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Nucleic Acids Research, 2002, Vol. 30, No. 24 5529-5538
© 2002 Oxford University Press

Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes

Arvind Raghavan1, Rachel L. Ogilvie1, Cavan Reilly2, Michelle L. Abelson1, Shalini Raghavan1, Jayprakash Vasdewani1, Mitchell Krathwohl3 and Paul R. Bohjanen*,1,3,4

1 Department of Microbiology, 2 Division of Biostatistics, School of Public Health, 3 Department of Medicine, Division of Infectious Diseases and 4 Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA

*To whom correspondence should be addressed at Department of Microbiology, University of Minnesota, 420 Delaware Street, SE, MMC 196, Minneapolis, MN 55455, USA. Tel: +1 612 625 7679; Fax: +1 612 626 0623; Email: bohjanen{at}mail.ahc.umn.edu

We used microarray technology to measure mRNA decay rates in resting and activated T lymphocytes in order to better understand the role of mRNA decay in regulating gene expression. Purified human T lymphocytes were stimulated for 3 h with medium alone, with an anti-CD3 antibody, or with a combination of anti-CD3 and anti-CD28 antibodies. Actinomycin D was added to arrest transcription, and total cellular RNA was collected at discrete time points over a 2 h period. RNA from each point was analyzed using Affymetrix oligonucleotide arrays and a first order decay model was used to determine the half-lives of approximately 6000 expressed transcripts. We identified hundreds of short-lived transcripts encoding important regulatory proteins including cytokines, cell surface receptors, signal transduction regulators, transcription factors, cell cycle regulators and regulators of apoptosis. Approximately 100 of these short-lived transcripts contained ARE-like sequences. We also identified numerous transcripts that exhibited stimulus-dependent changes in mRNA decay. In particular, we identified hundreds of transcripts whose steady-state levels were repressed following T cell activation and were either unstable in the resting state or destabilized following cellular activation. Thus, rapid mRNA degradation appears to be an important mechanism for turning gene expression off in an activation-dependent manner.


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