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. 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.