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Xenbase Image ID: 151527

Fig. 1. Analyses of tbp, tlf and tbp2 mRNA ablation, embryonic gene activation and α-amanitin treatment reveal TBP family-insensitive gene transcripts. (A) Box plots of the fold change of groups of transcripts upon TBP, TLF or TBP2 knockdown as measured by microarray. Expression ratio of stages 10.5 (early gastrula) and 7 (blastula) is also plotted (10/7). TBP-, TLF- and TBP2-dependent transcripts (first three panels) were identified using a consistent statistical change call between replicates for the initiation factor that was ablated, in addition to a fold change (log2 ratio<−1.5) in expression. The unaffected group of transcripts (fourth panel) was identified by selecting for developmentally upregulated transcripts (between stage 7 and 10.5) with no significant change upon injection of TBP family antisense oligos. Boxplots are standard box plots generated in R, showing the interquartile range (IQR) around the median; the whiskers extend from the minimum value to the maximum value unless the distance to the first and third quartiles is more than 1.5 times the IQR. The fold change cut off range is shaded gray in each panel. (B) Phenotype of control and α-amanitin-treated embryos at stage 10.5. (C) Effect of α-amanitin treatment on transcript levels of ‘unaffected’ TFI genes, demonstrating that these transcripts are newly made in the embryo, with the exception of gapdh (maternally provided control) and vegt which is also partly maternally provided. (D) K-means clustering of transcript expression ratios [antisense oligo-treated relative to control; stage 10.5 relative to stage 7; α-amanitin (α-ama) relative to control] of developmentally active transcripts (defined as transcripts that are either developmentally upregulated or affected by α-amanitin at stage 10.5). Each column represents one of two replicate experiments. A cluster of genes insensitive for TBP, TLF, or TBP2 depletion is marked on the left.

Image published in: Gazdag E et al. (2016)

Image downloaded from an Open Access article in PubMed Central. © 2016. Published by The Company of Biologists Ltd

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