Mapping of histone-binding sites in histone replacement-completed spermatozoa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA450284 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6979400_1.fastq.gz | Fastqsanger.gz | |||
| SRR6979400_2.fastq.gz | Fastqsanger.gz | |||
| SRR6979410_1.fastq.gz | Fastqsanger.gz | |||
| SRR6979410_2.fastq.gz | Fastqsanger.gz | |||
| SRR6979420_1.fastq.gz | Fastqsanger.gz |
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Project description:The majority of histones are replaced by protamines during spermatogenesis, but small amounts are retained in mammalian spermatozoa. Since nucleosomes in spermatozoa influence epigenetic inheritance, it is important to know how histones are distributed in the sperm genome. Conflicting data, which may result from different conditions used for micrococcal nuclease (MNase) digestion, have been reported: retention of nucleosomes at either gene promoter regions or within distal gene-poor regions. Here, we find that the swim-up sperm used in many studies contain about 10% population of sperm which have not yet completed the histone-to-protamine replacement. We develop a method to purify histone replacement-completed sperm (HRCS) and to completely solubilize histones from cross-linked HRCS without MNase digestion. Our results indicate that histones are retained at specific promoter regions in HRCS. This method allows the study of epigenetic status in mature sperm.
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Project description:This SuperSeries is composed of the SubSeries listed below.
2018-07-26 | GSE113150 | GEO
Project description:Small RNA expression analysis in histone replacement-completed sperm
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Project description:Majority of histones are replaced by protamine during spermatogenesis, but small amount of histones are retained in mammalian spermatozoa. Since nucleosomes in spermatozoa influence epigenetic inheritance, it is important how histones are distributed on sperm genome. We have found that the swim-up sperm used in many studies contains about 10% of immature sperm which do not yet complete the histone-to-protamine replacement. We have developed the novel method to purify the histone replacement-completed sperm (HRCS), and to completely solubilize nucleosomes from cross-linked HRCS without MNase digestion. Here, we analyzed H3 binding profiles in total sperm and HRCS by Chromatin IP – sequencing (ChIP-seq) analysis, and DNA methylation profiles in swim-up sperm and HRCS by target bisulfite sequencing (TGSB).
2018-07-26 | GSE112945 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE13863: Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa (Nimblegen) GSE19889: Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa (Illumina) Refer to individual Series
2010-05-16 | E-GEOD-19892 | biostudies-arrayexpress
Project description:Majority of histones are replaced by protamine during spermatogenesis, but small amount of histones are retained in mammalian spermatozoa. Since nucleosomes in spermatozoa influence epigenetic inheritance, it is important how histones are distributed on sperm genome. We have found that the swim-up sperm used in many studies contains about 10% of immature sperm which do not yet complete the histone-to-protamine replacement. We have developed the novel method to purify the histone replacement-completed sperm (HRCS), and to completely solubilize nucleosomes from cross-linked HRCS without MNase digestion. Here, we analyzed H3 binding profiles in total sperm and HRCS by Chromatin IP – sequencing (ChIP-seq) analysis, and DNA methylation profiles in swim-up sperm and HRCS by target bisulfite sequencing (TGSB).
2018-07-26 | GSE113137 | GEO
Project description:Increasing evidence indicates that paternal dietary conditions influence the metabolic disorders of offspring. Previous studies suggested the involvement of epigenetic regulation for such phenomena, but the mechanism remains elusive. To reveal the molecular function of stress-dependent epigenetic regulator ATF7 in paternal inheritance of dietry effect on offpring phenotype, we analyzed ATF7-binding profiles in testicular germ cells by ChIP-seq, DNA methylation profiles in sperm by TGBS, small RNA expression profiles in HRCS by RNA-seq,and whole expression profiles in offspring liver by expression array analysis, using wild-type and ATF7 heterozygous mutant mice fed with control diet or low-protein diet.
2020-03-09 | GSE123254 | GEO
Project description:In higher eukaryotes, histone methylation is involved in the maintenance of cellular identity during somatic development. During spermatogenesis, most nucleosomes are replaced by protamines. Therefore, it is unclear if histone modifications function in paternal transmission of epigenetic information. Here we show that active H3K4 di-methylation (H3K4me2) and repressive H3K27 tri-methylation (H3K27me3), two modifications important for Trithorax and Polycomb-mediated gene regulation, are present in chromatin of human spermatozoa and show methylation-specific distributions at regulatory regions. H3K4me2-marked promoters control gene functions in spermatogenesis and cellular homeostasis suggesting that this mark reflects germline transcription. In contrast, H3K27me3 marks promoters of key developmental regulators in sperm as in soma. Many H3K27me3-marked genes are never expressed in the male and female germline, and in early “totipotent” embryos, suggesting a function for Polycomb in repressing somatic determinants across generations. Targets of H3K4me2 and H3K27me3 are also modified in mouse spermatozoa, implicating an evolutionary conserved role for histone methylation in chromatin inheritance via the male germline.
2010-05-16 | GSE13863 | GEO
Project description:Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or no H2A.Z molecules. SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products. The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction. Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B and deposition of H2A.Z-H2B. These results suggest that the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction. Total nucleosomes from MNase-treated nuclear extracts were fractionated by sequential immunoprecipitation into homotypic H2A/H2A (AA), heterotypic H2A/H2A.Z (AZ), and homotypic H2A.Z/H2A.Z (ZZ) nucleosomes.
2010-10-12 | E-GEOD-24618 | biostudies-arrayexpress
Project description:In higher eukaryotes, histone methylation is involved in the maintenance of cellular identity during somatic development. During spermatogenesis, Since most nucleosomes are replaced by protamines during spermatogenesis . Iit is therefore unclear whether if histone modifications function in paternal transmission of epigenetic information. Here we show that H3K4 di-methylation (H3K4me2) and H3K27 tri-methylation (H3K27me3), two modifications important for Trithorax and Polycomb-mediated gene regulation, display methylation-specific distributions at regulatory regions in human spermatozoa. H3K4 dimethylation H3K4me2-marksed promoters of genes relevant control gene functions in spermatogenesis and cellular homeostasis suggesting that this mark reflects germline transcription. In contrast, H3K27 trimethylation (H3K27me3) marks promoters of key developmental regulators in sperm like in somatic cells. Promoters of orthologous genes are similarly modified in mouse spermatozoa. Further, particularly genes with extensive H3K27me3 coverage around transcriptional start sites are never expressed during male and female gametogenesis, nor in pre-implantation embryos. These data are compatible with a function for Polycomb in repressing somatic determinants across generations. Importantly, however, we observe only modest selective retention of nucleosomes at regulatory regions in human sperm suggesting that paternal transmission of H3K27me3-encoded epigenetic information may be subjected to variegation. Identification of nucleosome containing regions in 6 human sperm samples
2010-05-16 | E-GEOD-19889 | biostudies-arrayexpress