Animal model systems are essential to further our understanding of the developmental origins of congenital disease. Embryos of the amphibian Xenopus tropicalis represent an excellent model system for development and differentiation. The genome of this species has recently been sequenced, which has great potential to expedite analyses of the cellular and molecular basis of vertebrate development. While many of the Xenopus genes have been identified, the function of most of the intergenic DNA is still unknown and the annotation of functional elements such as enhancers is lacking. This is an important problem that has been identified by the Xenopus community as a priority for the use of this model system in biomedical research. Within the nucleus, genomic DNA is packaged in chromatin. The biochemical features of chromatin, such as post-translational modifications of histone proteins, determine its accessibility and function. Profiling these epigenetic modifications by chromatin immunoprecipitation (ChIP-sequencing) allows identification of the functional elements in the genome. The long-term objective of the research is to elucidate genome function in the context of embryonic development. The objective of this project is to generate epigenome and enhancer reference maps, which chart functional regions in the genome during early embryogenesis. The project has the following specific aims: (1.) Generate reference chromatin state maps at multiple stages of embryonic development. At the end of this project eight different histone modifications and DNA methylation will have been profiled at five stages of development, using a deep sequencing approach of the DNA enriched for these modifications. This provides an extensive catalogue of different types of regulatory activity in the genome, identifying both euchromatin and heterochromatin at multiple levels. (2.) Identify enhancers with their functional interactions to promoters. Enhancers are DNA elements important for the activation of genes in specific cells at specific stages of development. These important regions will be identified based on specific histone modifications. Enhancer interactions with promoters will be analyzed by ChIA-PET, a method that sequences cross-linked and ligated genomic DNA fragments. Accomplishing the specific aims will provide a well-annotated genome. The resulting Epigenome Reference Maps (aim #1) and Enhancer Resource (aim #2) will be extremely valuable assets for researchers. They will shed more light on normal development and accelerate the analysis of the developmental origins of disease.

Public Health Relevance

This project will identify functional elements of the genome in Xenopus, an important model system for embryogenesis. This much needed annotation will accelerate the analysis of the developmental origins of congenital disease.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Research Project (R01)
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Special Emphasis Panel (ZRG1-GGG-E (50))
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Coulombe, James N
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Stichting Katholieke Universiteit
Zip Code
6525 -EZ
Session, Adam M; Uno, Yoshinobu; Kwon, Taejoon et al. (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538:336-343
Bogdanović, Ozren; Smits, Arne H; de la Calle Mustienes, Elisa et al. (2016) Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet 48:417-26
van Kruijsbergen, Ila; Hontelez, Saartje; Elurbe, Dei M et al. (2016) Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos. Dev Biol :
van Kruijsbergen, Ila; Hontelez, Saartje; Veenstra, Gert Jan C (2015) Recruiting polycomb to chromatin. Int J Biochem Cell Biol 67:177-87
Paranjpe, Sarita S; Veenstra, Gert Jan C (2015) Establishing pluripotency in early development. Biochim Biophys Acta 1849:626-36
Hontelez, Saartje; van Kruijsbergen, Ila; Georgiou, Georgios et al. (2015) Embryonic transcription is controlled by maternally defined chromatin state. Nat Commun 6:10148
van Heeringen, Simon J; Akkers, Robert C; van Kruijsbergen, Ila et al. (2014) Principles of nucleation of H3K27 methylation during embryonic development. Genome Res 24:401-10
Smits, Arne H; Lindeboom, Rik G H; Perino, Matteo et al. (2014) Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs. Nucleic Acids Res 42:9880-91