The budding yeast, Saccharomyces cerevisiae, has been widely used as a model organism to study the molecular mechanisms that regulate gene expression in eukaryotic cells. In the yeast Cell Wall Integrity Pathway (CWI), the protein Kinase C, Pkc1, activates the MAP Kinase Slt2, which in turn targets the transcription factors Rlm1 and SBF (Swi4-Swi6) and the transcriptional complex Paf1C, to modulate and control the expression of cell wall integrity genes. To better describe the connection between the CWI components and the transcriptional regulation of the cell integrity genes, a series of Chromatin Immunoprecipitation (ChIP) assays were performed. Our results reveal that the MAPK Slt2, associates to the promoter of several cell wall housekeeping genes like FKS1, MNN1 and GAS1. The expression of these genes is reduced in slt2 and pkc1 mutant strains. However, neither the recruitment of the transcription factors Rlm1 and Swi6 to the promoter, nor the binding of the RNApol II or Paf1 to the initiation site is affected. When the association to the 3´ end of FKS1, MNN1 and GAS1 was analyzed, the RNApol II occupancy is not altered but, remarkably, the Paf1 association is importantly reduced in slt2 and pkc1 mutant strains. This result suggests that Slt2 is required for a stable association of Paf1C to the RNApol II along the cell wall genes and that in its absence, Paf1 dissociates from RNApol II causing a defect in RNA 3' end formation, which in turn leads to a reduced mRNA levels.