GSE173380
Illumina NGS RNA-seq and RRBS Sequencing on Rat Kidney
We reported the kidney transcriptome and methylome profiles of rat Brown Norway (BN) and Sprague Dawley (CD) strains at late pregnancy (day 18/21) compared to non-pregnancy. The renal transcriptome was characterized from 326 million single-end 100bp RNA-seq data. The methylome dataset included 234 million 75-bp RRBS DNA methylation reads. We identified 297 differentially expressed genes (DEGs) induced by pregnancy in CD rats and 174 DEGs induced in BN rats, based on the RNA-seq dataset.  237 of the 297 DEGs in CD pregnant rats and 114 of the 174 DEGs in BN pregnant rats are strain specific, indicating differential adaptation to pregnancy. Methylome data reveals that strain differences is the major factor in determining methylation differences. We also found that pregant BN showed higher methylation than non-pregnant BN at transcription starter site (TSS) and promoter regions. Functional analysis based on DEGs and DMGs revealed that pregnant BN rats showed renal transcriptomic changes that induce vitamin D deficiency and renal pro-inflammatory gene expression that can partly explain pregnancy-specific proteinuria. Integrated analysis based on transcriptome and methylome  suggested that modifications on DNA methylation were correlated with transcriptome changes for several significant biological processes and/or pathways. Overall design: Brown Norway (BN) rat pregnancies are characterized by preeclampsia-like symptoms, while Sprague-Dawley (CD) rats are regarded as a model of normal pregnancy. Using these two rat strains, we characterized the transcriptomic and methylomic changes in both BN and CD rats during pregnancy as compared to non-pregnancy, in aim to understand the temporal changes in renal physiological adaptation during pregancy.