Nucleic Acids Research Advance Access originally published online on February 23, 2009
Nucleic Acids Research 2009 37(7):2274-2282; doi:10.1093/nar/gkp088
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Nucleic Acids Research, 2009, Vol. 37, No. 7 2274-2282
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues
1RNA Biology Group and Epithelial Research Group, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle NE2 4HH and 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
*To whom correspondence should be addressed. Tel: +44 191 222 6990; Fax: +44 191 222 7424; Email: andreas.werner{at}ncl.ac.uk
Received November 3, 2008. Revised January 23, 2009. Accepted February 3, 2009.
Natural antisense transcripts (NATs) are important regulators of gene expression. Recently, a link between antisense transcription and the formation of endo-siRNAs has emerged. We investigated the bi-directionally transcribed Na/phosphate cotransporter gene (Slc34a1) under the aspect of endo-siRNA processing. Mouse Slc34a1 produces an antisense transcript that represents an alternative splice product of the Pfn3 gene located downstream of Slc34a1. The antisense transcript is prominently found in testis and in kidney. Co-expression of in vitro synthesized sense/antisense transcripts in Xenopus oocytes indicated processing of the overlapping transcripts into endo-siRNAs in the nucleus. Truncation experiments revealed that an overlap of at least 29 base-pairs is required to induce processing. We detected endo-siRNAs in mouse tissues that co express Slc34a1 sense/antisense transcripts by northern blotting. The orientation of endo-siRNAs was tissue specific in mouse kidney and testis. In kidney where the Na/phosphate cotransporter fulfils its physiological function endo-siRNAs complementary to the NAT were detected, in testis both orientations were found. Considering the wide spread expression of NATs and the gene silencing potential of endo-siRNAs we hypothesized a genome-wide link between antisense transcription and monoallelic expression. Significant correlation between random imprinting and antisense transcription could indeed be established. Our findings suggest a novel, more general role for NATs in gene regulation.