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Abstract
Chromatin architecture is fundamental in regulating gene expression. To investigate
when spatial genome organization is first established during development, we examined
chromatin conformation during Drosophila embryogenesis and observed the emergence
of chromatin architecture within a tight time window that coincides with the onset
of transcription activation in the zygote. Prior to zygotic genome activation, the
genome is mostly unstructured. Early expressed genes serve as nucleation sites for
topologically associating domain (TAD) boundaries. Activation of gene expression coincides
with the establishment of TADs throughout the genome and co-localization of housekeeping
gene clusters, which remain stable in subsequent stages of development. However, the
appearance of TAD boundaries is independent of transcription and requires the transcription
factor Zelda for locus-specific TAD boundary insulation. These results offer insight
into when spatial organization of the genome emerges and identify a key factor that
helps trigger this architecture.