Abstract: A major outstanding challenge in biology is to understand how the exact same genomic sequence present in every cell takes on alternate epigenetic landscapes to confer a myriad of cellular functions, all while using ubiquitous cellular machinery. In addition to histone modifications and DNA methylation, RNA has been long thought to be involved in the establishment and inheritance of these epigenetic states, but is far less understood. Indeed, recently three examples of large non-coding RNAs (HOTAIR, XIST and AIR) have been discovered that share a common theme: they physically associate with chromatin remodeling complexes and are required to guide chromatin formation at specific genomic loci. Although these examples suggest a general mechanism it is still unclear to what extent RNA plays a role in chromatin formation and the mechanisms by which this guidance occurs. Here we propose to comprehensively and systematically address the roles of large non-coding RNAs in the formation of chromatin structure. We will accomplish this by : (1) Identifying and characterize large noncoding RNAs that physically associate with chromatin remodeling complexes genome-wide across multiple yet related cell contexts;(2) Define the sites of regulations and the guidance mechanism to these genomic loci (3) Identify how these molecules and their mechanisms are misregulated in human disease. Together, our multifaceted experimental and computational approaches aim to 'crack the code'of epigenetic establishment and maintenance. This will transform our understanding of genome regulation and establish a new paradigm for RNA in the guidance of chromatin formation. Public Health Relevance:
Our research aims to understand a universal problem in human health: How does the same genome present in every cell take on alternate identities that orchestrate distinctive cell states and how are these states misregulated in diseases such as cancer. We recently discovered a novel class of large intergenic non-coding RNAs (lincRNAs) that have the ability to regulate cellular identity and are misregulated in human cancers. Thus, we seek to establish the fundamental principles and mechanisms by which lincRNAs regulate cellular identity and their role in human cancers. The ultimate goal of these innovative experimental and computational approaches is to develop novel RNA based cancer therapeutics.

Agency
National Institute of Health (NIH)
Institute
Office of The Director, National Institutes of Health (OD)
Type
NIH Director’s New Innovator Awards (DP2)
Project #
1DP2OD006670-01
Application #
7852410
Study Section
Special Emphasis Panel (ZGM1-NDIA-O (02))
Program Officer
Basavappa, Ravi
Project Start
2009-09-30
Project End
2010-10-31
Budget Start
2009-09-30
Budget End
2010-10-31
Support Year
1
Fiscal Year
2009
Total Cost
$621,576
Indirect Cost
Name
Beth Israel Deaconess Medical Center
Department
Type
DUNS #
071723621
City
Boston
State
MA
Country
United States
Zip Code
02215
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Hacisuleyman, Ezgi; Goff, Loyal A; Trapnell, Cole et al. (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21:198-206
Trapnell, Cole; Cacchiarelli, Davide; Grimsby, Jonna et al. (2014) The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 32:381-386
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Sun, Lei; Goff, Loyal A; Trapnell, Cole et al. (2013) Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci U S A 110:3387-92
Trapnell, Cole; Hendrickson, David G; Sauvageau, Martin et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31:46-53
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Kelley, David; Rinn, John (2012) Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol 13:R107

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