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Genome annotation by high-throughput 5' RNA end determination

Hwang, Byung Joon and Müller, Hans-Michael and Sternberg, Paul W. (2004) Genome annotation by high-throughput 5' RNA end determination. Proceedings of the National Academy of Sciences of the United States of America, 101 (6). pp. 1650-1655. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:HWApnas04b

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Abstract

Complete gene identification and annotation, including alternative transcripts, remains a challenge in understanding genome organization. Such annotation can be achieved by a combination of computational analysis and experimental confirmation. Here, we describe a high-throughput technique, trans-spliced exon coupled RNA end determination (TEC-RED), that identifies 5' ends of expressed genes in nematodes. TEC-RED can distinguish coding regions from regulatory regions and identify genes as well as their alternative transcripts that have different 5' ends. Application of TEC-RED to approximate to 10% of the Caenorhabditis elegans genome yielded tags 75% of which experimentally verified predicted 5'-RNA ends and 25% of which provided previously unknown information about 5'-RNA ends, including the identification of 99 previously unknown genes and 32 previously unknown operons. This technique will be applicable in any organisms that have a trans-splicing reaction from spliced leader RNA. We also describe an efficient sequential method for concatenating short sequence tags for any serial analysis of gene expression-like techniques.


Item Type:Article
Additional Information:Copyright © 2004 by the National Academy of Sciences. Communicated by Philip P. Green, University of Washington School of Medicine, Seattle, WA, December 16, 2003 (received for review November 20, 2003). Published online before print February 2, 2004, 10.1073/pnas.0308384100 We thank S. Gharib for DNA preparation, T. Blumenthal for discussions about operons, and C. Bastiani, T. Blumenthal, Y. Kee, E. Schwarz, and S. Vernooy for careful reading of the manuscript. This work was supported by the Howard Hughes Medical Institute, with which P.W.S. is an Investigator and B.J.H. and H.-M.M. were Associates, by a W. M. Keck Foundation/California Institute of Technology discovery award (to B.J.H. and P.W.S.), and by National Human Genome Research Institute/National Institutes of Health Genome Scholar and Faculty Transition Award K22HG02907-01 (to B.J.H.).
Subject Keywords:pre-messenger-RNA, C-elegans, spliced leader, gene, expression, sequences, operons, sage
Record Number:CaltechAUTHORS:HWApnas04b
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:HWApnas04b
Alternative URL:http://dx.doi.org/10.1073/pnas.0308384100
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1337
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:11 Jan 2006
Last Modified:26 Dec 2012 08:43

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