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Series GSE199084 Query DataSets for GSE199084
Status Public on May 03, 2022
Title Spontaneous and ART-induced large offspring syndrome: similarities and differences in DNA methylome
Organism Bos taurus
Experiment type Methylation profiling by high throughput sequencing
Summary Large/abnormal offspring syndrome (LOS/AOS) is a congenital overgrowth syndrome reported in ruminants produced by assisted reproduction (ART-LOS) which exhibit global disruption of the epigenome and transcriptome. LOS/AOS shares phenotypes and epigenotypes with the human congenital overgrowth condition Beckwith-Wiedemann syndrome. We have reported that LOS occurs spontaneously (SLOS), however, to date, no study has been conducted to determine if SLOS has the same methylome epimutations as ART-LOS. In this study, we performed whole genome bisulfite sequencing to examine global DNA methylation in SLOS and ART-LOS tissues. We observed unique patterns of global distribution of differentially methylated regions (DMRs) over different genomic contexts, such as promoters, CpG islands and surrounding regions, and repetitive sequences from different treatment groups. In addition, we identified hundreds of LOS-vulnerable DMRs across different cattle breeds when analyzing four idependent LOS experiments together. Specifically, there are 25 highly vulnerable DMRs that could potentially serve as molecular markers for the diagnosis of LOS, including at the promoters of DMRT2 and TBX18, at the imprinted gene bodies of IGF2R, PRDM8, and BLCAP/NNAT, and at multiple CpG islands. We also observed tissue-specific DNA methylation patterns between muscle and blood, and conservation of ART-induced DNA methylation changes between muscle and blood. We conclude that as in ART-LOS, alterations of the epigenome are involved in the etiology of SLOS. In addition, SLOS and ART-LOS share some similarities in methylome epimutations.
 
Overall design Whole genome bisulfite sequencing (WGBS) for tissues (mainly blood and muscle) of bovine calves from control and treatment groups. Animals from the US include three from the control group, eight from the SLOS group, and three which are relatives to one SLOS animal. Animals from Spain (ES) include three from the control group, four from the ART group, three from the reproductive fluid (RF) group, and two from the RF_necropsy group.
 
Contributor(s) Li Y, Sena Lopes J, Coy Fuster P, Rivera RM
Citation(s) 35466858
Submission date Mar 21, 2022
Last update date Aug 02, 2022
Contact name RocĂ­o Melissa Rivera
E-mail(s) riverarm@missouri.edu
Organization name University of Missouri, Columbia
Department Division of Animal Sciences
Street address 920 East Campus Drive
City Columbia
State/province MO
ZIP/Postal code 65211
Country USA
 
Platforms (1)
GPL24230 HiSeq X Ten (Bos taurus)
Samples (38)
GSM5963835 WGBS_US_Control_#1_Blood
GSM5963836 WGBS_US_Control_#2_Blood
GSM5963837 WGBS_US_Control_#3_Blood
Relations
BioProject PRJNA818312

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE199084_RAW.tar 10.8 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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