Methyl-Seq Analysis of d30 Pig Embryos Derived from Sows Feed Restricted During Lactation

Maternal nutrition during the peri-conception period has been shown to have health consequences for the offspring in several species.  These range from short term effects on fetal development to long term effects on adult health. 

This study extends previous gene expression studies (Oliver et al. 2011. Reprod Fertil Dev. 23(7):899-911) by using Methyl-seq to identify differentially methylated regions in d30 fetuses of sows feed restricted during lactation.  We have previously demonstrated that this treatment is associated with reduced fetal weights and alterations in litter sex ratio, and in particular sows that metabolize high amounts of energy for milk production compromise the development of the next litter (Patterson et al. 2011. Reprod Fertil Dev. 23(7):889-898).  Sows were categorized as Risk (mobilized > 40 MJ ME/d) and  Non-risk (mobilized < 20 MJ ME/d), and a pool of DNA was made for each category (Risk (n=3) and Non-risk (n=3)) using DNA from the fetuses.  Methyl-Miner (Invitrogen) was used to enrich for methylated sequences in each pool, and these were then used to create libraries for SOLiD4 (ABI) sequencing.  Data analyses to measure methylation sequence enrichment and to identify differentially methylated regions between Risk and Non-risk fetuses were conducted using the R based program MEDIPS (Weber et al. 2005. Nat Genet. 37(8):853-62).

We sequenced methylation enriched libraries for Risk and Non-risk d30 pig fetuses, and were able to identify DMRs in the fetuses that were associated with differences in the amount of energy the sow metabolized for feeding the weaned litter.