Topologically associating domains (TADs) and chromatin loops help specify promoter–enhancer communication, with CTCF defining their boundaries and anchors. During pluripotent stem cell differentiation, TAD borders strengthen, yet the mechanisms underlying this transition remain unclear. In our recent work, we show that differentiation from embryonic stem (ES) to neural stem (NS) cells triggers a widespread increase in interactions between CTCF and RNA-binding proteins (RBPs). Although dispensable in ES cells, RBPs enhance CTCF–DNA binding and nucleoplasmic CTCF clustering in NS cells, reinforcing TAD boundaries and loop formation. We identify Pantr1, a CTCF-associated non-coding RNA, as a key mediator of these CTCF–RBP interactions and a driver of chromatin consolidation in NS cells. Functionally, CTCF maintains neuronal gene silencing in NS cells, acting as a barrier to premature gene activation during brain development. Together, these findings uncover a mechanism that strengthens chromatin architecture upon loss of pluripotency and shapes promoter–enhancer interactions during differentiation.