Somatic Cell Contamination as an Inhibitor of Proper Sperm Methylation Analysis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE237402 | GEO | 2023/09/01
REPOSITORIES: GEO
Similar Datasets
Project description:We assessed a novel benchtop approach to detecting somatic cell contamination in human sperm epigenetic studies.
2017-12-16 | GSE108058 | GEO
Project description:To establish contamination profiles, the sperm donors with normal sperm counts were analyzed using an Infinium HumanMethylation450 array. Somatic cell lysis, sperm isolation, DNA extraction, and bisulfite conversion were performed as described by Aston et al. The bisulfite converted sperm DNA was hybridized to Illumina Infinium HumanMethylation450K microarrays at the University of Utah and run as recommended by the manufacturer (Bibikova et al. 2011). Unpaired blood samples were extracted using Qiagen's DNeasy Blood and Tissue kit and bisulfite converted using Zymo's EZ DNA Methylation kit. All procedures were performed according to the instructions of the manufacturer. Four permutations were run on each sample, including pure blood, half blood and half sperm by DNA concentration, half blood and half sperm by cell count, and pure sperm (n = 16). Concentration was normalized using a spectrophotometer. A Makler cell counting chamber was used to count white blood cells and sperm, which were then normalized in a 1:1 ratio.
2023-11-07 | GSE246935 | GEO
Project description:Somatic cell contamination in sperm human DNA methylatoin studies
| PRJNA422568 | ENA
Project description:In human sperm, preserved histones evading histone-to-protamine replacement were observed in certain genes and gene promoters, but also in distal intergenic and repetitive DNA regions. The substantiality of the latter and its putative biological role are still a subject of hot debate. To shed more light on this issue we analyzed H4K20me3, a histone mark regulating heterochromatic and repetitive DNA in somatic cells, which was recently detected in human sperm. Our immunohistochemical and western blot analyses revealed the presence of H4K20me3 in male germ cells at every stage of spermatogenesis and in mature sperms, respectively. By ChIP-sequencing of the motile sperm fractions from three biological replicates we found 4.56% of the sperm genome to be occupied by H4K20me3. By comparing the genome-wide binding sites of H4K20me3 in sperm cells and somatic cells (K562) we found correspondences in 77% of respective peaks. The majority of binding sites (70%) were detected in distal intergenic and intron regions. Intriguingly, H4K20me3 enrichments could be observed in both somatic and sperm cells within satellite repeats and retrotransposons, particularly in long interspersed nuclear repeats (LINEs) and retrotransposons containing long terminal repeats (LTR-retrotransposons). Broad cluster arrangements and strong enrichments in olfactory receptor genes were also characteristic for H4K20me3. This is the first time H4K20me3 is characterized at the genome-wide level in human sperm and compared to somatic cells. Our results reveal that H4K20me3 constitutes the majority of histones preserved in matured human sperm and maintains a somatic-like distribution pattern.
2019-04-03 | GSE129239 | GEO
Project description:we build the sperm proteome profile of aged and young males
2022-07-12 | PXD035466 | iProX
Project description:Genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm and an immortalized cell line using the meDIP technique and a custom oligonucleotide array targetting the vast majority of annotated TSSs and non-promoter CGIs in the human genome.
2008-04-30 | E-TABM-445 | biostudies-arrayexpress
Project description:food contamination metagenome Metagenome
| PRJNA340876 | ENA
Project description:A father’s lifetime experiences can be transmitted to his offspring to affect health and development. The mechanisms underlying paternal epigenetic transmission are unclear. Unlike somatic cells, there are few nucleosomes in sperm and their function in epigenetic inheritance is unknown. We generated transgenic mice in which overexpression of the histone H3 lysine 4 (H3K4) demethylase LSD1/KDM1A during spermatogenesis reduced H3K4 dimethylation in sperm. KDM1A overexpression in one generation severely impaired development and survivability of offspring. These defects persisted transgenerationally in the absence of KDM1A germ line expression and were associated with altered RNA profiles in sperm and offspring. We show that epigenetic inheritance of aberrant development can be initiated by histone demethylase activity in developing sperm, without changes to DNA methylation at CpG-rich regions.
2015-10-08 | GSE66050 | GEO
Project description:Mammalian sperm exhibit an unusual and heavily-compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, histone localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, along with appropriate lysis conditions, are required to reveal a sperm chromatin state distinct from any yet reported. Using ATAC-Seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with genes expressed during late spermiogenesis. Histone modification and chromosome folding studies also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies strongly argue that our knowledge of mammalian chromosome packaging remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.
2023-03-10 | GSE226684 | GEO
Project description:Mammalian sperm exhibit an unusual and heavily-compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, histone localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, along with appropriate lysis conditions, are required to reveal a sperm chromatin state distinct from any yet reported. Using ATAC-Seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with genes expressed during late spermiogenesis. Histone modification and chromosome folding studies also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies strongly argue that our knowledge of mammalian chromosome packaging remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.
2023-03-10 | GSE226686 | GEO