In metazoans, gene expression is regulated in a tissue/cell-type specific manner predominantly via stretches of noncoding sequence referred to as cis regulatory modules (CRMs) that regulate the expression of (typically) the adjacent gene(s). CRMs contain 1 or more DNA binding sites for 1 or more sequence-specific, regulatory transcription factors (TFs) that function to activate or repress the expression of target gene(s);CRMs that activate gene expression are frequently referred to as transcriptional enhancers, while those that repress gene expression are referred to as silencers. The goals of this renewal project are to extend our enhancer-FACS-Seq (eFS) technologies for high-throughput experimental assays to analyze additional functional features of tissue/cell-type-specific CRMs in vivo in whole Drosophila embryos in a genomic context, and to use them to identify cis regulatory codes that control gene expression in a tissue- and cell-type-specific manner. We will focus on the developing embryonic somatic mesoderm in Drosophila as our model system. We anticipate that our approaches and data should be applicable to other systems and organisms, including human.

Public Health Relevance

In metazoans, gene expression is regulated in a tissue- and cell-type specific manner predominantly via stretches of noncoding sequence referred to as cis regulatory modules (CRMs). In this project we will focus on the Drosophila embryonic mesoderm development as a model system. The overarching goals of this renewal project are to extend our technologies to analyze additional functional features of tissue/cell-type-specific CRMs and to elucidate cis regulatory codes in this important developmental tissue. We anticipate that the approaches and data resulting from this project will be generally applicable to other systems and organisms.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
2R01HG005287-04
Application #
8631657
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Pazin, Michael J
Project Start
2009-12-01
Project End
2017-01-31
Budget Start
2014-02-10
Budget End
2015-01-31
Support Year
4
Fiscal Year
2014
Total Cost
$503,861
Indirect Cost
$218,657
Name
Brigham and Women's Hospital
Department
Type
DUNS #
030811269
City
Boston
State
MA
Country
United States
Zip Code
02115
Christodoulou, Danos C; Wakimoto, Hiroko; Onoue, Kenji et al. (2014) 5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy. J Clin Invest 124:1364-70
Soruco, Marcela M L; Chery, Jessica; Bishop, Eric P et al. (2013) The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev 27:1551-6
Gisselbrecht, Stephen S; Barrera, Luis A; Porsch, Martin et al. (2013) Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. Nat Methods 10:774-80
Busser, Brian W; Gisselbrecht, Stephen S; Shokri, Leila et al. (2013) Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs. PLoS One 8:e69385
Chartier, Matthieu; Gaudreault, Francis; Najmanovich, Rafael (2012) Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. Bioinformatics 28:1438-45
Zhu, Xianmin; Ahmad, Shaad M; Aboukhalil, Anton et al. (2012) Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors. Development 139:1457-66
Aboukhalil, Anton; Bulyk, Martha L (2012) LOESS correction for length variation in gene set-based genomic sequence analysis. Bioinformatics 28:1446-54
Busser, Brian W; Shokri, Leila; Jaeger, Savina A et al. (2012) Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development 139:1164-74