Neonatal Hypothyroidism Rearranges the 3D Chromatin Structure in the Liver

Children with congenital hypothyroidism (1 in every ~2,500 live births) may develop a dramatic neurological, muscle-skeleton, and metabolic syndrome due to insufficient thyroid hormone (TH) signaling during development 1-3. While the mechanisms involved remain largely unknown, it is well established that the condition is irreversible if treatment is not initiated during the immediate post-natal period. Here we used high-throughput genomic and epigenomic techniques (Hi-C) to generate high-resolution, genome-wide 3D maps of chromatin interaction in mice with developmental liver-specific hypothyroidism (caused by Dio2 inactivation). The neonatal disruption of hepatic TH signaling only minimally affected genomic compartmentalization but caused substantial rearrangements (e.g. shifting or splitting) in thousands of topologically associating domains (TADs). The rearranged TADs contained DNA sites of hypermethylation, areas of reduced chromatin accessibility, and hundreds of repressed genes. In many instances, the enhancer-promoter (E-P) interaction in key repressed genes had been weakened, explaining the permanent change in how the liver handles excess fat or alcohol in the adult mouse 4-6. The Alb-D2KO mice, characterized by hepatocyte-specific Dio2 inactivation, were developed by crossbreeding floxed C57BL/6J D2 mice (dio2Flx) with mice expressing Cre-recombinase under the albumin promoter (Cre-ALB) [B6.Cg-Tg(Alb-cre)21Mgn/J; The Jackson Laboratory]. Cre-ALB mice were employed as control animals. All subjects in the study were male and 16 weeks old, and they were housed under standard conditions of room temperature (22 °C) and a 12-hour dark/light cycle. To ensure robustness and reliability, the Hi-C data assays were performed with duplicate biological replicates. A pool of four liver samples from each experimental group was utilized in these assays, contributing to the comprehensive analysis of spatial genomic interactions in the liver tissues of the mice under investigation.