Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells [Hi-C]

In metazoans, gene duplication has given rise to paralogous TFs, which have functionally diversified to control cellular commitment, differentiation, self-renewal and proliferation. While majority of paralogous TFs are dispersed across different chromosomes, some remain clustered—raising the question whether genomic proximity confers any evolutionary advantage for TF clusters.

To address this, we investigated a ~1 Mbp locus containing two ETS family paralogs, Ets1 and Fli1. Using a sub-diffraction sequential imaging technique called Optical Reconstruction of Chromatin Architecture (ORCA), we traced the 3D organization of this region in single alleles of T cells from genetically engineered mice with targeted deletions of key regulatory elements. We report that genetic deletion of the Ets1 super-enhancer re-wires the 3D chromatin landscape to favor Ets1-Fli1 promoter-promoter interactions characterized by transcriptional co-expression of both genes which safeguards Ets1 expression sustaining T cell development.