Cooperation is key – a new way of looking at MicroRNA and how it controls gene expression

A group of scientists at The Scripps Research Institute is reporting a discovery that sheds light on an area of research fundamental to everything from the normal processes that govern the everyday life of human cells to the aberrant mechanisms that underlie many diseases, including cancer and septic shock.

The discovery concerns tiny fragments of RNA known as microRNA and their relationship to the genetic transcripts known as messenger RNA (mRNA). All genes expressed in the human body must be transcribed as mRNA before they can be translated into proteins, and the stability of these mRNA transcripts is essential for control of genetic expression.

In the latest issue of the journal Cell, the Scripps Research team, led by Immunology Professor Jiahuai Han, describes how genetic control can be exerted in living cells through microRNA’s action in conjunction with several different proteins. “Most microRNA probably need the help of these other proteins and other molecules to target mRNA,” says Han. “[This targeting] not only depends on their complementary sequence but on whether these proteins are around to stabilize them.”

Han and his Scripps Research colleagues collaborated with researchers at the Novartis Institutes for Biomedical Research in Basel, Switzerland, and at the Hong Kong University of Science & Technology in Hong Kong, China for this study.

Stability is the Key to Control

Ever since biologists first started mapping genetic traits to particular genes, science and society have been fascinated by those tens of thousands of stretches of DNA within the nuclei of cells we call our genes.

One thing that has become clear in the last several decades, however, is that while our genes contribute to human health and disease, it is not always the genes themselves that matter, but rather how the genes are controlled that makes a difference. The regulation of gene expression is one of the most fundamental tasks of every cell in the body because many of our genes encode proteins that may only be needed occasionally. Indeed, having some of these proteins around when they are not needed can create any number of problems for an organism, and failing to properly control gene expression can be fatal. Indeed, aberrant expression of genes is the underlying cause of many different diseases.

For example, the expression of inflammatory cytokine proteins by immune system cells must be finely tuned so that these proteins do not cause more damage to the body than the bacterial infection they were produced to defeat. Excessive inflammation can lead to organ failure and death, and this is exactly what happens when people are stricken with septic shock. Likewise, the loss of control of genetic expression is the underlying cause of various forms of cancer–for instance the overexpression of genes that cause the cell to grow and the suppression of genes that curb cell growth.

Humans and other animals have evolved many overlapping ways of controlling gene expression. Many different controls determine when a DNA gene is transcribed into mRNA, and when and how the mRNA is translated into a protein. Many proteins are also tightly controlled through various post-translational modifications that activate or deactivate them.

Translation is the final step in the expression of every gene, and the cell exercises control over this process in numerous ways, and hence expression of a gene. One way to exert this control is ensuring that mRNAs that are not needed are destroyed. One of the ways that nature has evolved for destroying certain mRNAs is making them inherently unstable and prone to degradation.

This inherent instability is built into the 3’ tail of the mRNA in the form of noncoding stretches of RNA called AU-rich elements. Lots of genes, including inflammatory cytokines and cancer-causing oncogenes, have these AU-rich elements built in.

AU-rich element degradation involves a number of different proteins, including proteins that bind to the AU regions of the mRNA. These binding events may play a role in the stability and degradation of the mRNA. Despite much research over the last few years into exactly how this works, the question had not been answered.

“So far, it has not really been clear what the mechanism is,” says Han.

Now, Han and his colleagues are reporting in their Cell paper that the degradation mechanism involves tiny pieces of RNA known as microRNA. These microRNAs, which are generally only 17 or 20 nucleotides, were first identified about 20 years ago, and in the past few years scientists have realized that microRNA is a new category of regulatory molecules and identified hundreds of different microRNA in mammals.

The big question was, what are they doing? About a dozen years ago a few studies came out that showed that microRNA could suppress translation in certain Drosophila (fruit fly) genes if those genes contained sequences complementary to the microRNA’s sequence. But finding the targets of these microRNA proved difficult, and by the turn off the century, only a few had been identified.

When the human genome was solved and published in 2001, many scientists thought that the task of finding the mRNA to which the microRNA bound would be relatively straightforward. After all, a short stretch of nucleotides like a microRNA should be expected to bind to a piece of RNA of equal length and complementary sequence. And since these sequences of the microRNA were known, a computer search through the three billion letters of the human genome should find those matching sequences.

But this didn’t work. The homology searches yielded far fewer targets than expected and could not account for all known microRNAs. The reason, says Han, is that scientists were trying to predict the microRNA targets using the sequence homology of the full-length microRNAs.

In their Cell article, Han and his colleagues show that you don’t need the full-length complementary microRNA at all. They observed that microRNA was involved in the degradation of genes with AU rich elements, and that the microRNA used only eight bases to target the mRNA. Given that microRNAs have such a short targeting sequence, they may have broad targeting ability, says Han.

Significantly, the researchers found that for the AU-rich element degradation to work, the mRNA had to interact with multiple RNA binding proteins as well as microRNA. This suggests that the RNA binding proteins are there to facilitate the degradation and that microRNA is required as well. They believe that the microRNA and protein form a large complex of molecules, though they do not know exactly how many proteins and other molecules are involved.

The article, “Involvement of MicroRNA in AU-Rich Element-Mediated mRNA Instability” by Qing Jing, Shuang Huang, Sabine Guth, Tyler Zarubin, Andrea Motoyama, Jianming Chen, Franco Di Padova, Sheng-Cai Lin, Hermann Gram, and Jiahuai Han and appears in the March 11, 2005 issue of the journal Cell (120, 1-12).