Genome-wide analysis of RNA–protein interactions illustrates specificity of the mRNA export machinery

Nuclear export of mRNA is mediated by a complex machinery of RNA-binding proteins that recognizes and routes mRNAs through a messenger ribonucleoprotein (mRNP) network. The full spectrum of mRNA cargoes for any dedicated mRNA export factor is unknown. We identified the mRNAs that bind two conserved yeast mRNA export factors, Yra1 (refs. 1–5) and Mex67 (refs. 6,7), on a genome-wide scale and determined their level of binding. Yra1 and Mex67 bind approximately 1,000 and 1,150 mRNAs, respectively, corresponding to almost 20% of the yeast genome and roughly 36% of all transcriptional events each. The binding level of Yra1 targets is related to their transcriptional frequency, but that of Mex67 targets is not. Yra1-bound transcripts are enriched in mRNAs that are regulated by a number of transcription factors. Yra1- and Mex67-bound populations also show enrichment of mRNAs encoding distinct functional classes of proteins, some of which are regulated by these transcription factors. We determined that one such transcription factor, Abf1 (refs. 8–10), associates with Yra1. These results indicate a previously unidentified specificity of mRNA export factors, which coordinates the export of transcriptionally co-regulated, functional classes of transcripts, perhaps through interactions with the transcriptional machinery.