Fig. 1: Genome-wide Scr and Ubx ChIP-seq and transcriptomes from T1 and T3 leg discs. | Nature Communications

Fig. 1: Genome-wide Scr and Ubx ChIP-seq and transcriptomes from T1 and T3 leg discs.

From: Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

Fig. 1: Genome-wide Scr and Ubx ChIP-seq and transcriptomes from T1 and T3 leg discs.

a Medial view of T1 and T3 legs from adult males. Co coxa, Fe femur, Ti tibia, Ta tarsus. Compared to T3, T1 legs have larger coxa and shorter femurs and, in males, have a tightly packed row of specialized bristles called sex combs on the first tarsal segment (arrow). b Co-immunostaining of Scr and Ubx proteins in T1 and T3 leg discs in the wandering larva stage. Weak Scr signal in T3 leg disc is from adepithelial cells1. Scale bar: 100 μm. c Summary of Scr and Ubx functions in specifying T1 and T3 leg identities, respectively. d MA plot comparing the T1 and T3 leg disc transcriptomes. Differentially expressed genes (FDR < 0.01) are labeled red. Several genes investigated in this study are indicated. CR45559 is a lincRNA near the Scr locus. e Schematics (not to scale) of the 3xFLAG-tagged Scr and Ubx alleles generated by genome targeting (“Methods”)2. The wide boxes (Scr, orange; Ubx, green) indicate coding regions; the homeobox is purple and N-terminal 3xFLAG tags is red. The gray boxes are UTRs. The double-slash denotes large introns. The direction of transcription is indicated by an arrow at the transcription start site (TSS). f Genome browser view near the Ubx locus showing anti-FLAG ChIP-seq data from T1 or T3 leg discs dissected from isogenic stocks containing the 3xFLAG-Scr, 3xFLAG-Ubx, or no FLAG-tagged allele (w1118). Arrows indicate examples of different classes of binding: red: ScrT1 > UbxT3, black: ScrT1 ≈ UbxT3, green: ScrT1 < UbxT3. g Pie graphs showing the genomic classification of Scr and Ubx ChIP-seq peaks. TSS: transcription start site (promoter), defined as -1 kb to +100 bp from the +1 nucleotide of mRNA. TTS transcription termination site. h Hox–Exd-binding motifs are the most significantly enriched motifs in ScrT1 and UbxT3 peaks located in intergenic regions or introns (see Supplementary Fig. 3a for complete lists). Hox and Exd half-sites are indicated. Dashed ovals indicate positions that are known to differ for Scr-Exd and Ubx-Exd3.

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