Supplementary Figure 6: Smchd1-null embryos have altered posterior Hox-gene expression and skeletal abnormalities.
From: Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters
a. Images of a representative somite-matched, sex-matched pair of E9.5 embryos, Smchd1+/+ and Smchd1MommeD1/MommeD1. b. Principal component analysis (PCA) of RNA-seq libraries from the somite-matched female paired Smchd1+/+ (n=3) and Smchd1MommeD1/MommeD1 (n=4) samples. Smchd1+/+ samples are depicted in green, and Smchd1MommeD1/MommeD1 samples are depicted in blue. c. Gene expression data from somite-matched female paired Smchd1+/+ (n=3) (y-axis) against Smchd1MommeD1/MommeD1 (n=4) samples (x-axis). Genes that are differentially expressed between Smchd1+/+ and Smchd1MommeD1/MommeD1 samples (FDR<0.05) are shown in blue. The Hox genes are shown in green, X-linked DEG in red, clustered protocadherins in orange, and Smchd1 in purple. All other genes are represented in grey. Axes are mean log transformed reads per million. d-e. Representative images from n = 10 whole mount skeletons of Smchd1+/+ (d) and Smchd1MommeD1/MommeD1 (e) E17.5 embryos, stained with Alizaren red and Alician blue. Whole body image, higher magnification view of the cervical vertebrae, and higher magnification sagittal view of embryo shown in d. Smchd1MommeD1/MommeD1 embryo shows abnormal bifurcating morphology of C2, and absence of T13 rib, indicated by asterisks. Note image for C2 is not the same Smchd1MommeD1/MommeD1 embryo as full body and sagittal view. f. Summarised data from scoring of whole mount skeletons from Smchd1+/+ (n=10) and Smchd1MommeD1/MommeD1 (n=10) male embryos. Cervical, thoracic, lumbar and sacral vertebrae are indicated, with ribs shown by horizonal blue lines, sternum shown by vertical blue lines and sacrum shown by vertical red lines. Dark blue dots indicate dramatically reduced rib process. C2bif refers to a malformed C2 vertebra, where it bifurcates at the dorsal side.
