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| Status |
Public on Jul 06, 2012 |
| Title |
Developmental features of DNA methylation during activation of the embryonic zebrafish genome |
| Organism |
Danio rerio |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Zygotic genome activation (ZGA) occurs at the mid-blastula transition (MBT) in zebrafish and is a period of chromatin remodeling. Genome-scale gametic demethylation and remethylation occurs after fertilization, during blastula stages, but how ZGA relates to promoter DNA methylation states is unknown. Using methylated DNA immunoprecipitation coupled to high-density microarray hybridization (MeDIP-ChIP), we characterize genome-wide promoter DNA methylation dynamics before, during and after ZGA onset, in relation changes in post-translational histone modification and gene expression (Series GSE22830). A Kolmogorov-Smirnov (KS) test was applied with P <= 0.01 to identify methylation peaks.
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| Overall design |
MeDIP-chip experiments were performed on24 hpf zebrafish embryos and sperm. Samples were lysed and proteins digested by proteinase k treatment. DNA was extracted with phenol-chloroform-isoamylalcohol and ethanol precipitation. The DNA was RNAse treated and sonicated to fragment lengths between 300-1000 bp. From each stage, duplicate immuneoprecipitations were performed using anti-5-methylcytosine antibody (10 ng/µl; Mab-006-100; Diagenode) coupled to Dynabeads M-280 sheep anti-mouse IgG (Invitrogen). MeDIP and input DNA (150 ng each) were amplified (WGA-2; Sigma-Aldrich), cleaned up, eluted and processed for array hybridization. MeDIP and input DNA were labeled and co-hybridized onto the Nimbegen promoter arrays. The array covers 15 kb of upstream regulatory sequence and 5 kb downstream of the TSS of all zebrafish genes. A Kolmogorov-Smirnov (KS) test was applied with P <= 0.01 to identify methylation peaks.
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| Contributor(s) |
Collas P, Reiner AH |
| Citation missing |
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| Submission date |
Oct 26, 2011 |
| Last update date |
Jul 07, 2012 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
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| Department |
Institute of Basic Medical Sciences
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| Street address |
PO Box 1112 Blindern
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| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
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| Platforms (1) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA149411 |
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