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Fig. 3

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ZDB-FIG-240418-55

Publication

Ugolini et al., 2024 - Transcription bodies regulate gene expression by sequestering CDK9

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Fig. 3

Characterization of downregulated genes.

a, Average expression level in transcripts per million (TPM) in WT embryos for all genes (n = 32,428), non-expressed genes (n = 9,545), non-differentially expressed (DE) genes (n = 19,426) and upregulated (n = 716) and downregulated (n = 242) genes (mir430^−/− + inj MiR430 versus WT at 256-cell stage). Boxplots show median, quartiles, minimum and maximum, and 1.5× interquartile range. Outliers are not shown. b, Representative images of a DNA-FISH experiment for upregulated genes (green), downregulated genes (magenta) and mir430 (yellow) in a nucleus of a WT embryo at the 256-cell stage. N = 3. Nuclei were also stained with DAPI (blue). Images shown are maximum intensity projections. c,d, Schematic representation of oligopaint probe design for upregulated and downregulated genes (c) and the mir430 locus (d). Primers used for qPCR amplification and their complementarity within a probe are shown. Probe sequences are reported in Supplementary Table 2. Fwd, forward; Rev, reverse. e, Distributions of 3D distances of upregulated (up) genes from the mir430 locus (green) and downregulated (down) genes from the mir430 locus (red) in WT embryos. Quantification of one biological replicate was performed. N = 19 embryos, n = 643 nuclei. Source numerical data are available on GEO (GSE248237).

Expression Data

Expression Detail

Antibody Labeling

Phenotype Data

Phenotype Detail

Acknowledgments

This image is the copyrighted work of the attributed author or publisher, and ZFIN has permission only to display this image to its users. Additional permissions should be obtained from the applicable author or publisher of the image. Full text @ Nat. Cell Biol.