In human sperm, H4K20me3 is abundantly preserved in retrotransposons, satellite repeats and olfactory genes, and maintains herewith the somatic-like pattern
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ABSTRACT:
PROVIDER: PRJNA530568 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8838490.fastq.gz | Fastqsanger.gz | |||
| SRR8838491.fastq.gz | Fastqsanger.gz | |||
| SRR8838482.fastq.gz | Fastqsanger.gz | |||
| SRR8838492.fastq.gz | Fastqsanger.gz | |||
| SRR8838483.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Cellular senescence is a stable proliferation arrest and tumor suppressor mechanism. Abundance of histone modification, H4K20me3, has been reported to increase in senescent cells. Generally, H4K20me3 promotes formation of compacted transcriptionally silent constitutive heterochromatin, but its specific role in senescence is unknown. Here, we show that in senescent cells H4K20me3 is enriched at specific families of gene repeats (ZNFs, Olfactory Receptors, Protocadherins), and DNA sequences contained within senescence-associated heterochromatin (senescence-associated heterochromatin (SAHF)). Furthermore, in senescent cells, but not proliferating cells, H4K20me3 is also markedly enriched at bodies of repressed genes, including proliferation-promoting genes. Ectopic expression of SUV420H2, responsible for deposition of H4K20me3, reinforces senescence-associated proliferation arrest, and slows proliferation of transformed cells and tumorigenesis in vivo. These results indicate a dedicated role for H4K20me3 in control of nuclear organization and gene expression in senescent cells and stable senescence-associated proliferation arrest and tumor suppression.
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Project description:Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. Here we present a ChIP-Chip map of repressive and active histone modifications along mouse Chr.17 in embryonic, fibroblast cells. Our results show that the majority of H3K27me3 modifications form BLOCs rather than focal peaks. H3K27me3 BLOCs modify silent genes of all types and their flanking intergenic regions, indicating a negative correlation between H3K27me3 and transcription. However, non-transcribed gene-poor regions also lacked H3K27me3. We therefore performed a low resolution analysis of whole mouse Chr.17 which revealed that H3K27me3 specifically marks megabasepair sized domains that are enriched for genes, SINEs and active histone modifications. These genic H3K27me3 domains alternate with similar sized gene-poor domains that are deficient in active histone modifications, but enriched for LINE and LTR transposons as well as H3K9me3 and H4K20me3. Thus, a mouse autosome can be seen to contain alternating chromatin bands that predominantly separate genes from one retrotransposons class, which could offer unique chromatin compartments for the specific regulation of genes or the silencing of transposons. Keywords: Chip-chip, chromosome 17 wide unbiased mapping unbiased mapping of several histone modifications on chromosome 17 in two independent MEF cell lines
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Project description:We report the ChIP-SEQ results of H4K20me3 in BCSCsSETD4 and BCSCsGFP. To explore epigenetic regulation by H4K20me3 in BCSC quiescence, we performed chromatin immunoprecipitation sequencing (ChIP-seq) using BCSCsSETD4 and BCSCsGFP. Quiescent BCSCsSETD4 showed marked enrichment of H4K20me3 modifications relative to BCSCsGFP.
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Project description:Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. Here we present a ChIP-Chip map of repressive and active histone modifications along mouse Chr.17 in embryonic, fibroblast cells. Our results show that the majority of H3K27me3 modifications form BLOCs rather than focal peaks. H3K27me3 BLOCs modify silent genes of all types and their flanking intergenic regions, indicating a negative correlation between H3K27me3 and transcription. However, non-transcribed gene-poor regions also lacked H3K27me3. We therefore performed a low resolution analysis of whole mouse Chr.17 which revealed that H3K27me3 specifically marks megabasepair sized domains that are enriched for genes, SINEs and active histone modifications. These genic H3K27me3 domains alternate with similar sized gene-poor domains that are deficient in active histone modifications, but enriched for LINE and LTR transposons as well as H3K9me3 and H4K20me3. Thus, a mouse autosome can be seen to contain alternating chromatin bands that predominantly separate genes from one retrotransposons class, which could offer unique chromatin compartments for the specific regulation of genes or the silencing of transposons. Keywords: Chip-chip, chromosome 17 wide unbiased mapping
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Project description:Retrotransposons are widely spread in the mammalian genome and are usually silenced during development to avoid transposition-inducing mutations. But how they are repressed in embryos shortly before implantation remain to be identified, since the genome at this stage is globally hypomethylated. Here we show a histone chaperon, CAF-1, is responsible for retrotransposon silencing at the morula-blastocyst stages by depositing histone H4 lysine 20 trimethylation (H4K20me3). Knockdown of CAF-1 with a specific siRNA resulted in derepression of LINE-1, SINE-B2 and IAP associated with the decreased H4K20me3 level, and arrested embryonic development at the morula stage. The identical results were obtained with siRNAs against Suv420h1/2, H4K20 methyltransferases. Treatment with reverse transcriptase inhibitors rescued at least a part of these embryos. Thus, CAF-1 ensures the genomic integrity of preimplantation embryos by establishing repressive histone marks in the multiple retrotransposon classes. Comparative gene expression analyses using P150 knockdown (P150KD) embryos at morula stage were performed by microarray. P150KD embryos were produced with the injection of P150 siRNA into 1-cell embryos. As controls, siControl embryos were produced by the injection of control siRNA. These embryos were subjected to gene expression microarray.
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Project description:Retrotransposons are widely spread in the mammalian genome and are usually silenced during development to avoid transposition-inducing mutations. But how they are repressed in embryos shortly before implantation remain to be identified, since the genome at this stage is globally hypomethylated. Here we show a histone chaperon, CAF-1, is responsible for retrotransposon silencing at the morula-blastocyst stages by depositing histone H4 lysine 20 trimethylation (H4K20me3). Knockdown of CAF-1 with a specific siRNA resulted in derepression of LINE-1, SINE-B2 and IAP associated with the decreased H4K20me3 level, and arrested embryonic development at the morula stage. The identical results were obtained with siRNAs against Suv420h1/2, H4K20 methyltransferases. Treatment with reverse transcriptase inhibitors rescued at least a part of these embryos. Thus, CAF-1 ensures the genomic integrity of preimplantation embryos by establishing repressive histone marks in the multiple retrotransposon classes.
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