The sperm nucleus: chromatin, RNA, and the nuclear matrix

Abstract

Within the sperm nucleus, the paternal genome remains functionally inert and protected following protamination. This is marked by a structural morphogenesis that is heralded by a striking reduction in nuclear volume. Despite these changes, both human and mouse spermatozoa maintain low levels of nucleosomes that appear non-randomly distributed throughout the genome. These regions may be necessary for organizing higher order genomic structure through interactions with the nuclear matrix. The promoters of this transcriptionally quiescent genome are differentially marked by modified histones that may poise downstream epigenetic effects. This notion is supported by increasing evidence that the embryo inherits these differing levels of chromatin organization. In concert with the suite of RNAs retained in the mature sperm, they may synergistically interact to direct early embryonic gene expression. Irrespective, these features reflect the transcriptional history of spermatogenic differentiation. As such, they may soon be utilized as clinical markers of male fertility. In this review, we explore and discuss how this may be orchestrated.

Figure 1

The Potential Influence of Zygotic Genome Activation on Paternal Chromatin Structure. In mouse and human sperm the protamine genes are bound by nucleosomes residing within a potentiated DNase I-sensitive domain. These regions are differential marked by modified histones in each species. In mouse the bivalently marked spermatogenic promoters may reflect the early initiation of zygotic expression at the late 1-cell stage. Recruitment of transcriptional machinery (RNA polymerase; RNA POL II, and transcription factors; TFs) is coincident with the activation of silencing pathways (histone methyltransferases, HMTs; and Polycomb factors, PcG). The retention of the silencing H3K27me3 mark in promoters may prevent detrimental expression prior to gene silencing. In comparison, human zygotic genome activation occurs at the 4 or 8 cell stage. This affords the embryo time to silence these genes, which in sperm are marked with the active H3K4me3 modification lacking the repressive mark. In both species the protamine domain remains silenced throughout differentiation by adopting a highly condensed chromatin conformation. During male gametogenesis this region becomes potentiated in spermatocytes prior to its expression in round spermatids.

Figure 2

Nuclear Matrix Association within the Protamine Locus of Sperm and Somatic Cells. Genomic regions in sperm associated with DNA loops or the nuclear matrix within a ~120 Kb region of human chromosome 16 (chr 16: 11,223,803 – 11,341,499) are displayed as Log₂ values (Loop/Matrix). This region contains the complete protamine domain as well as the neighboring SOCS1 gene. Genes are denoted by black arrows: PRM1 > PRM2 > PRM3 > TNP2 > SOCS. The relative histone enrichment across this region is illustrated in blue (GEO Series GSE15690). (A) Nuclear matrices were extracted from sperm from four fertile donors. Following EcoR I digestion matrix- and loop-associated DNA were labeled and competitively hybridized to Nimblegen CGAR0150-WHG8 CGH arrays. Loop- or matrix-association was determined as previously described (Linnemann et al. 2007). (B) Composite of percent normalized values from all four fertile donors. (C) Loop- and matrix-associated DNA from HeLa and AoAF cells were identified as previously described (Linnemann & Krawetz 2009, Linnemann et al. 2009).