Lopsided mRNA Expression of Fine Tuning of Protein Production

    Messenger RNA (mRNA) has long been thought of as the middleman in the central dogma of molecular biology (DNA makes RNA and then RNA makes protein), which shuttles genetic information from DNA in the nucleus into the cytoplasm for translation into protein. But new research at The Rockefeller University suggests the molecule is up to something unexpected.

    By uncovering widespread disparities in the expression of components of mRNA molecules–something assumed not to occur–the scientists say they have found intriguing expression patterns that suggest unexpected functions for certain regions within mRNA molecules.

    “The lopsided ratios we found in the expression of two parts of the mRNA, one that carries the code for a protein and one that does not, do not appear to occur randomly,” explained senior author Mary Hynes, Ph.D., research associate professor in the laboratory of neural specification and development at Rockefeller University. “We suspect some of these skewed ratios may act as a mechanism for regulating protein production, particularly during embryonic development but also in the adult.”

    The findings from this study were published recently in Neuron through an article entitled “Widespread Differential Expression of Coding Region and 3′ UTR Sequences in Neurons and Other Tissues.”

    A typical mRNA molecule contains a protein-coding sequence (CDS) that is flanked by two noncoding regions—3′ and 5′ untranslated regions (UTRs). The UTRs have been found to be involved in regulating gene expression, as many have binding sites for regulatory proteins and microRNA’s. It has long been assumed by scientists that the CDS and UTRs move together as a single mRNA molecule.

    Using a technique called translating ribosome affinity purification (TRAP), the researchers isolated purified mRNA from dopamine neurons of embryonic mice. When they viewed the expression patterns for the isolated mRNA, to their surprise they observed that some genes in dopamine neurons showed abundant expression of 3′ UTR mRNA sequences and little to no expression of the CDS for these mRNAs. For example, two genes in the Sox family, Sox11, and Sox12, which are known to help determine the fate of cells during development, followed this unusual expression pattern.

    This contradicts the common thinking that once an mRNA is transcribed from a gene, the 5′ and 3′ UTRs and the CDS act as a unit until protein is produced and the mRNA is degraded.

    In order to verify their findings and observe if this phenomenon was restricted to dopamine neurons, development, or the nervous system, the team used green probes to mark coding sequences and red to mark the 3′ UTRs of 19 genes in embryonic and adult tissue.

    “Based on prior understanding, it was expected that every cell in the tissue should show up as either yellow, when both are expressed, or black, when neither are,” Dr. Hynes noted. “But to our surprise, when we examined Sox11 mRNA in the brain we found many neurons that were red, or expressing mostly UTR, as well as many that were green, or expressing mostly coding sequences.”

    The Rockefeller researchers went on to show that this pattern was true for every gene they examined and that differential expression of UTR and coding sequences occurs in the embryo, in the adult, and outside of the nervous system. Even widely expressed genes such as β-actin, a structural protein essential for cell movement, showed differences in UTR and CDS expression.

    Interestingly, when the researchers focused specifically on developing dopamine neurons, they found that many of the genes with high UTR-to-CDS ratios turned out to play roles specifically in development while the genes with comparable ratios were more often involved in generic cellular processes.

    “During development, a neuron may need to express a certain gene, but only a particular amount of it,” remarked Dr. Hynes. “Either too much or too little might be harmful and lead to irreversible fate changes. So, we think this could be a mechanism for finely titrating the proteins levels from an active gene.”

    Dr. Hynes concluded that “going forward, I think that when an RNA sequencing experiment suggests that a gene is highly expressed, researchers will want to take a closer look at the relative levels of these two components to get a more accurate picture of what is being expressed.”