Key gene regulatory sequences with distinctive ontological signatures associate with differentially endonuclease-accessible mouse sperm chromatin

Abstract

Using a well-established endonuclease-based chromatin dissection procedure in conjunction with both experimental comparative genome hybridisation (CGH) array profiling and in silico data mining, we show that mouse spermatozoa contain chromatin that is sensitive and resistant to digestion with micrococcal nuclease (MNase). Sequences represented in the micrococcal nuclease digestion solubilised (MNDS) but not the MND insoluble (MNDI) chromatin are strongly enriched in chromosomal regions of high gene density. Furthermore, by fluorescence in situ hybridisation (FISH) analysis, we show that MNDS and MNDI DNAs occupy distinct domains of decondensed mouse sperm nuclei that may also retain abundant histones. More detailed in silico analysis of CGH probe location in relation to known promoters and sequences recognised by CCCTC binding factor (CTCF) shows a significant excess of both in MNDS chromatin. A functional analysis of gene promoters reveals strong ontological signatures for ion transport on methylated promoters associated with CTCF binding sequences in MNDS chromatin. Sensory perception is the only strong ontological signature present in MNDI chromatin, driven by promoters that are not associated with CTCF regardless of their methylation status.

High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and Sperm

“…Two studies isolated solubilized mononucleosome-sized fragments after MNase digestion of human sperm, finding enrichment over the promoters of key developmental regulators, with a very strong correlation with GC content (Brykczynska et al, 2010; Hammoud et al, 2009; Vavouri and Lehner, 2011). Somewhat different results were obtained via tiling microarray analysis of DNA released after light restriction enzyme or MNase digestion of human and mouse sperm, with gene and promoter-rich regions flanked by CTCF sites very broadly overrepresented in much longer (Megabase-scale) domains (Arpanahi et al, 2009; Saida et al, 2011). …”

Paternal Poly (ADP-ribose) Metabolism Modulates Retention of Inheritable Sperm Histones and Early Embryonic Gene Expression

“…CTCF-binding sites are highly enriched in MNase-sensitive sperm DNA fractions in both, humans [4] and mice [31]. Future studies addressing how the sites of histone retention in sperm are determined are clearly required.…”

Sperm selection for assisted reproduction by prior hyaluronan binding: the HABSelect RCT

“…Work conducted in this and other laboratories suggests that the DNA in human and mouse sperm is carefully and systematically organised in the nucleus into distinct geographical domains ( Figure 1). [30][31][32] These studies showed that some domains are enriched in histones, 33 which can account for their hitherto unexplained persistence in sperm nuclei alongside the more abundant protamines. 34,35 Histone-bound sperm chromatin domains are enriched in developmental gene sequences expressed in early embryogenesis.…”

“…34,35 Histone-bound sperm chromatin domains are enriched in developmental gene sequences expressed in early embryogenesis. 30,32,33 We hypothesised that damage to these domains was critically relevant for subsequent early embryonic development and could account for the early pregnancy failure observed after both IVF and ICSI-based procedures. 36 Failure of the embryo to thrive following successful implantation may be related to the fragmented or deranged paternal DNA resulting in sequences that are important for early embryological function remaining bound to histones.…”