Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa

Abstract

In mammals, fusion of two morphologically distinct gametes, oocytes and spermatozoa, leads to the formation of totipotent embryos. Acquisition of totipotency is thought to be mediated by extensive epigenetic reprogramming of parental genomes, affecting DNA methylation and histone modifications, and possibly replication timing and transcriptional activity in parental specific manners [1][2][3][4] . It is currently unclear to what extent differential reprogramming of maternal and paternal genomes is due to differences in chromatin states inherited from the oocyte and spermatozoon [4][5][6][7][8][9][10][11] . Beyond DNA methylation 1,2,6,12 , it is unknown which types of parental chromatin states are maintained or reprogrammed in early embryos. If certain parental chromatin states did escape reprogramming in the early embryo, such information could constitute an "intrinsic intergenerational epigenetic program directing gene expression in the next generation 13 . If these chromatin states also escaped reprogramming during gametogenesis, the inheritance program would function transgenerationally 13 . An increasing number of studies point to inter-or transgenerational transmission of acquired phenotypic traits that are related to temporal exposure of (grand-)parents to alternative instructive environmental cues [14][15][16][17][18] . Mechanistically, such phenotypic changes may be related to (transient) alterations of an intrinsic inheritance program.A role of histones and associated posttranslational modifications in maternal and paternal transmission of intrinsic or acquired epigenetic information is largely unknown 13 . In many metazoans, male germ cells undergo during their final differentiation into sperm an extensive chromatin remodeling process during which 3 genomic DNA becomes newly packaged into a highly condensed configuration by sperm specific proteins. In mammals, removal of histones is generally not complete 10,11,[19][20][21][22][23][24] . Furthermore, remaining histones have been reported to stay associated with the paternal genome during de novo chromatin formation in the zygote following fertilization 9 .We and others recently showed that histones lasting in human sperm are to some extent enriched at regulatory sequences of genes 10,11 . We also demonstrated that H3K4me3-and H3K27me3-marked histones are retained at promoters of specific sets of genes in mouse spermatozoa 11. The extent of evolutionary conservation of nucleosome retention at gene regulatory sequences in spermatozoa and the mechanistic principles of such retention are, however, unknown.To address 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. We show here that combinatorial effects of sequence composition, histone variants and histone modifications uniquely determine the packaging of sperm DNA. Nucleosomes in sperm mainly localize to unmethylated CpG-rich sequences in a histone variant specif...

Effect of high fat diet on paternal sperm histone distribution and male offspring liver gene expression

“…3B,D), as was previously reported. 16,19 Overall, we observed a higher normalized read density at protein-coding promoter regions in HFD (HFD7) compared to LFD (LFD8), consistent with the results of the peak analysis.…”

“…Although most of the histone proteins are replaced by protamines during spermatogenesis, several recent reports suggest that a portion of the haploid genome is retained in nucleosomes, [16][17][18][19][20] with about 1-4% being retained in the murine genome. To address the effect of diet on sperm histone content, we performed chromatin immunoprecipitation (ChIP) using specific antibodies against histone H3.…”

“…[15][16][17][18][19][20] Recent studies have also detected specific histone tail modifications at retained histones and the presence of small RNA in sperm. 3,10,16,[19][20][21] After fertilization of the oocyte, protamines are stripped from the paternal genome and nucleosomes are reassembled. 22 It remains to be shown whether H3 retention in sperm can transfer transgenerational epigenetic information.…”

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice

“…The first high-resolution genome-wide map of human spermatozoa histones shows a strong enrichment in methylated histone H3K4me3 at many promoters of developmental genes, genes encoding signaling factors, imprinted gene clusters, microRNA and HOX gene clusters (17). These studies showed that the promoters in sperm are enriched in H3K4me3 and H3K27me3, and it was suggested that genes with these marks play a particularly important role in epigenetic inheritance (16–18). On the other hand, more recent nucleosome mapping studies showed that sperm nucleosome fraction is enriched in gene-poor regions and is generally depleted from the promoters (19,20).…”

“…Nucleosomes in sperm are also enriched in CpG islands (18). Recently, a strong association between nucleosome retention at CpG islands in sperm and the establishment of unmethylated regions in the early mammalian embryo was shown (28).…”