The ChIP-sequencing tracks were produced as part of a project funded by NICHD to generate epigenome reference maps of Xenopus tropicalis embryos. Intergenic DNA contains functional genomic elements which are largely unannotated. The biochemical features of chromatin, such as post-translational modifications of histone proteins, determine its accessibility and function. The combination of different histone modifications can also be used to partition the genome in distinct chromatin states, such as promoters, enhancers, transcribed regions, and repressed heterochromatin.
ChIP-sequencing was performed as described (Akkers et al. 2009, Akkers et al. 2012, Van Heeringen et al. 2014). The genome browser tracks have been generated for the histone modifications H3K4me1, H3K4me3, H3K9ac, H3K9me2, H3K9me3, H3K27me3, H3K36me3 and H4K20me3, in addition to RNA polymerase II and p300. At five stages of development (NF stages 9, 10.5, 12.5, 16 and 30) they have been mapped with or without repetitive reads, to allow assessing histone modfications at repetitive heterochromatic regions as well as unique regions within the genome. In addition they have been mapped to the two newest X.tropicalis genome assemblies (v7.1 and v8.0).
The data were generated in the Gert Jan Veenstra lab at Radboud University (The Netherlands). The unpublished data can be freely used on a per gene locus basis. Please contact Gert Jan Veenstra (email g.veenstra [@] science.ru.nl) for all other use.
Akkers RC, Jacobi UG, Veenstra GJ. 2012. Chromatin immunoprecipitation analysis of Xenopus embryos. Methods Mol Biol. 2012;917:279-92. doi: 10.1007/978-1-61779-992-1_17. PMID: 22956095
Akkers RC, van Heeringen SJ, Jacobi UG, Janssen-Megens EM, Françoijs KJ, Stunnenberg HG, Veenstra GJ. 2009. A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Dev Cell. 2009 Sep;17(3):425-34. doi: 10.1016/j.devcel.2009.08.005. PMID: 19758566
van Heeringen SJ, Akkers RC, van Kruijsbergen I, Arif MA, Hanssen LL, Sharifi N, Veenstra GJ. 2014. Principles of nucleation of H3K27 methylation during embryonic development. Genome Res. 2014 Mar;24(3):401-10. doi: 10.1101/gr.159608.113. Epub 2013 Dec 11. PMID: 24336765