Held Jointly with the
2004 SIAM Annual Meeting

Oregon Convention Center
Portland, Oregon

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Comparative Gene Structure and Gene Expression: Lessons from the Arabidopsis Genome

Terry Gaasterland, Rockefeller University

Several recent surveys of gene expression indicate that genome transcription activity extends well beyond mRNA, tRNA and rRNA gene expression. Large scale studies that completely tiled human chromosomes 21 and 22 onto 2-color or 1-color microarrays and hybridized with total RNA found considerable transcriptional activity in intergenic, intronic, and UTR antisense regions (Rinn et al 2003; Kapranov et al 2002). Studies that used chromatin immuno-precipitation to isolate DNA bound to selected transcription factors followed by hybridization on DNA microarrays (ChIP-chip studies) have found unexpected binding events in regions annotated as intergenic (Euskirchen et al 2004; Martone 2003; Kampa et al 2004; Cawley et al 2004). In contrast, ChIP-chip studies of POL-II binding sites have tended to identify primarily previously annotated coding regions (Ren & Dynlacht 2004). Other data sources include SAGE-like surveys of gene expression using the Massively Parallel Signature Sequence (MPSS) technology, which invariably yield substantial evidence for transcription outside of previously annotated genes as well as quantitative gene expression levels for annotated genes.

Some of the additional transcription is explained by the presence of small non-coding RNA genes in intergenic regions. In the case of microRNAs, transcripts from these ~150-350 nucleotide (nt) genes fold into secondary structures with long, imperfect hairpins that are processed by a protein complex that recognizes and cleaves double-stranded RNA to release short ~19-23 nt single-stranded RNA molecules. These microRNAs are complementary to mRNA transcripts and suppress protein expression by repressing translation or by triggering mRNA degradation. In plants, microRNAs tend to bind within coding regions; in animals, they bind to the 3'UTR.

This talk presents observations about control of gene and protein expression in Arabidopsis thaliana based on the following data sources: tissue specific MPSS data and Affymetrix gene expression data on stress response, genome-wide prediction of binding site clusters for known transcription factors, evaluation of alternative splicing evident in cDNA and EST sequences, and microRNA identification and mRNA target prediction (Hoth et al 2003). These data have all been combined to yield a model of microRNA regulation of gene and protein expression in plants.

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2. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. Large-scale transcriptional activity in chromosomes 21 and 22. Science. 2002 296(5569):916-9.
3. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB Binds to Multiple Loci on Human Chromosome 22. Mol Cell Biol. 2004 24(9):3804-14.
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6. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004 116(4):499-509.
7. Ren B, Dynlacht BD. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol. 2004;376:304-15.
8. Hoth S, Ikeda Y, Morgante M, Wang X, Zuo J, Hanafey MK, Gaasterland T, Tingey SV, Chua NH. Monitoring genome-wide changes in gene expression in response to endogenous cytokinin reveals targets in Arabidopsis thaliana. FEBS Lett. 2003 554(3):373-80.


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