Identification of Alternative Splicing Changes in Erythroid Differentiation Using Human Exon Arrays.

Terminal erythroid differentiation is accompanied by extensive structural remodeling as the cell enucleates and eventually assumes the biconcave disk morphology of the mature cell. Previous studies have documented many changes at the transcriptional level essential for erythroid differentiation. Changes in erythroid gene expression also occur at the level of pre-mRNA alternative splicing: the activation of 4.1R (EPB41) exon 16 splicing in late erythroblasts increases 4.1R affinity for spectrin-actin and mechanically strengthens the plasma membrane. We hypothesize that analogous changes in alternative splicing affect the structure and function of other erythroid proteins. To identify additional alternative splicing switches in erythroid genes, a genome-wide exon expression analysis was carried out using the new Affymetrix Human Exon 1.0 ST Array. Unlike traditional gene expression microarrays, this array has single exon resolution and can detect changes in expression due to alternative splicing. Samples for array analyses were prepared from RNA of human erythroid progenitor cells grown in culture for 7, 10, and 14 days, corresponding to basophilic, polychromatic, and orthochromatic stages. Analysis of this exon array data confirmed that 4.1R exon 16 splicing was activated in day 14 cells, and that a known inhibitor of exon 16 splicing, hnRNP A1, was down-regulated in coordination with the 4.1R splicing switch. As another positive control, we confirmed in array data the expression of a known erythroid-specific 3′ end in beta-spectrin mRNA in all three time points of erythroblasts, while array data from muscle tissue showed expression of only the non-erythroid 3′ end of beta-spectrin. Array data is now being analyzed to identify new cases of alternative splicing during erythropoiesis, and confirmation of several candidate splicing switches by RT-PCR and quantitative PCR is under way. A number of genes, including PIK3R1, SLC12A6, and TNPO2, show changes in alternative 5′ first exon usage during late erythropoiesis. A splicing change involving an internal cassette exon in MBNL2, which encodes a splicing regulator, was identified by array data and confirmed by RT-PCR. In addition, overall gene expression analyses confirm up-regulation of known genes expressed during erythroid differentiation, including Band 3, GLUT1, ALAS2, and BCL2L1. This preliminary analysis demonstrates the application of exon arrays toward the identification of splicing switches that occur during differentiation of human erythroblasts. Further validation of putative alternative splicing events is in progress, and investigation of the regulation of the validated events and the physiological implications of the predicted changes in the proteins will be pursued in the future.