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| Status |
Public on Dec 12, 2017 |
| Title |
‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming [RRBS] |
| Organism |
Danio rerio |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
The function and retention/reprogramming of epigenetic marks during the germline-to-embryo transition is a key issue in developmental and cellular biology, with relevance to stem cell programming and trans-generational inheritance. In zebrafish, DNAme patterns are programmed in transcriptionally-quiescent early cleavage embryos; paternally-inherited patterns are maintained, whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a ‘placeholder’ nucleosome, containing the histone H2A variant H2A.Z(FV) and H3K4me1, occupies virtually all regions lacking DNAme in both sperm and cleavage embryos – residing at promoters encoding housekeeping and early embryonic transcription factors. Upon genome-wide transcriptional onset, genes with the Placeholder become either active H3K4me3-marked or silent H3K4me3/K27me3-marked (bivalent). Importantly, functional perturbation causing Placeholder loss confers DNAme acquisition, whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation. Thus, during transcriptionally quiescent stages (gamete-zygote-cleavage), an H2A.Z(FV)/H3K4me1-containing Placeholder nucleosome deters DNAme, poising parental genes for either gene-specific activation or facultative repression.
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| Overall design |
DNA methylation was analyzed for Sperm and Sphere stage embryos that were either mutant for the anp32e gene, or were injected with either an SRCAP morpholino or recombinant Anp32e protein.
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| Contributor(s) |
Murphy PJ, Wu S, James CR, Wike CL, Cairns BR |
| Citation(s) |
29456083 |
| |
| Submission date |
Feb 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Murphy |
| Organization name |
University of Rochester
|
| Street address |
601 Elmwood Ave
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
|
| Samples (25)
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| This SubSeries is part of SuperSeries: |
| GSE95033 |
‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming |
|
| Relations |
| BioProject |
PRJNA375791 |
| SRA |
SRP100179 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95032_Anp32e_Mat-Null_merged_RRBS_fraction_DNAme.bw |
26.2 Mb |
(ftp)(http) |
BW |
| GSE95032_Anp32e_Pat-Null_merged_RRBS_fraction_DNAme.bw |
20.4 Mb |
(ftp)(http) |
BW |
| GSE95032_Anp32e_Sperm_merged_RRBS_fraction_DNAme.bw |
12.5 Mb |
(ftp)(http) |
BW |
| GSE95032_Anp32e_Sphere_merged_RRBS_fraction_DNAme.bw |
5.8 Mb |
(ftp)(http) |
BW |
| GSE95032_Haploid_RRBS_Fraction_DNAme.bw |
6.4 Mb |
(ftp)(http) |
BW |
| GSE95032_Rcmb_Anp32e_INJ_merged_RRBS_fraction_DNAme.bw |
4.6 Mb |
(ftp)(http) |
BW |
| GSE95032_SRCAP_MO_1_RRBS_fraction_DNAme.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE95032_SRCAP_MO_2_RRBS_fraction_DNAme.bw |
1.2 Mb |
(ftp)(http) |
BW |
| GSE95032_Sperm_RRBS_Fraction_DNAme.bw |
11.2 Mb |
(ftp)(http) |
BW |
| GSE95032_Sphere_RRBS_Fraction_DNAme.bw |
13.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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