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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures^1,[w]

Department of Botany, Miami University, Oxford, Ohio 45056 (J.C.L., P.C.W., Q.Q.L.); Ohio Supercomputer Center, Columbus, Ohio 43212 (E.A.S.); Cray, Inc., Brighton, Michigan 48116 (D.G.S.); and The Institute of Genomic Research, Rockville, Maryland 20850 (B.J.H.)

Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3'-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3'-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3'-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3'-ends for gene annotation.

² Present address: Department of Medicine, Mount Sinai School of Medicine, 1425 Madison Ave., New York, NY 10029–6574.

^[w] The online version of this article contains Web-only data.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.060541.

^* Corresponding author; e-mail liq{at}muohio.edu; fax 513–529–4243.

Received January 31, 2005; returned for revision April 29, 2005; accepted May 3, 2005.

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