Integrating ATAC-seq and RNA-seq reveals tissue-specific genes and repressed networks in the placenta

We performed ATAC-seq on placenta dissected from e9.5 timed-pregnant mice in order to generate genome-wide chromatin accessibility maps. Integrating this data with previously published RNA-seq data showed that: 1) genes that have high expression and high ATAC-seq read coverage at the transcription start site (TSS) were enriched for house-keeping functions; 2) genes that have high expression and medium-low coverage at the TSS were enriched for placenta-specific genes and functions; 3) genes that have low expression and high TSS coverage are actively repressed. From the actively repressed genes, we extracted a protein-protein interaction network enriched for neuronal functions. These data increase our understanding of active and repressed gene networks in the e9.5 placenta. The analysis also provides a method for identifying repressed networks and tissue-specific genes by integrating ATAC-seq and RNA-seq data. Please note that the RNA-Seq data are already deposited and available under GSE65808. Overall design: Examination of chromatin accessibility in the e9.5 mouse placenta