Analyzing the effects of Cis-elements and trans-factors on the stability of the Gal1 mRNP

Abstract

The highly dynamic and nonrandom spatial organization of the eukaryotic nucleus plays an important role in the regulation of gene expression. For example, in S. cerevisiae, several conditionally expressed genes relocate to the nuclear periphery upon activation. Moreover, these genes can be retained at the nuclear periphery for a considerable time after transcriptional shutoff. Sequence specific DNA binding proteins, transcription, chromatin remodeling, and mRNP quality control factors have all been implicated in perinuclear gene repositioning, but their relative contributions to the events of gene recruitment, capture and retention at the periphery remain unresolved. Sus1 is a conserved eukaryotic protein involved in transcription, mRNA export and perinuclear gene repositioning. Here, we show that the functions of Sus1p in perinuclear repositioning of GAL genes and its chromatin-linked functions can be genetically uncoupled, and that the role of Sus1p in the retention of mRNA in gene-proximal foci is chromatin-independent. Histone variant H2A.Z, likewise has been suggested to play a role in the post-transcriptional association of the yeast genes with the nuclear periphery. Our findings indicate that the loss of H2A.Z doesn’t alter gene-proximal mRNA retention, but has a differential effect on perinuclear repositioning of GAL genes. H2A.Z affects recruitment of GAL1 promoter-driven genes to the nuclear periphery in a 3’UTR-dependent manner, but its effect on posttranscriptional retention of GAL1 genes at the nuclear periphery is locus specific. Our previous analysis has also shown that the retention of RNA at the site of transcription is dependent on 3’end of the Gal1. Our results indicate that the absence of AU-rich element (ARE) sequence in Gal1 3’UTR may be one of the factor leading to Gal1 mRNP formation at the transcription site. Moreover, our data shows that by introducing the ARE sequence (TATTTAT), between the two cleavage sites of Gal1 3’UTR, it not only reduces the number of cells that for Gal1 mRNP but also abolishes the synthesis of extended transcript at Gal1 locus.