used to define pathways in mammalian organ development. Because the central focus of the SysCODE Consortium is to define such pathways in the developing tooth germ, pancreatic islet and heart valve, Projects 2, 3 and 4 of this U54 Consortium will use RNA profiling to define RNA levels during development. We have recently developed a novel RNA profiling procedure, PMAGE, that circumvents potential issues encountered with conventional microarray platforms in the analysis of low abundance transcripts. The PMAGE method combines the frequency distribution technique pioneered by SAGE (serial analysis of gene expression) with the high throughput Polony DNA sequencing technique to produce histograms, which accurately profile the RNAs in tissues or cells. That is, a single 14 base pair tag is produced from a single RNA molecule, the tags are stored in PMAGE libraries, and about 2 million tags are sequenced per library. The RNA profiles obtained by this method contain about 30-fold more tags than the majority of SAGE libraries, and hence are able to measure the level of RNAs expressed at less than 0.3 RNA copies per cell. This enhanced sensitivity thus encompasses potential low abundance RNAs, such as those encoding transcription factors and other regulatory molecules that may be important to a molecular understanding of organogenesis. The ability to comprehensively define levels of transcription factors should therefore provide novel insights into organ development. We propose to create, under the aegis of this P30 Core grant, a PMAGE Technology Development Core facility that will enable Consortium investigators to determine expression profiles from total RNA. We expect to produce about 50 PMAGE RNA profiles in the first year and 250 RNA profiles during the grant period. These RNA profiles will provide unique insights into the mechanisms by which the tooth germ, pancreatic islet and heart valve form. In particular we will define the complete catalogue of transcription factors that are required for the development of these tissues. PERFORMANCE SITE(S) (organization, city, state) Dept of Genetics, Harvard Medical School, Boston, MA 02115 PHS 398 (Rev. 09/04) Page 2 Form Page 2

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Linked Center Core Grant (PL1)
Project #
5PL1HL092552-05
Application #
8115992
Study Section
Special Emphasis Panel (ZRR1-SRC (99))
Program Officer
Applebaum-Bowden, Deborah
Project Start
2007-09-30
Project End
2013-06-30
Budget Start
2011-07-01
Budget End
2013-06-30
Support Year
5
Fiscal Year
2011
Total Cost
$254,250
Indirect Cost
Name
Harvard University
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
047006379
City
Boston
State
MA
Country
United States
Zip Code
02115
Eminaga, Seda; Christodoulou, Danos C; Vigneault, Francois et al. (2013) Quantification of microRNA expression with next-generation sequencing. Curr Protoc Mol Biol Chapter 4:Unit 4.17
Alcalai, Ronny; Wakimoto, Hiroko; Arad, Michael et al. (2011) Prevention of ventricular arrhythmia and calcium dysregulation in a catecholaminergic polymorphic ventricular tachycardia mouse model carrying calsequestrin-2 mutation. J Cardiovasc Electrophysiol 22:316-24
Christodoulou, Danos C; Gorham, Joshua M; Herman, Daniel S et al. (2011) Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Curr Protoc Mol Biol Chapter 4:Unit4.12
Christodoulou, Danos C; Gorham, Joshua M; Kawana, Masataka et al. (2011) Quantification of gene transcripts with deep sequencing analysis of gene expression (DSAGE) using 1 to 2 µg total RNA. Curr Protoc Mol Biol Chapter 25:Unit25B.9
Morita, Hiroyuki; Nagai, Ryozo; Seidman, J G et al. (2010) Sarcomere gene mutations in hypertrophy and heart failure. J Cardiovasc Transl Res 3:297-303
Wang, Libin; Seidman, Jonathan G; Seidman, Christine E (2010) Narrative review: harnessing molecular genetics for the diagnosis and management of hypertrophic cardiomyopathy. Ann Intern Med 152:513-20, W181
Artunduaga, Maria A; Quintanilla-Dieck, Maria D L; Greenway, Steven et al. (2009) A classic twin study of external ear malformations, including microtia. N Engl J Med 361:1216-8
Herman, Daniel S; Hovingh, G Kees; Iartchouk, Oleg et al. (2009) Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection. Nat Methods 6:507-10