Cytoplasmic 5′-3′ exonuclease Xrn1p is also a genome-wide transcription factor in yeast

The 5′ to 3′ exoribonuclease Xrn1 is a large protein involved in cytoplasmatic mRNA degradation as a critical component of the major decaysome. Its deletion in the yeast Saccharomyces cerevisiae is not lethal, but it has multiple physiological effects. In a previous study, our group showed that deletion of all tested components of the yeast major decaysome, including XRN1, results in a decrease in the synthetic rate and an increase in half-life of most mRNAs in a compensatory manner. Furthermore, the same study showed that the all tested decaysome components are also nuclear proteins that bind to the 5′ region of a number of genes. In the present work, we show that disruption of Xrn1 activity preferentially affects both the synthesis and decay of a distinct subpopulation of mRNAs. The most affected mRNAs are the transcripts of the highly transcribed genes, mainly those encoding ribosome biogenesis and translation factors. Previously, we proposed that synthegradases play a key role in regulating both mRNA synthesis and degradation. Evidently, Xrn1 functions as a synthegradase, whose selectivity might help coordinating the expression of the protein synthetic machinery. We propose to name the most affected genes “Xrn1 synthegradon.”
José E. Pérez-Ortín is supported by grants from the Spanish MCINN and the European Union (FEDER) (BFU2010-21975-C03-01), and from the Generalitat Valenciana (PROMETEO 2011/088). Sebastián Chávez is supported by grants from the Spanish MCINN (BFU2010-21975-C03-02) the Regional Andalusian Government (P07-CVI-02623 and P08-CVI-03508), and the European Union (FEDER). Mordechai Choder is supported by the Israel Science Foundation (1283/07), US-Israel Binational Foundation and the Rappaport Foundation. Daniel A. Medina was a recipient of a Santiago Grisolía fellowship from the Generalitat Valenciana.