:1-11
Mani, Sneha Ramesh; Megosh, Heather; Lin, Haifan (2014) PIWI proteins are essential for early Drosophila embryogenesis. Dev Biol 385:340-9
Peng, Jamy C; Lin, Haifan (2013) Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism. Curr Opin Cell Biol 25:190-4
Darricarrere, Nicole; Liu, Na; Watanabe, Toshiaki et al. (2013) Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity. Proc Natl Acad Sci U S A 110:1297-302
Mani, Sneha Ramesh; Juliano, Celina E (2013) Untangling the web: the diverse functions of the PIWI/piRNA pathway. Mol Reprod Dev 80:632-64
Huang, Xiao A; Yin, Hang; Sweeney, Sarah et al. (2013) A major epigenetic programming mechanism guided by piRNAs. Dev Cell 24:502-16