Studies of Xenopus embryos have contributed much to our understanding of early vertebrate embryogenesis. The Xenopus tropicalis genome has been sequenced and the next challenge will be to characterize the functionally relevant sequences in this genome. The long-term goal of the application's research is to increase our understanding of the transcriptional regulation of the genome during early Xenopus embryogenesis. The objective of the research proposed here is to use genome-tiling microarrays to identify all expressed and gene-regulatory sequences in the Xenopus genome during the early stages of embryonic development, and to uncover the dynamics of transcription regulatory mechanisms during these stages. Studies of mammalian genomes and our own preliminary data indicate that genome tile path microarrays can be used to identify novel genes and their regulatory sequences in a comprehensive and unbiased way.
The aims of the project are (1) to determine the complete Xenopus transcriptome in early embryogenesis by hybridizing the entire non-repetitive X. tropicalis genome on NimbleGen genome-tiling microarrays with cDNA obtained from different developmental stages; (2) to determine the relevant promoters and other regulatory sequences in the Xenopus genome during early embryogenesis by hybridizing the entire non-repetitive X. tropicalis genome on NimbleGen genome-tiling microarrays with DNA isolated by chromatin immunoprecipitation (ChIP) using antibodies against epigenetic marks and transcription factors; (3) to determine the temporal regulation of the genome at the onset of embryonic transcription by integrating expression and ChIP temporal profiles of embryonic gene activation. This will give insight into the developmental regulation of genome organization and will lay a solid foundation to assess the complete early embryonic transcriptional network. The proposed project will develop Xenopus genome-tiling microarray tools and generate comprehensive catalogues of transcribed and regulatory sequences; both will be extremely valuable resources for the research community. Therefore, it is expected that the proposed work will promote the use and exploitation of Xenopus in biomedical research, advance the characterization of genes and pathways in vertebrate development, and provide a long-lasting impetus to public health research. ? ? ?
| 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 |
| Paranjpe, Sarita S; Jacobi, Ulrike G; van Heeringen, Simon J et al. (2013) A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. BMC Genomics 14:762 |
| Bogdanovic, Ozren; van Heeringen, Simon J; Veenstra, Gert Jan C (2012) The epigenome in early vertebrate development. Genesis 50:192-206 |
| van Heeringen, Simon J; Akhtar, Waseem; Jacobi, Ulrike G et al. (2011) Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome Res 21:410-21 |
| Bogdanovic, Ozren; Long, Steven W; van Heeringen, Simon J et al. (2011) Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Res 21:1313-27 |
| van Heeringen, Simon J; Veenstra, Gert Jan C (2011) GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments. Bioinformatics 27:270-1 |
| Bartlett, Heather; Veenstra, Gert Jan C; Weeks, Daniel L (2010) Examining the cardiac NK-2 genes in early heart development. Pediatr Cardiol 31:335-41 |
| Akkers, Robert C; van Heeringen, Simon J; Manak, J Robert et al. (2010) ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation. PLoS One 5:e8820 |
| Akkers, Robert C; van Heeringen, Simon J; Jacobi, Ulrike G et al. (2009) A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Dev Cell 17:425-34 |
| Bogdanovi?, Ozren; Veenstra, Gert Jan C (2009) DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 118:549-65 |
