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 and are activated substantially earlier and shape the minor wave of genome activation. The mechanisms underlying the minor wave of genome activation are little understood. We explored the genomic organisation and cis-regulatory mechanisms of a transcription body, in which the minor wave of genome activation is first detected in zebrafish. We identified the miR-430 cluster with excessive copy number and highest density of Pol II-transcribed promoters in the genome, that is required for forming the transcription body. However, this transcription body is not essential for, nor encompasses minor wave transcription globally. Instead, distinct minor wave-specific promoter architecture suggests promoter-autonomous mechanisms regulate the minor wave of genome activation. These minor wave specific features also suggest distinct transcription initiation mechanisms between the minor and major wave of genome activation.