The transcription factor Sfp1 imprints specific classes of mRNAs and links their synthesis and cytoplasmic decay

To function as a system, transcription and post-transcriptional stages must communicate - the underlying mechanism of which is still little studied. Here we focus on S. cerevisiae genes, transcription of which is regulated by Sfp1 that binds their promoters. We show that Sfp1 also binds downstream chromatin regions, thereby changing Pol II configuration, resulting in enhanced Pol II backtracking and possibly Rpb4 dissociation. Unexpectedly, this transcription factor binds >264 transcripts of these genes - near their 3’ ends – and regulates their deadenylation and stability. The interaction of Sfp1 with these mRNAs is controlled by the promoter and it occurs concomitantly with its dissociation from the chromatin. Collectively, we propose that Sfp1 accompanies Pol II and binds the RNA co-transcriptionally. It then accompanies these mRNAs to the cytoplasm and regulates their stability. Thus, Sfp1 co-transcriptional binding imprints the mRNA fate and serves as a paradigm for posttranscriptional regulation of specific mRNAs by the transcription apparatus. UV Cross-linking and cDNA analyses of N-termally HTP tagged Sfp1 in the presence or absence of Rbp4. Independent replicate experiments were performed with each strain.