"mRNA Imprinting": Regulation of Gene Expression by Co-transcriptionally Associating Proteins

The coordination between stages of the RNA life-cycle is important for proper gene expression. We hypothesized that the decision making process of whether to express a gene (or a gene family) and the extent of its expression involves communication between all stages. Moreover, we found that the fate of a certain mRNA is already determined during transcription, even before its synthesis is completed. We surmise that co-transcriptional binding of factors, "mRNA imprinting", affects the fate of many mRNAs.

We have ascertained a broad scope of over 50 proteins that associate with the mRNA during transcription. Amongst these proteins are a number of splicing factors, capping and polyadenylation factors and factors know to mediate mRNA export. Additionally, some of these proteins are known to associate with mature, cytoplasmic mRNA. Interactions of some proteins change under different conditions or stresses, such as heat shock and starvation. In response to stress, several chaperones bind mRNAs during transcription. This attachment to nascent mRNA may play a role in the heat shock response. Hence, mRNA imprinting is a widespread phenomenon whose functions may extend beyond the realm of transcription.