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Series GSE42629 Query DataSets for GSE42629
Status Public on Jun 15, 2013
Title Density and methylation state of CpG dinucleotides define histone variant specific retention of nucleosomes in mouse spermatozoa
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Nucleosomes are the principal packaging units of chromatin and critical for gene regulation and genome stability. In mammals, a subset of nucleosomes fail to be replaced by protamines during spermatogenesis and are retained in mature spermatozoa providing opportunities for paternal epigenetic transmission. In humans, the remaining 10% localize at regulatory elements of genes. To assess evolutionary conservation and to dissect the molecular logic underlying nucleosome retention, we determined the genome wide nucleosome occupancy in mouse spermatozoa that only contain 1% residual histones. In striking contrast to mammalian somatic cells and haploid round spermatids, we observe high enrichment of nucleosomes at CpG-rich sequences throughout the genome, at conserved regulatory sequences as well as at intra- and intergenic regions and repetitive DNA. This preferred occupancy occurs mutually exclusive with DNA methylation both in mouse and human sperm. At unmethylated CpG-rich sequences, residing nucleosomes are largely composed of the H3.3 histone variant, and trimethylated at lysine 4 (H3K4me3). Both canonical H3.1/H3.2 and H3.3 variant histones are present at promoters marked by Polycomb-mediated H3K27me3, which is strongly predictive for gene repression in pre-implantation embryos. Our data indicate important roles of DNA sequence composition, DNA methylation, variant H3.3 and canonical H3.1/H3.2 histones and associated modifications in nucleosome retention versus eviction during the histone-to-protamine remodeling process in elongating spermatids and potentially in epigenetic inheritance by nucleosomes between generations.
Overall design Identification of histone, histone variant and histone modification states in round spermatids and sperm
Contributor(s) Erkek S, Hisano M, Murr R, Schuebeler D, Stadler M, Peters A
Citation(s) 23770822
Submission date Nov 29, 2012
Last update date May 15, 2019
Contact name Antoine Peters
Organization name Friedrich Miescher Institute for Biomedical Research (FMI)
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (21)
GSM1046827 Sperm Nucleosome replicate1
GSM1046828 Sperm Nucleosome replicate2
GSM1046829 Sperm H3.3
BioProject PRJNA182375
SRA SRP017350

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Supplementary file Size Download File type/resource
GSE42629_RAW.tar 642.9 Mb (http)(custom) TAR (of TAB, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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