• RNA-seq identified thousands of changes in alternative gene isoform expression changes during erythropoiesis.• MBNL1 regulates alternative splicing in terminal erythropoiesis.The scope and roles of regulated isoform gene expression during erythroid terminal development are poorly understood. We identified hundreds of differentiation-associated isoform changes during terminal erythropoiesis. Sequences surrounding cassette exons of skipped exon events are enriched for motifs bound by the Muscleblind-like (MBNL) family of splicing factors. Knockdown of Mbnl1 in cultured murine fetal liver erythroid progenitors resulted in a strong block in erythroid differentiation and disrupted the developmentally regulated exon skipping of Ndel1 mRNA, which is bound by MBNL1 and critical for erythroid terminal proliferation. These findings reveal an unanticipated scope of the alternative splicing program and the importance of Mbnl1 during erythroid terminal differentiation. (Blood. 2014;124(4):598-610)
IntroductionTerminal erythroid differentiation is characterized by 4 to 5 terminal cell divisions accompanied by hemoglobinization, a decrease in cell size, chromatin condensation, and finally expulsion of the nucleus and other organelles. Previous studies have primarily focused on the roles of intracellular signal transduction proteins, transcription factors, and chromatin modifiers in erythropoiesis.1,2The roles of alternative mRNA isoforms and associated regulatory factors in terminal erythroid differentiation are not well established, but an understanding of these could shed light on erythroid developmental biology. [3][4][5] Differential joining of exons in mRNAs via alternative splicing can substantially alter the functions of the corresponding encoded proteins. 6 One classical example of regulated pre-mRNA splicing during erythroid development is the splicing switch of exon 16 in the mRNA encoding the cytoskeletal protein 4.1R (band 4.1). The inclusion of exon 16 in late erythroblasts enhances the affinity of 4.1R protein for spectrin and actin, thereby stabilizing the erythroid membrane under mechanical stress. [7][8][9] It is likely that there are other stage-specific splicing changes crucial for modifying protein functions in erythropoiesis. Previous studies used exon microarrays to identify a handful of novel splicing events and alternative choices of first exons in human erythroid cells, but the scope of analysis was limited by the availability of probes.10 Recent genome-wide analyses of alternative isoform gene expression using RNA-seq have revealed large-scale splicing differences between mammalian tissues, cell, and disease states, [11][12][13] but similar comprehensive studies have not been performed in the context of erythroid differentiation.The Muscleblind-like (MBNL) family of sequence-specific premRNA splicing factors bind RNA through pairs of highly conserved zinc fingers, recognizing YGCY (where Y 5 C or U) and similar motifs.14-18 MBNL proteins are predominantly expressed in skeletal muscle, neuronal tissu...