Xenopus genome browser track hub
Epigenome reference maps
A track data hub has been generated providing access to Veenstra lab chromatin state maps, including ChIP-sequencing tracks of eight histone modifications, RNA polymerase II and the enhancer-binding protein p300 during Xenopus tropicalis development from blastula to larval stages.
Intergenic DNA contains functional genomic elements such as enhancers 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.
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).
(Click for larger image)X.tropicalis Epigenome reference maps published: Hontelez et al. (December 2015)
X.tropicalis assembly v9 added to trackhub (February 2016)
X.laevis assembly v9.1 and ChIP tracks added to trackhub (unpublished, March 2016)
Xenopus track hub instructions
The data can be browsed using a track data hub for the UCSC browser. Do the following to use this track hub:
- Visit the UCSC genome browser
- Click the button "track hubs"
- Select the tab "My Hubs"
- Copy-paste the following URL in the text box:
- Click "Add Hub"
- In the "Group" drop-down menu (to the left of the search box, where you normally select "Mammal" or "Vertebrate"), select the "Xenopus UCSC hub" group
- Select the Xenopus genome and assembly of interest
- Browse the genome or modify track settings (right click on the track, or use track controls under main graphic)
- X. tropicalis v7.1, v8.0 and v9.0 with the Epigenome reference maps
- X. laevis v7.1 and v9.1
Genome data publications
Hontelez S., I. van Kruijsbergen, G. Georgiou, S. J. van Heeringen, O. Bogdanovic, R. Lister, G.J.C. Veenstra. 2015. Embryonic transcription is controlled by maternally defined chromatin state. Nature Commun., 6, 10148 (doi: 10.1038/ncomms10148).
Nature Communications PDF NCBI GSE67974
Heeringen, S.J. van, R.C. Akkers, I. van Kruijsbergen, M.A. Arif, L.L.P. Hanssen, N. Sharifi, G.J.C. Veenstra. 2014. Principles of nucleation of H3K27 methylation during embryonic development. Genome Research, 24, 401-410 (doi: 10.1101/gr.159608.113).
Genome Research PDF NCBI GSE41161
Paranjpe SS, U.G. Jacobi, S.J. van Heeringen, G.J.C. Veenstra. 2013. A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. BMC Genomics, 14,762 (doi:10.1186/1471-2164-14-762).
BMC Genomics NCBI GSE43652
Bogdanovic, O., S.W. Long, S. J. van Heeringen, A.B. Brinkman, J.L. Gómez-Skarmeta, H.G. Stunnenberg, P.L. Jones and G.J.C. Veenstra. 2011. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Research, 21, 1313-1327 (doi: 10.1101/gr.114843.110).
Genome Research Online NCBI GSE23913
Van Heeringen, S.J., W. Akhtar, U.G. Jacobi, R.C. Akkers, Y. Suzuki, G.J.C. Veenstra. 2011. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome Research, 21, 410-421.
Genome Research Online NCBI GSE21482
Akkers, R.C., S.J. van Heeringen, U.G. Jacobi, E.M. Janssen-Megens, K.J. Françoijs, H.G. Stunnenberg and G.J.C. Veenstra. 2009. A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Developmental Cell, 17, 425-434.
Dev.Cell Online PubMed Central NCBI GSE14025