Genomic analysis has revealed the existence of a large number of long noncoding RNAs (lncRNAs) with different functions in a variety of organisms, including yeast. Cells display dramatic changes of gene expression upon environmental changes. Upon osmostress, hundreds of stress-responsive genes are induced by the stress-activated protein kinase (SAPK) p38/Hog1. Using whole-genome tiling arrays, we found that Hog1 induces a set of lncRNAs upon stress. One of the genes expressing a Hog1-dependent lncRNA in antisense orientation is CDC28, the cyclin-dependent kinase 1 (CDK1) that controls the cell cycle in yeast. Cdc28 lncRNA mediates the establishment of gene looping and the relocalization of Hog1 and RSC from the 3′ UTR to the +1 nucleosome to induce CDC28 expression. The increase in the levels of Cdc28 results in cells able to reenter the cell cycle more efficiently after stress. This may represent a general mechanism to prime expression of genes needed after stresses are alleviated.

This work was supported by grants from the Spanish Ministry of Economy and Competitiveness (BFU2012-33503 and FEDER to F.P., BFU2011-26722 to E.d.N.), the Fundación Marcelino Botín (FMB), and the Consolider Ingenio 2010 programme CSD2007-0015 (to F.P.). This work was supported by the National Institutes of Health and Deutsche Forschungsgemeinschaft (L.M.S.). F.P. and E.d.N. are recipients of an ICREA Acadèmia award (Generalitat de Catalunya).