Figure 8. Tracheal DT cell growth... | Rockefeller University Press

Figure 8.

$Tracheal DT cell growth deficit in rib mutants and Rib-bound tracheal genes. (A) Top: Comparison of WT and rib mutant trachea from stage 16 embryos. Yellow outline encloses DT segments corresponding to Tr.3–Tr.5 and reveals the failure in tube elongation and fusion in rib mutants. Scale bar: 10 µm. Inset: Arrowheads indicate DT segments from Tr.3–Tr.5 in whole embryos. Scale bar: 50 µm. Bottom: Cell volumetry shows decreased size in rib mutant DT cells compared with stage-matched WT embryos. A total of 260 cells (5 embryos/group; stages 15, 16) with clear marker staining, from segments Tr.3–Tr.5, whose entire volume could be unambiguously measured, were volume-rendered (two-tailed, unpaired t test; group median and quartiles labeled). Scale bar: 10 µm. (B) Cell counts of WT and rib mutant tracheal DT (Tr. 3–Tr. 5). n = 6 embryos/group; two-tailed, unpaired t test; mean with SEM. (C) Functional clustering of Rib-bound tracheal genes under GO terms according to DAVID. The top 10 GO terms with their associated enrichment scores are shown. See Table S5 for meta data. (D) Mapping of Rib binding peaks relative to the TSS of the closest gene and sorted by DAVID GO terms in the embryonic trachea shows a preponderance of target binding peaks localizing to regions distant from the TSS compared with the SG (Fig. 3 D). Rib binds only a small fraction of tracheal-expressed RPGs (GO cluster rank 93 covers 13 ribosomal and several nonribosomal genes), and primarily to sequences distal from the TSS-proximal promoter. Red line indicates median distance from the peak to TSS (+1 bp). n = number of peaks versus (number of genes).$

Tracheal DT cell growth deficit in rib mutants and Rib-bound tracheal genes. (A) Top: Comparison of WT and rib mutant trachea from stage 16 embryos. Yellow outline encloses DT segments corresponding to Tr.3–Tr.5 and reveals the failure in tube elongation and fusion in rib mutants. Scale bar: 10 µm. Inset: Arrowheads indicate DT segments from Tr.3–Tr.5 in whole embryos. Scale bar: 50 µm. Bottom: Cell volumetry shows decreased size in rib mutant DT cells compared with stage-matched WT embryos. A total of 260 cells (5 embryos/group; stages 15, 16) with clear marker staining, from segments Tr.3–Tr.5, whose entire volume could be unambiguously measured, were volume-rendered (two-tailed, unpaired t test; group median and quartiles labeled). Scale bar: 10 µm. (B) Cell counts of WT and rib mutant tracheal DT (Tr. 3–Tr. 5). n = 6 embryos/group; two-tailed, unpaired t test; mean with SEM. (C) Functional clustering of Rib-bound tracheal genes under GO terms according to DAVID. The top 10 GO terms with their associated enrichment scores are shown. See Table S5 for meta data. (D) Mapping of Rib binding peaks relative to the TSS of the closest gene and sorted by DAVID GO terms in the embryonic trachea shows a preponderance of target binding peaks localizing to regions distant from the TSS compared with the SG (Fig. 3 D). Rib binds only a small fraction of tracheal-expressed RPGs (GO cluster rank 93 covers 13 ribosomal and several nonribosomal genes), and primarily to sequences distal from the TSS-proximal promoter. Red line indicates median distance from the peak to TSS (+1 bp). n = number of peaks versus (number of genes).

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