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Fig. 1

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ZDB-FIG-230710-43

Publication

Hadzhiev et al., 2023 - The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation

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Fig. 1

De novo assembly of the miR-430 cluster from long-read sequencing data

(A) Schematic of the most common miR-430 gene structure (top), the duplex consisting of promoter region (red) and two pre-miRNA triplets (blue) each containing miR-430a, miR-430b, and miR-430c (gray) pre-miR-430 subtypes. Bottom: the miR-430 gene cluster structure in current reference assembly (GRCz11).

(B) Genome browser view of the miR-430 gene cluster assembled from long reads. The tracks show a low-resolution continuity structure of the gene cluster (top), long-read coverage histogram (middle), and the read to contig assembly layout (bottom). Raw reads with 50 or more promoters are shown as red horizontal bars with the promoter number indicated on top of them.

(C) Left: number of BLAST hits in raw long reads of single gene promoters and miR-430. Right: estimated miR-430 promoter number normalized to that of single-copy genes.

(D) Estimated miR-430 promoter number (red line) by digital droplet PCR (ddPCR) for three zebrafish strains and the assembled contig. Error bars are standard deviation from the mean of the miR-430 promoter estimate normalized to each of the 6 single-copy genes and 6 technical ddPCR replicates respectively.

(E) Rainfall plot representing the promoter density across each chromosome of the newly assembled zebrafish genome (GRCz11 reference guided). Red arrow indicates the mirR-430 gene cluster. Abbreviations: TSS, transcription start site; AB, TU-AB, TU, and TL are zebrafish strains used in (C) and (D).

See also Figure S1 and Tables S1 and S5.

Expression Data

Expression Detail

Antibody Labeling

Phenotype Data

Phenotype Detail

Acknowledgments

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Reprinted from Developmental Cell, 58, Hadzhiev, Y., Wheatley, L., Cooper, L., Ansaloni, F., Whalley, C., Chen, Z., Finaurini, S., Gustincich, S., Sanges, R., Burgess, S., Beggs, A., Müller, F., The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation, 155170.e8155-170.e8, Copyright (2023) with permission from Elsevier. Full text @ Dev. Cell