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Poster number 36 submitted by Daniel Coughlin

Prediction and Detection of Mouse tRNA Genes

Daniel J Coughlin (Department of Biological Chemistry, University of Michigan), Thomas Babak (Banting & Best Department of Medical Research, University of Toronto), Tim Hughes (Banting & Best Department of Medical Research, University of Toronto), David R Engelke (Department of Biological Chemistry, University of Michigan)

Abstract:
tRNA biogenesis has been thoroughly studied in bacteria andyeast, including transcription, maturation, and amino-acylation. Additionally important, tRNA genes themselves have been implicated in silencing of neighboring genes as well as being anchor points important in nuclear organization. In higher eukaryotes there is little known about how many tRNA genes are present, their expression, and what effect this has on local transcription and genomic organization. The primary focus of our research is the determination and verification of tRNA genes in the mouse genome.

We scanned the May 2004 Mus musculus genome with two tRNA detection programs, Aragorn (1) and tRNAscan-SE (2), that identify genomic sequences consistent with the conserved sequences and secondary structure of tRNAs. tRNAscan-SE searches for base pairing of clover leaf stems, poly-T RNA polymerase III (polIII) termination sequence, and A and B boxes which are polIII transcription factor recognition sites. Aragorn analyzes predicted secondary structure for tRNA homologies.

In order to verify the predictions, microarray chips were designed with multiple probes tiling each of the ~1,800 predicted tRNA genes. Fluorescently labeled RNA, from different mouse tissue and developmental stages, was used to probe the microarray. Over 500 of the predicted tRNAs were detected on the microarray. Confirmation of expression by Northern blot, comparative analysis of the different tRNA scanning programs, and analysis of the detected tRNAs will be presented.

References:
(1) Laslett, D. and B. Canback. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11-16.
(2) Lowe, T.M. and S.R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.

Keywords: tRNA, Mouse, bioinformatics