Tet inactivation disrupts YY1 binding and long-range chromatin interactions to cause developmental defects in embryonic heart

Tet-mediated DNA methylation oxidation plays an important role in shaping the epigenetic landscapes and chromatin accessibility during gene expression. While several studies demonstrated pivotal roles of Tet proteins in regulating embryonic development, little is known about their functions in heart development. Here we systemetically analyzed DNA methylation and hydroxymethylation dynamics during early cardiac development in both human and mice. We discovered that cardiac-specific deletion of Tet2 and Tet3 in mice (Tet2/3-DKO) led to ventricular non-compaction cardiomyopathy (NCC) with embryonic lethality. Single-cell and bulk RNA-seq analyses revealed dramatic decrease of cardiomyocytes in Tet2/3-DKO heart tissues. Impaired DNA demethylation and chromatin accessibility in Tet2/3-DKO mice further compromised chromatin association of a key transcription factor, Ying-yang1 (YY1), and reduced long-range promoter-enhancer interactions at key genes involved in cardiac development. Taken together, our studies establish the physiological role of Tet proteins in the regulation of DNA methylation dynamics and chromatin configuration during embryonic heart development in mammals. In this study, we systematically investigated the DNA methylation and hydroxymethylation dynamics during early cardiac development in both human and mice. Furthermore, we generated a cardiac specific Tet2 and Tet3 double deficient mouse model to investigate the function of Tet-mediated DNA modifications during early cardiac development. These mice developed severe developmental defects in the ventricular wall reminiscent of non-compaction cardiomyopathy (NCC). With this disease-relevant in vivo model, we further unveiled previously-unrecognized roles of Tet-mediated DNA hydroxymethylation in regulating chromatin accessibility to facilitate the genomic recruitment of one key transcription factor, Ying-Yang 1 (YY1). More excitingly, our study uncovered a crucial role of Tet/5hmC in modulating chromatin long-range interactions to coordinate higher-order chromatin organization during embryonic heart development.