Enhancers are remotely acting non-coding DNA elements that regulate the tissue-specific and developmental expression of genes. Enhancers are thought to be a major driver of vertebrate evolution, and there is increasing evidence that they play important roles in human disorders. Two complementary, powerful approaches to identify tissue-specific enhancers at a genomic scale are the use of extreme evolutionary conservation of non-coding sequences and, more recently, the mapping of enhancer-associated epigenomic marks by chromatin immunoprecipitation coupled to sequencing (ChIP-seq). Surprisingly, ChIP-seq studies of different embryonic mouse tissues revealed that enhancers active in some tissues, such as the embryonic brain, are under severe evolutionary sequence constraint whereas enhancers active in other tissues, such as the embryonic heart, are only mildly constrained. These results raise the possibility that patterns of evolutionary constraint generally differ between enhancers active in different tissues. Alternatively, it is possible that he degree of enhancer constraint in a specific tissue changes during development, and those differences in timing of these changes account for the observed differences in enhancer conservation between tissues. I propose to examine these two possibilities through a combination of experimental and computational approaches aimed at the identification and sequence analysis of genome-wide sets of enhancers active in the mouse from mid-gestation through adulthood in three tissues with different developmental trajectories.
The specific aims i nclude: 1) Identify active enhancers through ChIP-seq performed on brain, liver and heart tissue sampled across eight time points of pre- and postnatal mouse development;2) Classify the degree of evolutionary constraint associated with active enhancers in the three tissues at all time points sampled;3) Validate changes in activity through development in vivo using mouse transgenic enhancer assays for a selected set of enhancers. This study is expected to elucidate the evolutionary constraint signatures of enhancers active in different tissues at the same developmental time point, as well as possible constraint differences between enhancers active in the same tissue at different developmental stages. Importantly, the results will help to explain why gene expression in evolutionarily old organ systems like the heart appears to be under the control of poorly conserved enhancers. This is expected to have direct implications for our understanding of the role of enhancers in vertebrate evolution. In addition to enabling fundamental evolutionary insights, the data sets generated through this proposal will also provide a valuable resource for biomedical studies, since they are expected to reveal large numbers of currently unrecognized enhancers with transient developmental activities in three tissues of major biomedical interest.

Public Health Relevance

It has become clear that non-coding DNA, once considered junk, contains functional elements that control the precise regulation of gene expression central to development and disease. The goal of this proposal is to characterize active enhancers in forebrain, heart, and liver tissue across development in a mammalian model system, producing insights into the evolution and function of a class of DNA elements that are highly relevant to human disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Postdoctoral Individual National Research Service Award (F32)
Project #
1F32GM105202-01A1
Application #
8595085
Study Section
Special Emphasis Panel (ZRG1-F08-A (20))
Program Officer
Reddy, Michael K
Project Start
2013-08-01
Project End
2015-07-31
Budget Start
2013-08-01
Budget End
2014-07-31
Support Year
1
Fiscal Year
2013
Total Cost
$52,190
Indirect Cost
Name
Lawrence Berkeley National Laboratory
Department
Type
DUNS #
078576738
City
Berkeley
State
CA
Country
United States
Zip Code
94720
Wu, Han; Nord, Alex S; Akiyama, Jennifer A et al. (2014) Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet 10:e1004610
Attanasio, Catia; Nord, Alex S; Zhu, Yiwen et al. (2014) Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res 24:920-9
Pattabiraman, Kartik; Golonzhka, Olga; Lindtner, Susan et al. (2014) Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex. Neuron 82:989-1003
Dickel, Diane E; Zhu, Yiwen; Nord, Alex S et al. (2014) Function-based identification of mammalian enhancers using site-specific integration. Nat Methods 11:566-71
Attanasio, Catia; Nord, Alex S; Zhu, Yiwen et al. (2013) Fine tuning of craniofacial morphology by distant-acting enhancers. Science 342:1241006
Sanchez-Castro, Marta; Gordon, Christopher T; Petit, Florence et al. (2013) Congenital heart defects in patients with deletions upstream of SOX9. Hum Mutat 34:1628-31