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| Status |
Public on Jun 15, 2009 |
| Title |
Distinctive Chromatin in Human Sperm Packages Genes that Guide Embryo Development: ChIP-chip |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
Methylation profiling by genome tiling array
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| Summary |
As nucleosomes are widely replaced by protamine in mature human sperm, epigenetic contributions to embryo development appear limited. However, our genome-wide approaches find nucleosomes at low levels genome-wide, but also significantly enriched at imprinted gene clusters, miRNA clusters, HOX gene clusters, and the promoters of other developmental transcription and signaling factors. Developmental promoters were often DNA hypomethylated, and bore histone modifications localized to discrete locations: H3K4me2 is enriched at certain developmental promoters, whereas large blocks of H3K4me3 localize to a subset of developmental promoters, regions in HOX loci, certain non-coding RNAs, and generally to paternally-expressed imprinted loci. In contrast, H3K4me3 is generally absent at paternally-repressed imprinted loci. Interestingly, repressive H3K27me3 is enriched at many developmental promoters that lack early expression in embryos, with significant overlap with bivalent (H3K4me3/H3K27me3) promoters in ES cells. Taken together, epigenetic marking in sperm is extensive, and correlated with developmental regulators.
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| Overall design |
*Use of ChIP-chip to identify regions enriched for methylated DNA, protamine, histone, and several histone variants in human sperm.
*Histone Localization: Chromatin was prepared from 40 million sperm as described previously (1) in the absence of crosslinking reagent, treated with sequential and increasing MNase (10U-160U), and centrifuged to sediment protamine-associated DNA, releasing mononucleosomes. The pooled mononucleosomes were gel purified (~140-155 bp) for sequencing and array analysis. Histone localization on arrays was performed using a single donor with 3 biological replicas and normalized to total genomic DNA (control).
*Chromatin IP and Preparation for Genomics Methods: ChIP methods were as described previously (2) but were performed without a cross linking agent and slight modifications to the salt levels, 250 mM NaCl, 200 mM LiCl, and replaced the TE wash with 150 mM PBS wash. ChIPs hybridized to arrays were performed from a single donor: H3K4me2 had 2 biological replicas, H3k4me3 had 3-replicas, TH2B had 2 replicas, and all the modifications data were normalized to the gel purified array monucleosomes.
*Methylation Profiling Using MeDIP: This procedure was described previously (3). Samples were hybridized to Agilent expanded promoter arrays, treated according to standard Agilent conditions, and scanned in an Agilent scanner. Sperm MeDIP had three replicas and Fibroblast had 2 replicas. Both Sperm and Fibroblast MeDIPs were normalized to their corresponding input fractions.
1. Zalenskaya, I.A., Bradbury, E.M. & Zalensky, A.O. Chromatin structure of telomere domain in human sperm. Biochem Biophys Res Commun 279, 213-8 (2000).
2. Gordon, M. et al. Genome-Wide Dynamics of SAPHIRE, an Essential Complex for Gene Activation and Chromatin Boundaries. Mol Cell Biol 27, 4058-69 (2007).
3. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457-66 (2007).
The '*EnrichedRegions.xls' supplementary files list the enriched regions. See 'GSE15701_EnrichedRegions_README.txt'.
The '*OligoRatioData.zip' folders have the supplementary files containing oligo ratio data (log2(AveTreatment/AveControl)). See 'GSE15701_OligoRatioData_README.txt'.
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| Contributor(s) |
Hammoud SS, Nix DA, Zhang H, Carrell DT, Cairns BR |
| Citation(s) |
19525931 |
| Submission date |
Apr 16, 2009 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Bradley R. Cairns |
| Organization name |
HHMI and Huntsman Cancer Institute
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| Department |
Oncological Sciences
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| Street address |
2000 Circle of Hope
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84102 |
| Country |
USA |
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| Platforms (2) |
| GPL4124 |
Agilent-014706 Human Promoter ChIP-on-Chip Set 244K, Microarray 1 of 2 G4489A (Feature Number version) |
| GPL4125 |
Agilent-014707 Human Promoter ChIP-on-Chip Set 244K, Microarray 2 of 2 G4489A (Feature Number version) |
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| Samples (36)
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| GSM402834 |
H3K4Me3, Replica 3 and 1, Slide 2 |
| GSM402835 |
H3K4Me3, Replica 2, Slide 1 |
| GSM402836 |
H3K4Me3, Replica 2, Slide 2 |
| GSM402837 |
TH2B, Replica 1, Slide 1 |
| GSM402838 |
TH2B, Replica 1, Slide 2 |
| GSM402839 |
TH2B, Replica 2, Slide 1 |
| GSM402840 |
TH2B, Replica 2, Slide 2 |
| GSM402841 |
InputFibroblast and MeDIPFibroblast, Replica 1, Slide 1 |
| GSM402842 |
InputFibroblast and MeDIPFibroblast, Replica 1, Slide 2 |
| GSM402843 |
InputFibroblast and MeDIPFibroblast, Replica 2, Slide 1 |
| GSM402844 |
InputFibroblast and MeDIPFibroblast, Replica 2, Slide 2 |
| GSM402845 |
InputSpermD1 and Histone-MNAseSpermD1, Replica 1, Slide 1 |
| GSM402846 |
InputSpermD1 and Histone-MNAseSpermD1, Replica 1, Slide 2 |
| GSM402847 |
InputSpermD1 and Histone-MNAseSpermD1, Replica 2, Slide 1 |
| GSM402848 |
InputSpermD1 and Histone-MNAseSpermD1, Replica 2, Slide 2 |
| GSM402849 |
InputSpermD1 and Histone-MNAseSpermD1, Replica 3, Slide 1 |
| GSM402850 |
InputSpermD1 and Histone-MNAseSpermD1, Replica 3, Slide 2 |
| GSM402851 |
InputSpermD1 and ProtamineSpermD1, Replica 1, Slide 1 |
| GSM402852 |
InputSpermD1 and ProtamineSpermD1, Replica 1, Slide 2 |
| GSM402853 |
InputSpermD1 and ProtamineSpermD1, Replica 2, Slide 1 |
| GSM402854 |
InputSpermD1 and ProtamineSpermD1, Replica 2, Slide 2 |
| GSM402855 |
InputSpermD2 and MeDIPSpermD2, Replica 1, Slide 1 |
| GSM402856 |
InputSpermD2 and MeDIPSpermD2, Replica 1, Slide 2 |
| GSM402857 |
InputSpermD2 and MeDIPSpermD2, Replica 2, Slide 1 |
| GSM402858 |
InputSpermD2 and MeDIPSpermD2, Replica 2, Slide 2 |
| GSM402859 |
InputSpermD2 and MeDIPSpermD2, Replica 3, Slide 1 |
| GSM402860 |
InputSpermD2 and MeDIPSpermD2, Replica 3, Slide 2 |
| GSM402861 |
InputSpermD4 and MeDIPSpermD4, Replica 1, Slide 1 |
| GSM402862 |
InputSpermD4 and MeDIPSpermD4, Replica 1, Slide 2 |
| GSM402863 |
InputSpermD4 and MeDIPSpermD4, Replica 2, Slide 1 |
| GSM402864 |
InputSpermD4 and MeDIPSpermD4, Replica 2, Slide 2 |
| GSM402865 |
InputSpermD4 and MeDIPSpermD4, Replica 3, Slide 1 |
| GSM402866 |
InputSpermD4 and MeDIPSpermD4, Replica 3, Slide 2 |
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| This SubSeries is part of SuperSeries: |
| GSE15594 |
Distinctive Chromatin in Human Sperm Packages Genes that Guide Embryo Development |
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| Relations |
| BioProject |
PRJNA123019 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE15701_EnrichedRegions_README.txt |
1.9 Kb |
(ftp)(http) |
TXT |
| GSE15701_H3K4Me2_EnrichedRegions.xls.gz |
477.3 Kb |
(ftp)(http) |
XLS |
| GSE15701_H3K4Me2_OligoRatioData.zip.gz |
3.8 Mb |
(ftp)(http) |
ZIP |
| GSE15701_H3K4Me3_EnrichedRegions.xls.gz |
488.7 Kb |
(ftp)(http) |
XLS |
| GSE15701_H3K4Me3_OligoRatioData.zip.gz |
3.8 Mb |
(ftp)(http) |
ZIP |
| GSE15701_Histone_EnrichedRegions.xls.gz |
457.2 Kb |
(ftp)(http) |
XLS |
| GSE15701_Histone_OligoRatioData.zip.gz |
3.8 Mb |
(ftp)(http) |
ZIP |
| GSE15701_MeDIP_Fibroblast_EnrichedRegions.xls.gz |
527.8 Kb |
(ftp)(http) |
XLS |
| GSE15701_MeDIP_Fibroblast_OligoRatioData.zip.gz |
3.8 Mb |
(ftp)(http) |
ZIP |
| GSE15701_MeDIP_Sperm-Fibroblast_EnrichedRegions.xls.gz |
1.1 Mb |
(ftp)(http) |
XLS |
| GSE15701_MeDIP_Sperm-Fibroblast_OligoRatioData.zip.gz |
3.8 Mb |
(ftp)(http) |
ZIP |
| GSE15701_MeDIP_Sperm_EnrichedRegions.xls.gz |
535.2 Kb |
(ftp)(http) |
XLS |
| GSE15701_MeDIP_Sperm_OligoRatioData.zip.gz |
3.8 Mb |
(ftp)(http) |
ZIP |
| GSE15701_OligoRatioData_README.txt |
551 b |
(ftp)(http) |
TXT |
| GSE15701_Protamine_EnrichedRegions.xls.gz |
1.1 Mb |
(ftp)(http) |
XLS |
| GSE15701_Protamine_OligoRatioData.zip.gz |
3.8 Mb |
(ftp)(http) |
ZIP |
| GSE15701_RAW.tar |
2.4 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE15701_TH2B_EnrichedRegions.xls.gz |
463.9 Kb |
(ftp)(http) |
XLS |
| GSE15701_TH2B_OligoRatioData.zip.gz |
3.8 Mb |
(ftp)(http) |
ZIP |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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