Differential mRNA Processing in Hematopoietic Stem Cells

Teresa V. Bowman^a^,b, Andrew J. McCooey^a, Akil A. Merchant^a^,c, Carlos A. Ramos^a^,c, Patricia Fonseca^d, Alan Poindexter^e, Steven B. Bradfute^a^,f, Daniela M. Oliveira^a, Rahshaana Green^a, Yayun Zheng^a, Kathyjo A. Jackson^a^,g, Stuart M. Chambers^a^,b, Shannon L. McKinney-Freeman^a^,f, Kevin G. Norwood^a, Gretchen Darlington^d^,h, Preethi H. Gunaratne^d^,i, David Steffen^d^,e^,i, Margaret A. Goodell^a^,b^,d^,f^,g

^a Cell and Gene Therapy Center,
^b Cell and Molecular Biology Program,
^c Departments of Medicine and
^d Molecular and Human Genetics,
^e Bioinformatics Research Center,
^f Departments of Immunology,
^g Pediatrics, and
^h Molecular and
ⁱ Cellular Biology, Baylor Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA

Key Words. RNA processing • Hematopoietic stem cells • cDNA library • Stem cell activation

Correspondence: Margaret A. Goodell, Ph.D., Center for Cell and Gene Therapy, Baylor College of Medicine, N1030, One Baylor Plaza, Houston, Texas 77030, USA. Telephone: 713-798-1265; Fax: 713-798-1230; e-mail: goodell{at}bcm.tmc.edu

Received November 8, 2005; accepted for publication December 14, 2005.
Hematopoietic stem cells (HSCs) maintain tissue homeostasisby rapidly responding to environmental changes. Although thisfunction is well understood, the molecular mechanisms governingthis characteristic are largely unknown. We used a sequenced-basedstrategy to explore the role of both transcriptional and post-transcriptionalregulation in HSC biology. We characterized the gene expressiondifferences between HSCs, both quiescent and proliferating,and their differentiated progeny. This analysis revealed a largefraction of sequence tags aligned to intronic sequences, whichwe showed were derived from unspliced transcripts. A comparisonof the biological properties of the observed spliced versusunspliced transcripts in HSCs showed that the unspliced transcriptswere enriched in genes involved in DNA binding and RNA processing.In addition, levels of unspliced message decreased in a transcript-specificfashion after HSC activation in vivo. This change in unsplicedtranscript level coordinated with increases in gene expressionof splicing machinery components. Combined, these results suggestthat post-transcriptional regulation is important in HSC activationin vivo.