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| Status |
Public on Jan 13, 2011 |
| Title |
Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm |
| Organism |
Danio rerio |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
Methylation profiling by genome tiling array
Expression profiling by array
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| Summary |
In mature human sperm, genes of importance for embryo development (i.e. transcription factors) lack DNA methylation and bear nucleosomes with distinctive histone modifications, suggesting the specialized packaging of these developmental genes in the germline. Here, we explored the tractable zebrafish model and found conceptual conservation as well as several new features. Biochemical and mass spectrometric approaches reveal the zebrafish sperm genome packaged in nucleosomes and histone variants (and not protamine), and we find linker histones high and H4K16ac absent - key factors which may contribute to genome condensation. We examined several activating (H3K4me2/3, H3K14ac, H2AFV) and repressing (H3K27me3, H3K36me3, H3K9me3, hypoacetylation) modifications/compositions genome-wide, and find developmental genes packaged in large blocks of chromatin with coincident activating and repressing marks and DNA hypomethylation, revealing complex ‘multivalent’ chromatin. Notably, genes that acquire DNA methylation in the soma (muscle) are enriched in transcription factors for alternative cell fates. Remarkably, we find H3K36me3 located in ‘silent’ developmental gene promoters, and not present at the 3’ ends of coding regions of genes heavily transcribed during sperm maturation, suggesting different rules for H3K36me3 in the germline and soma. We also reveal the chromatin patterns of transposons, rDNA, and tRNAs. Finally, high levels of H3K4me3 and H3K14ac in sperm are correlated with genes activated in embryos prior to the mid-blastula transition (MBT), whereas multivalent genes are correlated with activation at or after MBT. Taken together, gene sets with particular functions in the embryo are packaged by distinctive types of complex and often atypical chromatin in sperm.
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| Overall design |
[DNA profiling]: H3K4me3, H3K4me2, H3K14ac, H3K36me3, H3K27me3, H3K9me3, and H2AFV ChIP-chip in zebrafish sperm; DNA methylation in zebrafish sperm and muscle by MeDIP-chip. (two replicates and dye-swaps for all experiments). Antibodies: H3K4me3 (Abcam ab8580 and Active Motif 39159), H3K4me2 (Abcam ab7766), H3K14Ac (Upstate 07-353), H2AZ (Abcam ab4174), H3K27me3 (Upstate 07-449), H3K9me3 (Active Motif 39161), H3K36me3 (Abcam ab9050), 5-methylcytidine (Eurogentec BI-MECY-1000). Supplementary files: Processed data files reporting calculated enrichment log2 ratio (mean ChIP/mean Input in the log2 ratio). Note: For analysis, "mean Input" from H3K4me3-rep1 ch1, H3K4me2-rep1 ch2, and H3K36me3-rep2 ch1 for all ChIP eluates.
[mRNA profiling]: Transcripts in zebrafish mature sperm using zebrafish expression microarray from Agilent. (two replicates)
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| Contributor(s) |
Wu S, Zhang H, Cairns BR |
| Citation(s) |
21383318 |
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| Submission date |
Jan 13, 2011 |
| Last update date |
Apr 06, 2012 |
| Contact name |
Shan-Fu Wu |
| E-mail(s) |
shan-fu.wu@hci.utah.edu
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| Phone |
(801)585-1823
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| Organization name |
University of Utah
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| Department |
Oncological Sciences
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| Lab |
Cairns lab
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| Street address |
2000 Circle of Hope
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platforms (3) |
| GPL6600 |
Zebrafish 12kb promoter 244K array_slide 1 of 2 |
| GPL6601 |
Zebrafish 12kb promoter 244K array_slide 2 of 2 |
| GPL7302 |
Agilent-015064 D. rerio (Zebrafish) Oligo Microarray 4x44K G2519F (Probe Name version) |
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| Samples (38)
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| GSM654994 |
sperm H3K4me3 ChIP replicate 1 (slide 1 of 2) |
| GSM654995 |
sperm H3K4me3 ChIP replicate 2 (slide 1 of 2) |
| GSM654996 |
sperm H3K4me2 ChIP replicate 1 (slide 1 of 2) |
| GSM654997 |
sperm H3K4me2 ChIP replicate 2 (slide 1 of 2) |
| GSM654998 |
sperm H3K14ac ChIP replicate 1 (slide 1 of 2) |
| GSM654999 |
sperm H3K14ac ChIP replicate 2 (slide 1 of 2) |
| GSM655000 |
sperm H3K27me3 ChIP replicate 1 (slide 1 of 2) |
| GSM655001 |
sperm H3K27me3 ChIP replicate 2 (slide 1 of 2) |
| GSM655002 |
sperm H2AFV ChIP replicate 1 (slide 1 of 2) |
| GSM655003 |
sperm H2AFV ChIP replicate 2 (slide 1 of 2) |
| GSM655004 |
sperm H3K36me3 ChIP replicate 1 (slide 1 of 2) |
| GSM655005 |
sperm H3K36me3 ChIP replicate 2 (slide 1 of 2) |
| GSM655006 |
sperm H3K9me3 ChIP replicate 1 (slide 1 of 2) |
| GSM655007 |
sperm H3K9me3 ChIP replicate 2 (slide 1 of 2) |
| GSM655008 |
sperm MeDIP replicate 1 (slide 1 of 2) |
| GSM655009 |
sperm MeDIP replicate 2 (slide 1 of 2) |
| GSM655010 |
muscle MeDIP replicate 1 (slide 1 of 2) |
| GSM655011 |
muscle MeDIP replicate 2 (slide 1 of 2) |
| GSM655012 |
sperm H3K4me3 ChIP replicate 1 (slide 2 of 2) |
| GSM655013 |
sperm H3K4me3 ChIP replicate 2 (slide 2 of 2) |
| GSM655014 |
sperm H3K4me2 ChIP replicate 1 (slide 2 of 2) |
| GSM655015 |
sperm H3K4me2 ChIP replicate 2 (slide 2 of 2) |
| GSM655016 |
sperm H3K14ac ChIP replicate 1 (slide 2 of 2) |
| GSM655017 |
sperm H3K14ac ChIP replicate 2 (slide 2 of 2) |
| GSM655018 |
sperm H3K27me3 ChIP replicate 1 (slide 2 of 2) |
| GSM655019 |
sperm H3K27me3 ChIP replicate 2 (slide 2 of 2) |
| GSM655020 |
sperm H2AFV ChIP replicate 1 (slide 2 of 2) |
| GSM655021 |
sperm H2AFV ChIP replicate 2 (slide 2 of 2) |
| GSM655022 |
sperm H3K36me3 ChIP replicate 1 (slide 2 of 2) |
| GSM655023 |
sperm H3K36me3 ChIP replicate 2 (slide 2 of 2) |
| GSM655024 |
sperm H3K9me3 ChIP replicate 1 (slide 2 of 2) |
| GSM655025 |
sperm H3K9me3 ChIP replicate 2 (slide 2 of 2) |
| GSM655026 |
sperm MeDIP replicate 1 (slide 2 of 2) |
| GSM655027 |
sperm MeDIP replicate 2 (slide 2 of 2) |
| GSM655028 |
muscle MeDIP replicate 1 (slide 2 of 2) |
| GSM655029 |
muscle MeDIP replicate 2 (slide 2 of 2) |
| GSM655039 |
sperm expression replicate 1 |
| GSM655040 |
sperm expression replicate 2 |
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| Relations |
| BioProject |
PRJNA136217 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE26609_H2AFV_sp_ChIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE26609_H3K14ac_sp_ChIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE26609_H3K27me3_sp_ChIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE26609_H3K36me3_sp_ChIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE26609_H3K4me2_sp_ChIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE26609_H3K4me3_sp_ChIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE26609_H3K9me3_sp_ChIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE26609_RAW.tar |
2.4 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE26609_muscle_MeDIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE26609_sperm_MeDIP.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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