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| Status |
Public on Nov 28, 2013 |
| Title |
Principles of nucleation of H3K27 methylation during embryonic development |
| Organism |
Xenopus tropicalis |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 K27 trimethylation (H3K27me3). However, the developmental origins of this regulation are unknown. Here, we report on H3K27me3 deposition dynamics in Xenopus embryos, on sequence elements that initiate deposition during pluripotency, and the sequence characteristics that segregate Polycomb-regulated domains from the rest of the genome. Strikingly, although PRC2 binds widely to active enhancers, H3K27me3 is only deposited at a small subset of these sites. Using a Support Vector Machine algorithm these sequences can be predicted accurately on basis of DNA sequence alone, with a sequence signature conserved between humans, frog and fish. The results suggest a genetic-default model in which genomic sequence constrains Polycomb regulation.
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| Overall design |
ChIP-seq profiles of three histone modifications (H3K4me3, H3K27me3 and H3K4me1) and RNA Polymerase II, EZH2 and Jarid2 of Xenopus tropicalis embryos during development
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| Contributor(s) |
van Heeringen SJ, Akkers RC, van Kruijsbergen I, Hanssen L, Sharifi N, Veenstra GC, Arif M |
| Citation(s) |
24336765 |
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| Submission date |
Sep 26, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
g.veenstra@science.ru.nl
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| Phone |
+31 24 3610541
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| Organization name |
Radboud University
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| Department |
Molecular Developmental Biology
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| Street address |
Geert Grooteplein 28
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| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
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| Platforms (2) |
| GPL13741 |
Illumina Genome Analyzer IIx (Xenopus (Silurana) tropicalis) |
| GPL15472 |
Illumina HiSeq 2000 (Xenopus (Silurana) tropicalis) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA175996 |
| SRA |
SRP015902 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41161_RAW.tar |
1.9 Gb |
(http)(custom) |
TAR (of BED, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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