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Nucleic Acids Research 2005 33(17):e148; doi:10.1093/nar/gni149
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Published online 4 October 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Isolation of mRNA from specific tissues of Drosophila by mRNA tagging

Zhiyong Yang1, Howard J. Edenberg2 and Ronald L. Davis1,3,*

1Department of Molecular and Cellular Biology, Baylor College of Medicine Houston, TX 77030, USA 2Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine Houston, TX 77030, USA 3Center for Medical Genomics, Indiana University School of Medicine Indianapolis, IN 46202, USA

*To whom correspondence should be addressed. Tel: +1 713 798 6641; Fax: +1 713 798 8005; Email: rdavis{at}bcm.tmc.edu

Received February 1, 2005. Revised April 6, 2005. Accepted September 18, 2005.

To study the function of specific cells or tissues using genomic tools like microarray analyses, it is highly desirable to obtain mRNA from a homogeneous source. However, this is particularly challenging for small organisms, like Caenorhabditis elegans and Drosophila melanogaster. We have optimized and applied a new technique, mRNA tagging, to isolate mRNA from specific tissues of D.melanogaster. A FLAG-tagged poly(A)-binding protein (PABP) is expressed in a specific tissue and mRNA from that tissue is thus tagged by the recombinant PABP and separated from mRNA in other tissues by co-immunoprecipitation with a FLAG-tag specific antibody. The fractionated mRNA is then amplified and used as probe in microarray experiments. As a test system, we employed the procedures to identify genes expressed in Drosophila photoreceptor cells. We found that most known photoreceptor cell-specific mRNAs were identified by mRNA tagging. Furthermore, at least 11 novel genes have been identified as enriched in photoreceptor cells. mRNA tagging is a powerful general method for profiling gene expression in specific tissues and for identifying tissue-specific genes.


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