title: Integrative DNA methylation and gene expression analyses identify DNA packaging and epigenetic regulatory genes associated with low motility sperm.
abstract: BACKGROUND
  In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function.
  
  
  RESULTS
  Sperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic. DNA methylation was measured with the Illumina Infinium array at 27,578 CpG loci. Unsupervised clustering of methylation data differentiated the 21 sperm samples by their motility values. Recursively partitioned mixture modeling (RPMM) of methylation data resulted in four distinct methylation profiles that were significantly associated with sperm motility (P = 0.01). Linear models of microarray analysis (LIMMA) was performed based on motility and identified 9,189 CpG loci with significantly altered methylation (Q<0.05) in the low motility samples. In addition, the majority of these disrupted CpG loci (80%) were hypomethylated. Of the aberrantly methylated CpGs, 194 were associated with imprinted genes and were almost equally distributed into hypermethylated (predominantly paternally expressed) and hypomethylated (predominantly maternally expressed) groups. Sperm mRNA was measured with the Human Gene 1.0 ST Affymetrix GeneChip Array. LIMMA analysis identified 20 candidate transcripts as differentially present in low motility sperm, including HDAC1 (NCBI 3065), SIRT3 (NCBI 23410), and DNMT3A (NCBI 1788). There was a trend among altered expression of these epigenetic regulatory genes and RPMM DNA methylation class.
  
  
  CONCLUSIONS
  Using integrative genome-wide approaches we identified CpG methylation profiles and mRNA alterations associated with low sperm motility.
authors.affiliation: Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Sara E
authors.initials: SE
authors.lastname: Pacheco
authors.forename: E Andres
authors.initials: EA
authors.lastname: Houseman
authors.forename: Brock C
authors.initials: BC
authors.lastname: Christensen
authors.forename: Carmen J
authors.initials: CJ
authors.lastname: Marsit
authors.forename: Karl T
authors.initials: KT
authors.lastname: Kelsey
authors.forename: Mark
authors.initials: M
authors.lastname: Sigman
authors.forename: Kim
authors.initials: K
authors.lastname: Boekelheide
mesh_terms: D016000:Cluster Analysis; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D042003:DNA Packaging / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics*; D020869:Gene Expression Profiling; D056426:Genetic Loci / Q000235:genetics; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013081:Sperm Motility / Q000235:genetics*; D013094:Spermatozoa / Q000166:cytology* / Q000378:metabolism; D018511:Systems Integration
chemical_list: D012333:RNA, Messenger