Systematic discovery of the grammar of translational inhibition by RNA hairpins.pdfVIP

1 Systematic discovery of the grammar of translational inhibition by RNA hairpins Clark Jeffries1*, Diana O. Perkins2, Michael Jarstfer3 1Renaissance Computing Institute and School of Pharmacy, Campus Box 7360, University of North Carolina at Chapel Hill, Chapel Hill NC 27599-7360 USA Email: clark_jeffries@ , FAX 919-843-7624, TEL 919-260-6576 2 Department of Psychiatry, University of North Carolina at Chapel Hill, USA Email: diana_perkins@ 3 School of Pharmacy, University of North Carolina at Chapel Hill, USA Email: jarstfer@ * Corresponding author _________________________________________________________________ Research supported by: (Jeffries) 5-P20-RR020751-01-02 from the National Institutes of Health/National Center for Research Resources; (Perkins) USP#SMH01905-01 North Carolina Foundation of Hope, Anonymous donor administered through the San Francisco Foundation; (Jarstfer) Elsa U. Pardee Foundation and NSF MCB 0446019. The contents of this paper are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health/National Center for Research Resources or the other supporting Foundations. 2 Introduction This paper addresses the problem of discovering from databases the organizational principles of regulation of gene expression. Text-based searches for gene relationships inherently must be artificially terminated. By contrast, we present a hybrid algorithm of text and biochemical alignment searches that inherently terminates. The product of the algorithm is a gene organization hypothesis. The hybrid search works, we assert, because some genes are not just selfish (seeking above all else their own survival and proliferation in future generations); they are also devious in the sense that their transcription byproducts automatically inhibit translation of other genes with counteracting functions (so they quietly undermi