Supplementary Figure 4: Effects of the deletion of HS-29 on local gene expression and chromatin state in primary erythroid cells.

(a) MA plot for RNA-seq data derived from WT and D29 erythroid cells. Data represent n = 3 independent experiments in which 3 animals were analysed in total. Mean RNA abundance is plotted on the x-axis and enrichment is plotted on the y-axis. No significant changes in local gene expression were detected as shown on the plot by the genes highlighted in blue: Snrnp25, Rhbdf1, Mpg. Controls are shown in different colours: Mitoferrin-1 (Slc25a37, green), a highly expressed erythroid gene; Sh3pxd2b and Il9r (red), repressed in erythroid; Nprl3 (yellow), a housekeeping gene within the α-globin locus that is unaffected by HS-29 deletion. The five most significant outliers were investigated and only one gene was located in cis to α-globin (Irgm2, >25 Mb removed), making it unlikely that these expression changes represent direct effects from HS-29 deletion. Significance was tested with a Wald test (DEseq2, n = 3 independent experiments in which 3 animals were analysed). (b) Normalised ATAC-Seq and ChIP-seq read-densities (RPKM; 2 independent experiments in which 2 animals were analysed in total) for H3K27me3, H3K4me3, and CTCF at the α-globin locus both in WT and D29 primary erythroid cells. Shaded grey bar indicates HS-29. The dashed box highlights the region over the Rhbdf1 and Mpg genes, magnified in top panels for ease of data visualisation.