Differential mRNA Processing in Hematopoietic Stem Cells

¹ Cell and Gene Therapy Center, Cell and Molecular Biology Program, Baylor College of Medicine, Houston, Texas
² Cell and Gene Therapy Center, Baylor College of Medicine, Houston, Texas
³ Cell and Gene Therapy Center, Department of Medicine, Baylor College of Medicine, Houston, Texas
⁴ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
⁵ Bioinformatics Research Center, Baylor College of Medicine, Houston, Texas
⁶ Cell and Gene Therapy Center, Department of Immunology, Baylor College of Medicine, Houston, Texas
⁷ Cell and Gene Therapy Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
⁸ Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
⁹ Department of Molecular and Human Genetics, Baylor Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
¹⁰ Department of Molecular and Human Genetics, Bioinformatics Research Center, Baylor Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
¹¹ Cell and Gene Therapy Center, Cell and Molecular Biology Program, Department of Molecular and Human Genetics, Department of Immunology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas

^* To whom correspondence should be addressed. E-mail: goodell{at}bcm.tmc.edu.

	Abstract

Hematopoietic stem cells (HSCs) maintain tissue homeostasis by rapidly responding to environmental changes. Although this function is well understood, the molecular mechanisms governing this characteristic are largely unknown. We utilized a sequenced-based strategy to explore the role of both transcriptional and post-transcriptional regulation in HSC biology. We characterized the gene expression differences between HSCs, both quiescent and proliferating, and their differentiated progeny. This analysis revealed a large fraction of sequence tags aligned to intronic sequences, which we showed were derived from unspliced transcripts. A comparison of the biological properties of the observed spliced versus unspliced transcripts in HSCs showed that the unspliced transcripts were enriched in genes involved in DNA binding and RNA processing. Additionally, levels of unspliced message decreased in a transcript-specific fashion following HSC activation in vivo. This change in unspliced transcript level coordinated with increases in gene expression of splicing machinery components. Combined, these results suggest post-transcriptional regulation is important in HSC activation in vivo.