title: 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.
authors.affiliation: Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds, UK.
authors.forename: Myriam
authors.initials: M
authors.lastname: Saida
authors.forename: David
authors.initials: D
authors.lastname: Iles
authors.forename: Abdul
authors.initials: A
authors.lastname: Elnefati
authors.forename: Martin
authors.initials: M
authors.lastname: Brinkworth
authors.forename: David
authors.initials: D
authors.lastname: Miller
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000378:metabolism*; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002467:Cell Nucleus / Q000378:metabolism / Q000648:ultrastructure; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism*; D055028:Comparative Genomic Hybridization; D019175:DNA Methylation; D057225:Data Mining; D004822:Epididymis / Q000166:cytology; D006657:Histones / Q000378:metabolism; D006868:Hydrolysis; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D051379:Mice; D008836:Micrococcal Nuclease / Q000378:metabolism*; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism; D011119:Polynucleotides / Q000737:chemistry / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000378:metabolism*; D012995:Solubility; D013094:Spermatozoa / Q000378:metabolism / Q000648:ultrastructure*
chemical_list: D001426:Bacterial Proteins; D000076246:CCCTC-Binding Factor; D002843:Chromatin; C000619698:Ctcf protein, mouse; D006657:Histones; D009707:Nucleosomes; D011119:Polynucleotides; D012097:Repressor Proteins; D008836:Micrococcal Nuclease