Fig. 2 | Nature Communications

Fig. 2

From: A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation

Fig. 2

Characterisation of the miR430 clustered locus demonstrates usage of multiple promoters. a, b Multi-site mapping of CAGE-seq provides evidence for activity of the miR430 cluster at early blastula stages. Schematic demonstrates transcription start sites (TSS) and internal RNA Drosha processing sites post (high stage) and pre-MBT (64-cell stage). The start position of microRNA offset RNA (moRNA) at the Drosha cutting site detected by CAGE is indicated. Black short bars indicate mature miRNA positions, long bar indicates predicted promoter region around the TSS. b At least 8 promoters are predicted by CAGE on the zebrafish reference genome (GRCz10). Candidate promoters are indicated by P1-P8, tag per million (TPM) signal is shown with a log scale. An additional cluster of miR430 genes without CAGE predicted promoter is shown on the left. c Promoter sequence alignment indicates SNPs among candidate promoters, which allow unique mapping of nascent RNA sequencing data for mapping of promoter usage. Orange box indicates predicted TATA box at the canonical position from the main TSS mapped by CAGE-seq. P3 and P9 carry unique bases for unique detection of transcripts driven by these promoters. d nascent RNA-seq data uniquely mapped to the miR430 locus demonstrates start site region utilization by at least two promoters indicated by CAGE-seq. RNA sequencing peaks drop at precursor gene start due to lack of SNP in the highly repetitive miRNA precursor region