Fig. 3
m6A-dependent regulation of erythroid gene expression programs. a Global m6A levels quantified by colorimetric assay in lv-sgRNA-KO transduced HEL cells are significantly reduced following WTAP-KO, METTL3-KO and METTL14-KO, and unchanged following LMO2-KO (n = 3, mean ± SEM. Student’s t-test two-sided, *** indicates p < 0.001). b A heatmap for RNA-seq analysis of HEL cells following KO of METTLE3 and WTAP, as well as select erythroid genes, shows clustering of the two components of the m6A MTase complex and a unique transcriptional profile vs. GATA1 and LMO2-KO. c GSEA analysis of METTL3-KO and WTAP-KO HEL cell RNA-seq, using custom gene sets for transcriptionally up and down genes during erythropoiesis as defined by ref. 40, shows enrichment for genes upregulated following m6A loss in HEL cells, which are downregulated during erythropoiesis and genes that are downregulated following m6A loss in HEL cells, which are upregulated during erythropoiesis. d A heatmap of transcriptional changes observed during normal erythropoiesis compared to m6A MTase KO HEL cells and KO HEL cells for select erythroid transcriptional regulators shows similar inverse patterns of gene expression. e A heatmap of gene expression changes from RNA-seq data for select erythroid transcriptional regulators and their targets from sgGATA1-KO, sgLMO2-KO, sgWTAP-KO, and sgMETTL3-KO HEL cells, showing decreased expression of the target genes in the absence of changes in transcription factor expression following m6A loss. The complete dataset is available in Supplementary Data 3. *Indicates significant changes relative to non-targeting control (sgNTC) (FDR < 0.05)
