Xenopus genome browser track hub

  tracks!

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)

NEWX.tropicalis Epigenome reference maps published: Hontelez et al. (December 2015)
NEWX.tropicalis assembly v9 added to trackhub (February 2016)
NEWX.laevis assembly v9.1 and ChIP tracks added to trackhub (unpublished, March 2016)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:

  1. Visit the UCSC genome browser
  2. Click the button "track hubs"
  3. Select the tab "My Hubs"
  4. Copy-paste the following URL in the text box:
    http://trackhub.science.ru.nl/hubs/xenopus/hub.txt
  5. Click "Add Hub"
  6. 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
  7. Select the Xenopus genome and assembly of interest
  8. Browse the genome or modify track settings (right click on the track, or use track controls under main graphic)
The track hub contains the following genome assemblies: The generation of Epigenome reference maps is supported by the US National Institutes of Health (NICHD, grant R01HD069344). Please note that the track hub includes published data but also provides pre-publication access to data. The unpublished data can be freely used on a per gene locus basis. Please contact Gert Jan Veenstra for other use. Published data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession numbers (listed with the publications below).


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).
www Nature Communications          download PDF          data NCBI GSE67974
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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).
www Genome Research          download PDF          data NCBI GSE41161
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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).
www BMC Genomics          data NCBI GSE43652
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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).
www Genome Research Online          Email          data NCBI GSE23913         
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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.
www Genome Research Online          Email          data NCBI GSE21482         
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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.
www Dev.Cell Online          Email          PMC PubMed Central          data NCBI GSE14025         

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Radboud University Faculty of Science Radboud Institute for Molecular Life Sciences Dept. Molecular Developmental Biology