Paired-Tag single-cell joint profiling of H3K27me3-H3K4me1 and transcriptome revealed prenatal e-cigarette induced abnormal neuronal lineage development in rat neonatal prefrontal cortex

We performed single-nucleus joint profiling of transcriptome and histone modifications, namely H3K27me3 and H3K4me1, in prenatal electronic cigarette exposed neonatal rat prefrontal cortex. We found that e-cig not only induced unique histone mark patterns for H3K27me3-H3K4me1 within the gene body in many cell type-specific marker genes, e.g., Fibcd1, Slc1a3, Apq4, and Rfx4, but also caused a differential gene expression for these genes. We demonstrated that H3K27me3-H3K4me1 bivalency regulated the neuronal lineage differentiation by controlling the accessibility of promoter regions in genes responsible for cell specifications. Prenatal e-cig exposure also caused differential gene expressions in both excitatory and inhibitory neurons in many genes involved in specific neuronal functions, which was orchestrated by different H3K27me3-H3K4me1 methylations. Furthermore, prenatal e-cig smoking altered the gene expression of circadian genes involved in circadian entrainment and circadian rhythm including calcium signaling genes Cacna1c, Camk2b, and Ryr2; cAMP and protein kinase signaling transduction gene Adcy1 and Prkcb; as well as synaptic transmitter receptor Gria4. These results suggested that nicotine addiction could be epigenetically imprinted at a very early stage of brain development. Our study showed a profound effect of epigenomic regulation of histone marks by prenatal e-cig exposure on neuronal lineage development and highlighted a new underlying epigenetic mechanism of nicotine addiction, which could potentially lead to the identification of therapeutical targets for nicotine abuse disorders. Overall design: Pregnant rats were exposed to e-cigarette vapor during E4 to E20. Paired-Tag single-cell joint profilling were performed on transciptome and H3K27me3-H3K4me3 in postnatal day 7 ( P7) brain prefront cortex to study the epigenetic influence of maternal vaping on rat neonates' brain development.