Comment[ArrayExpressAccession] E-GEOD-58747 MAGE-TAB Version 1.1 Public Release Date 2014-07-16 Investigation Title Perturbed adult sperm methylome after in utero undernutrition is associated with transmission of metabolic disease Comment[Submitted Name] Perturbed adult sperm methylome after in utero undernutrition is associated with transmission of metabolic disease Experiment Description The pre and postnatal environment can affect both an individual’s risk of adult onset metabolic disease and that of subsequent generations. Although animal models and epidemiological data implicate epigenetic inheritance, little is known of the mechanisms involved. In a robust intergenerational model of developmental programming we demonstrate that the nutritional environment experienced in utero by F1 generation embryos alters the DNA methylome of the F1 adult male germ line in a locus-specific manner, without affecting overall methylation levels. Differentially methylated regions are mostly hypomethylated and are enriched in nucleosome retaining regions in adult sperm. A substantial fraction is resistant to early embryo methylation reprogramming, and thus have the potential to alter F2 generation development. Altered expression of transcripts neighbouring differentially methylated regions are evident in tissues of F2 offspring despite lack of persistence of differential methylation. Transmitted methylation variation in the germline at key regulatory loci may therefore contribute to the development of metabolic disease in the subsequent generation. 2 biological replicates of pooled sperm samples for each control (C) or undernutrition (UN) model Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Shi Radford Ito Shi Corish Yamazawa Isganaitis Seisenberger Hore Reik Erkek Peters Patti Ferguson-Smith Person First Name Hui Elizabeth Mitsiteru Hui Jennifer Kazuki Elvira Stefanie Timothy Wolf Serap Antoine Mary-Elizabeth Anne Person Mid Initials J C Person Email hs523@cam.ac.uk Person Affiliation University of Cambridge Person Address Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, United Kingdom Person Roles submitter Protocol Name P-GSE58747-4 P-GSE58747-1 P-GSE58747-3 P-GSE58747-2 Protocol Description preprocessing of the raw reads were performed using FastQC and TrimGalore to remove poor quality bases and adapter sequences reads post-QC were mapped to mouse reference genome NCBIM37/mm9 using BWA v0.6.2 mapped reads were subject to further QC by SAMtools to remove unmapped, unpaired reads and reads with mapping quality score less than 10 differentially methylated regions (DMRs) were identified using MEDIPS DNA methylation levels across the whole genome were assessed using sliding windows (size 500bp and 200bp to shift the window) Genome_build: mm9 Supplementary_files_format_and_content: bigWig files, scores represent methylation levels Serial centrifugations were used to purify sperm from potential contaminating cells (such as epithelium or white blood cells). Sperm DNA was extracted by standard phenol-chloroform extraction, with an overnight proteinase K reaction at 55 degrees. DNA was sonicated, paired end adaptors ligated and 12 cycles of whole-genome amplification employed using PhusionTM High-Fidelity Taq and paired end Illumina primers. Libraries were electrophoresed in 2% 1x TAE agarose gels at 95V in 1x TAE buffer followed by excision of a 200bp range band either 200-400bp to 300-500bp according to the peak fragment size. Identical size ranges were obtained for control and UN libraries. qPCR for known methylated and unmethylated regions confirmed library quality. Sperm was isolated from 2 month old male offspring of control dams or dams undernourished by 50% during the last week of gestation. Protocol Type normalization data transformation protocol sample treatment protocol nucleic acid library construction protocol growth protocol Experimental Factor Name TREATMENT Experimental Factor Type treatment Publication Title In utero effects. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism. Publication Author List Radford EJ, Ito M, Shi H, Corish JA, Yamazawa K, Isganaitis E, Seisenberger S, Hore TA, Reik W, Erkek S, Peters AH, Patti ME, Ferguson-Smith AC PubMed ID 25011554 Publication DOI 10.1126/science.1255903 Comment[SecondaryAccession] GSE58747 Comment[GEOReleaseDate] 2014-07-16 Comment[ArrayExpressSubmissionDate] 2014-06-23 Comment[GEOLastUpdateDate] 2014-09-05 Comment[AEExperimentType] methylation profiling by high throughput sequencing Comment[SecondaryAccession] SRP043514 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR1448853-SRR1448857 SDRF File E-GEOD-58747.sdrf.txt