Differently regulated gene-specific activity of enhancers located at the boundary of sub-topologically associated domains

Enhancers activate transcription through long-distance physical interactions with their cognate promoters within a particular sub-topologically-associated domain (sub-TAD). The T-cell receptor alpha (TCRalpha) enhancer (Ealpha) is located at the sub-TAD boundary between the TCRalpha and DAD1 genes, and is able to regulate transcription toward both sides in an approximately 1Mb region. Our analyses of transcriptional enhancer-dependence during T-cell development and non-T-lineage tissues revealed that Ealpha can activate transcription of specific 3prime-sub-TAD genes, when it is inactive to transcribe the TCRalpha gene. Hence, distinct requirements for Ealpha function are necessary at specific genes at both sub-TADs, implying that enhancers do not merely function as chromatin loop anchors that nucleate the formation of factor condensates to increase gene transcription initiated at their cognated promoters. The observed different regulated Ealpha activity for activating specific genes at its flanking sub-TADs may be a feature for enhancers located at a sub-TAD boundary.