The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.

Lampbrush chromosomes (LBCs) are giant meiotic bivalents that have served as a classic model system for studying chromatin organization and RNA synthesis for over a century. Despite their importance, the molecular mechanisms underlying distinctive LBC chromomere-loop architecture have remained poorly understood. Moreover, the influence of hypertranscription on chromatin organization during oogenesis remains enigmatic. Here, we provide comprehensive analysis of LBC organization by integrating single-cell Hi-C, RNA-seq, NOMe-seq, FISH mapping, and chromatin simulations. Single-nucleus Hi-C revealed CTCF-independent contact domains with stable boundaries defined by convergently oriented transcription units (TUs). Contact domains identified through Hi-C analysis correspond to insulated chromomeres in LBCs. Small transcriptionally inactive contact domains surrounded by divergently oriented TUs form "chromatin knots," which are often detached from the chromosome axis. Transcription loops frequently manifest as a "cross" pattern with reduced contacts within chromatin domains. Integrative analysis of the whole-genome data uncovers the mechanisms underlying LBC structure, revealing how hypertranscription modulates chromatin stiffness and repositions SMC complexes to establish the distinctive chromomere-loop organization. Biophysical modeling through polymer simulation reproduces key features of LBCs, including transcription loop formation, chromomere compaction, and insulation patterns. These findings offer a unifying framework for understanding remarkable transcription-dependent organization of LBCs.