XB-ART-57326Nat Commun January 1, 2020; 11 (1): 3491.
Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription.
Sperm contributes genetic and epigenetic information to the embryo to efficiently support development. However, the mechanism underlying such developmental competence remains elusive. Here, we investigated whether all sperm cells have a common epigenetic configuration that primes transcriptional program for embryonic development. Using calibrated ChIP-seq, we show that remodelling of histones during spermiogenesis results in the retention of methylated histone H3 at the same genomic location in most sperm cell. This homogeneously methylated fraction of histone H3 in the sperm genome is maintained during early embryonic replication. Such methylated histone fraction resisting post-fertilisation reprogramming marks developmental genes whose expression is perturbed upon experimental reduction of histone methylation. A similar homogeneously methylated histone H3 fraction is detected in human sperm. Altogether, we uncover a conserved mechanism of paternal epigenetic information transmission to the embryo through the homogeneous retention of methylated histone in a sperm cells population.
PubMed ID: 32661239
PMC ID: PMC7359334
Article link: Nat Commun
Species referenced: Xenopus laevis
Genes referenced: ascl2 atf1 bmi1 cbx3 cfap52 cpeb1 elf3 foxq1 h2ac21 h2bc21 hmga2 hmgb1 hmgb2 hmgb3 hmgn2 meis1 meis2 nfya nfyb nhlh1 nr4a2 osr2 pam sox7 sp1 spdef spib stat1 tbx3 tcf12 tcf3 wdr5 zbtb33 zic3 znf143 znf281
Antibodies: H3C1 Ab10 Hist1H3A Ab2 Histone H2B Ab10 Histone H4 Ab11 Hmgb1 Ab1 Tri-Methyl H3f3a Ab19
GEO Series: GSE125982: NCBI
Article Images: [+] show captions
|Fig. 1: Somatic level of histone H3/H4 is retained as nuclesosomes and subnucleosomes in sperm chromatin. a Xenopus laevis sperm core histones content relative to that found in a somatic cell (XL-177) as measured by quantitative WB (H2A, H2B, H3 n = 2, H4 n = 3, biologically independent samples error bar on H4 shows standard deviation). b DNA fragments generated by MNase digestion of Xenopus laevis sperm and somatic cell. c Schematic representation of the possible origin of subnucleosomal sized fragments generated by MNase treatment of sperm chromatin. d Nucleoproteic particles generated by MNase treatment of sperm are centrifugated on a sucrose gradient. Subsequently, particles isolated along the gradient are analysed for associated DNA fragment length (electrophoresis) and for associated proteins (mass spectrometry). e WB analysis confirms mass spectrometry analysis. Similar ratio of H3 to H4, and decreased level H2B to H4 are detected in subnucleosomes compared with nucleosomes. Xenopus sperm and mESCs are shown as control. Graphs below show the quantification of WB data (n = 2, biologically independent samples). f Model of core histone composition of Xenopus laevis sperm nucleosomal and subnucleosomal particle. Source data related to a, b, d and e are provided as Source Data files.|
|Fig. 2: Nucleosome loss/retention associated with spermiogenesis occurs non-randomly in a large fraction of the genome. a Relative abundance (left) and genome coverage (right) of nucleosomes and subnucleosomes in the sperm chromatin. The left pie chart reports the fraction of DNA fragments from Xenopus Laevis sperm corresponding to each type of particle; the right pie chart reports the fraction of genome covered by each type of particle. b Fraction of the genome with homogeneous particles composition. The bar graph indicates the percentage of the genome that possess nucleosomal or subnucleosomal structure across most sperm of the population sequenced (genome binned in 50 bp windows). c Fold enrichment (observed/random) over 1000 randomisations for homogeneous nucleosomes (left) or subnucleosomes (right) composition at the indicated genomic features; ***: empirical p value <1e−3. Input data from two independent replicates were pooled. d PAM (partitioning around medoids) clustering of promoter (TSS +/−2 kb) according to enrichment for nucleosomes or subnucleosomes. e Model of nucleosomes and subnucleosomes distribution in sperm and spermatid. Source data related to a, b and d are provided as Source Data files.|
|Fig. 7: Homogeneous retention of methylated nucleosome in a human sperm population. a Percentage of the genome (left) and percentage of peaks (right) with different levels of H3K4 or H3K27 methylation density in human sperm. b PAM clustering of H3K4 and H3K27 HMD levels at promoter regions (TSS +/−2 kb) in human sperm. c Genome browser screenshots of TBX3 and BMI1 HMDs in human sperm. d Percentage of gene orthologues with peaks of histone methylation in both human and Xenopus sperm. e Barplots of the average percentage (%) of 5mC methylation at H3K27me3 peaks stratified by methylation level (left); error bars: sem; barplot of the percentage of H3K27me3 peaks showing absence of 5mC methylation (right) (5mC methylation: single-sperm bisulfite sequencing data from ref. 31). f Barplots indicating −log10 (p value) for enrichment of sperm TSSs with HMD > 80 for H3K4 or H3K27 in set of genes with TSSs showing different chromatin accessibility level in eight cell embryos (open and closed corresponds to TSSs open or closed in all cells of a eight cell embryos), whereas divergent corresponds to TSSs either open or closed in different cells (ATAC-seq data from ref. 31); p values determined by χ2 proportion test evaluating if the proportion of gene of interest is higher (green) or lower (red) than the genome-wide proportion (i.e., expected proportion). g Model of epigenetic homogeneity in Xenopus and human sperm. The cartoon summarises the observed trends in retention of modified histones across the genome in those species. Source data related to b and e are provided as Source Data files.|
External Resources: GSE125982
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