Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells

Highlights

• Commitment to T lineages is paired with global changes in the regulome and 3D nucleome

• Transformation of these chromatin organizations is concerted for T cell commitment

• Concerted changes of the regulome and 3D nucleome underlie transcriptomic changes

• BCL11B contributes to the maintenance of the 3D nucleome in T cells

Summary

How chromatin reorganization coordinates differentiation and lineage commitment from hematopoietic stem and progenitor cells (HSPCs) to mature immune cells has not been well understood. Here, we carried out an integrative analysis of chromatin accessibility, topologically associating domains, AB compartments, and gene expression from HSPCs to CD4⁺CD8⁺ T cells. We found that abrupt genome-wide changes at all three levels of chromatin organization occur during the transition from double-negative stage 2 (DN2) to DN3, accompanying the T lineage commitment. The transcription factor BCL11B, a critical regulator of T cell commitment, is associated with increased chromatin interaction, and Bcl11b deletion compromised chromatin interaction at its target genes. We propose that these large-scale and concerted changes in chromatin organization present an energy barrier to prevent the cell from reversing its fate to earlier stages or redirecting to alternatives and thus lock the cell fate into the T lineages.