A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis.
Alternative pre-messenger RNA splicing remodels the human transcriptome in a spatiotemporal manner during normal development and differentiation. Here we explored the landscape of transcript diversity in the erythroid lineage by RNA-seq analysis of five highly purified populations of morphologically distinct human erythroblasts, representing the last four cell divisions before enucleation. In this unique differentiation system, we found evidence of an extensive and dynamic alternative splicing program encompassing genes with many diverse functions. Alternative splicing was particularly enriched in genes controlling cell cycle, organelle organization, chromatin function and RNA processing. Many alternative exons exhibited differentiation-associated switches in splicing efficiency, mostly in late-stage polychromatophilic and orthochromatophilic erythroblasts, in concert with extensive cellular remodeling that precedes enucleation. A subset of alternative splicing switches introduces premature translation termination codons into selected transcripts in a differentiation stage-specific manner, supporting the hypothesis that alternative splicing-coupled nonsense-mediated decay contributes to regulation of erythroid-expressed genes as a novel part of the overall differentiation program. We conclude that a highly dynamic alternative splicing program in terminally differentiating erythroblasts plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells.
Department of Computer Science, University of California, Berkeley, CA 94720, USA, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Red Cell Physiology Laboratory, New York Blood Center, New York, NY 10065, USA, Department of Mathematics, University of California, Berkeley, CA 94720, USA and Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA.
Harold
H
Pimentel
Marilyn
M
Parra
Sherry
S
Gee
Dana
D
Ghanem
Xiuli
X
An
Jie
J
Li
Narla
N
Mohandas
Lior
L
Pachter
John G
JG
Conboy
D017398:Alternative Splicing; D002478:Cells, Cultured; D004900:Erythroblasts / Q000378:metabolism; D041905:Erythroid Cells / Q000166:cytology / Q000378:metabolism; D004920:Erythropoiesis / Q000235:genetics*; D006801:Humans; D059365:Nonsense Mediated mRNA Decay; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
D016601:RNA-Binding Proteins