The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation

In anamniote embryos, the major wave of zygotic genome activation starts during the mid-blastula transition. However, some genes escape global genome repression, are activated substantially earlier, and contribute to the minor wave of genome activation. The mechanisms underlying the minor wave of genome activation are little understood. We explored the genomic organization and cis -regulatory mechanisms of a transcrip-tion body, in which the minor wave of genome activation is first detected in zebrafish. We identified the miR-430 cluster as having excessive copy number and the highest density of Pol-II-transcribed promoters in the genome, and this is required for forming the transcription body. However, this transcription body is not essential for, nor does it encompasse, minor wave transcription globally. Instead, distinct minor-wave -specific promoter architecture suggests that promoter-autonomous mechanisms regulate the minor wave of genome activation. The minor-wave-specific features also suggest distinct transcription initiation mecha-nisms between the minor and major waves of genome activation.

Automated summary

In anamniote embryos, the major wave of zygotic genome activation occurs during the mid-blastula transition, while some genes escape repression and contribute to the minor wave. The mechanisms underlying the minor wave of genome activation are not well understood. This study investigated a specific transcription body involved in the minor wave of activation in zebrafish and found that it is not essential for global transcription in the minor wave. Instead, distinct promoter architectures and promoter-autonomous mechanisms regulate the minor wave of genome activation.