The broad objective of this proposal is to identify and characterize mammalian gene regulatory networks controlled by endogenously expressed double-stranded RNA (dsRNA) and to determine their function. DsRNA triggers a number of different gene silencing processes commonly referred to as RNA silencing. The identification of dsRNA triggers of gene silencing and the elucidation of their functions is a complex task because dsRNA is produced from many different sources (repetitive gene loci, miRNA genes, sense/antisense overlapping mRNA transcripts) in a tissue-specific and developmentally regulated manner. In retrospect, it is surprising that such a fundamental mode of genetic regulation has been overlooked. Comprehensively collecting the sequence information of RNA silencing regulators and targets will provide new starting points for human genetic studies aimed at characterizing the factors contributing to multigenic or idiopathic diseases. The analysis will be a team effort that brings together four laboratories interested in understanding the mechanisms and function of RNA silencing as a fundamental gene regulatory mechanism. These laboratories are specialized in biochemistry, computational biology, immunology and metabolic disease.
The specific aims of the proposed project are: 1. Comprehensive recording of small RNA profiles of mammalian cell lines and tissues. 2. Development of computational and experimental methods for the identification and validation of targets of RNA silencing and RNA silencing regulatory networks. 3. Cell culture and in vivo functional characterization of RNA silencing regulatory networks using classic and conditional knockout technology in mice, in particular those related to the development of the immune system and the pancreas, as well as computational modeling of these networks. 4. Linkage analysis of genetic variation in RNA silencing regulatory networks in type 2 diabetes, supported by a relational database of small RNAs and their respective mRNA target sites available to the medical and general scientific community.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
5P01GM073047-03
Application #
7174767
Study Section
Special Emphasis Panel (ZRG1-F08 (40))
Program Officer
Rhoades, Marcus M
Project Start
2005-02-01
Project End
2010-01-31
Budget Start
2007-02-01
Budget End
2008-01-31
Support Year
3
Fiscal Year
2007
Total Cost
$1,217,772
Indirect Cost
Name
Rockefeller University
Department
Genetics
Type
Other Domestic Higher Education
DUNS #
071037113
City
New York
State
NY
Country
United States
Zip Code
10065
Nakanishi, Kotaro; Ascano, Manuel; Gogakos, Tasos et al. (2013) Eukaryote-specific insertion elements control human ARGONAUTE slicer activity. Cell Rep 3:1893-900
Skalsky, Rebecca L; Corcoran, David L; Gottwein, Eva et al. (2012) The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog 8:e1002484
Rajasethupathy, Priyamvada; Antonov, Igor; Sheridan, Robert et al. (2012) A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 149:693-707
Farazi, Thalia A; Horlings, Hugo M; Ten Hoeve, Jelle J et al. (2011) MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res 71:4443-53
Hafner, Markus; Renwick, Neil; Brown, Miguel et al. (2011) RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 17:1697-712
Gottwein, Eva; Corcoran, David L; Mukherjee, Neelanjan et al. (2011) Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe 10:515-26
Lipchina, Inna; Elkabetz, Yechiel; Hafner, Markus et al. (2011) Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. Genes Dev 25:2173-86
Hafner, Markus; Landthaler, Markus; Burger, Lukas et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129-41
Hafner, Markus; Landthaler, Markus; Burger, Lukas et al. (2010) PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp :
Betel, Doron; Koppal, Anjali; Agius, Phaedra et al. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 11:R90

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