The Temporal Expression and Regulation of an Imprinted Gene Network during Postnatal Liver Development in Mice

Abstract

Postnatal liver maturation involves a unique process after birth, in which hepatocytes proliferate and differentiate simultaneously until the organ gains a mature gene expression profile and adult hepatic functions. During this developmental period, most liver functions, including drug metabolism, are not fully mature as the genes involved are not expressed at adult levels. It is known that the neonatal liver undergoes extensive changes in its transcriptome during early life as it matures from a hematopoietic to a metabolic organ, however genetic mechanisms regulating postnatal liver maturation are largely unknown. The goal of our study is to understand how an imprinted gene network controls organ growth and hepatocyte proliferation and promotes the expression of mature hepatic genes during postnatal liver maturation. Mouse is selected as a model. RNA‐Seq was performed on mouse livers collected at 6 ages of postnatal development: days ‐2 (day 17 of gestation), 1, 5, 20, 25, and 60 (adult). A total of 88 genes that were previously proven to be imprinted in mice, meaning they have monoallelic expression, were selected for further analysis. A total of 46 of these genes were found to be expressed in the liver during at least one of the ages. The majority of expressed genes (27) had decreasing expression with age, showing high expression levels closer to birth, then little to no expression in adult ages, with a coordinated notable decrease in expression at day 20. Imprinted genes with the highest expression at neonatal ages included the long non‐coding RNA (lncRNA) H19 and its neighborhood genes, along with another lncRNA maternally expressed 3 (Meg3) and the genes in its cluster. Generally, the majority of imprinted genes are found in clusters on the chromosomes. After examining the expression of imprinted genes in each cluster, it was found that groups of genes with decreasing expression with age all contained an imprinted lncRNA, suggesting that lncRNAs may be critical for controlling the coordinate decline of many imprinted genes levels during postnatal development. To investigate a possible factor responsible for the decline of many imprinted genes with age, we also performed RNA‐Seq on farnesoid X receptor (Fxr) null mice at matching ages to wild type mice. FXR is a nuclear receptor involved in bile acid homeostasis that increases in expression postnatally and is expressed at high levels in adults. We found that Fxr null mice have significantly higher expression of 28 imprinted genes in liver during neonatal ages. H19 and Meg3 showed the greatest increase in expression, suggesting FXR may play a role, possibly through the activation of small heterodimer partner (SHP), in repressing the expression of many imprinted genes. The expression of imprinted genes in the liver seems to be highly coordinated with both the age of mice and their inclusion in certain clusters on chromosomes. Imprinted genes are known to be critical for mammalian development, and we suggest they may control the maturation of the postnatal liver. Our study also suggests that lncRNAs and the nuclear receptor FXR play a role in coordinating the expression patterns of imprinted genes with age and therefore can have a significant effect on liver development and function.Support or Funding InformationNIH/NIEHS R01ES019487