Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control
RESEARCH ARTICLE Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control Ophir Shalem1,2☯¤a, Eilon Sharon1,2☯¤b, Shai Lubliner1,2, Ifat Regev1,2, Maya Lotan- Pompan1,2, Zohar Yakhini3,4, Eran Segal1,2* 1 Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel, 2 Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel, 3 Department of Computer Science, Technion, Haifa, Israel, 4 Agilent Laboratories, Tel Aviv, Israel ☯ These authors contributed equally to this work. ¤a Current address: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America ¤b Current address: Department of Genetics, Stanford University, Stanford, California, United States of America * Eran.Segal@weizmann.ac.il Abstract OPEN ACCESS Citation: Shalem O, Sharon E, Lubliner S, Regev I, The 3’end genomic region encodes a wide range of regulatory process including mRNA sta- Lotan-Pompan M, Yakhini Z, et al. (2015) Systematic bility, 3’ end processing and translation. Here, we systematically investigate the sequence ’ Dissection of the Sequence Determinants of Gene 3 determinants of 3’ end mediated expression control by measuring the effect of 13,000 de- End Mediated Expression Control. PLoS Genet 11(4): ’ e1005147. doi:10.1371/journal.pgen.1005147 signed 3 end sequence variants on constitutive expression levels in yeast. By including a high resolution scanning mutagenesis of more than 200 native 3’ end sequences in this de- Editor: Hiten D. Madhani, University of California San Francisco, UNITED STATES signed set, we found that most mutations had only a mild effect on expression, and that the vast majority (~90%) of strongly effecting mutations localized to a single positive TA-rich el- Received: June 4, 2014 ement, similar to a previously described 3’ end processing efficiency element, and resulted Accepted: March 17, 2015 in up to ten-fold decrease in expression.
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