First discovered a few years ago, microRNAs are short strings of RNA that are made in large amounts in every cell from plant to humans. Biochemists, including co-author Thomas Tuschl, Ph.D., found that microRNAs bind to messenger RNAs, which are the blueprints for proteins, and either target them for destruction or inhibit them from making proteins.
"There was a lot of beautiful biochemistry showing how microRNAs are made and processed," says Gaul, head of the Laboratory for Developmental Neurogenetics. "But we didn't really know how important they are for the development of an organism and its function."
To solve this question, Gaul and colleagues systematically blocked each of the 46 known microRNAs that are active during early development of the fruit fly. This is difficult to do by traditional genetic means, so they inject young fly embryos with short strings of RNA that bind to the microRNAs and prevent them from finding their target messenger RNAs. The researchers found that over half of the microRNAs were not only essential for development, but also affected it in very specific ways.
"Many of the fundamental processes in development are regulated by microRNAs," Gaul says, "including body patterning, morphogenesis, nervous system and muscle development. In particular, though, we found that cell survival relies very heavily on them."
Cell death in development is not uncommon. The developing embryo makes an overabundance of many cell types, like nerve cells, which it then removes later in a process of fine-tuning. In fact, the genes in flies that carry out a cell's death sentence, Hid, Grim and Reaper, are expressed in many healthy cells, poised to do their job at a moment's notice.
Gaul's new research shows that it is microRNAs that stand between a cell's survival and its death at the hands of Hid, Grim and Reaper. The microRNAs bind to the messenger RNA of the death genes and prevent their proteins from being made. But when the microRNAs are blocked, Hid, Grim and Reaper proteins are produced, causing massive cell death and killing the fly embryo.
The microRNAs that block cell death all belong to the largest microRNA family in the fruit fly. The family is made up of 13 members, which are identical in sequence at one end but different at the other. There has been some debate on whether differences at this end are important, but Gaul's research now shows that they are central for helping the microRNAs find the right targets.
"Our findings show that while similar defects are seen when the different family members are blocked, they are not identical," Gaul says. "And we find that different family members interact differently with the three death genes."
Deciding between life and death is only one of many split-second decisions that a cell may have to make. By regulating which messenger RNAs are used to make protein, microRNAs can help cells react to an event without the nucleus being involved. For example, the ending of a nerve cell can be very far away from its nucleus. Localizing and regulating messenger RNAs at the nerve endings enables the nerves to react very fast to an incoming signal, instead of every signal being transmitted to the nucleus and back.
Gaul's lab has many more interesting microRNAs to examine, a number of which are conserved between flies and humans. The next experiments will look to further match up different microRNAs with their targets. But Gaul is also very interested in how microRNAs themselves are regulated.
"We wanted to know if microRNAs were important and if they were specific, and we got those answers - they affect fundamental pathways and have a limited number of critical targets," Gaul says. "Now we want to connect the microRNAs both to their upstream regulation and to their downstream targets to see where they fit in the developmental gene networks."
Dan Leaman, John Fak, Michael Pearce and Ulrich Unnerstall from the Laboratory of Developmental Neurogenetics, and Po Yu Chen and Abdullah Yalcin from Thomas Tuschl's Laboratory of RNA Molecular Biology at Rockefeller University; Debora S. Marks from the Department of Systems Biology at Harvard Medical School in Boston, Massachusetts; and Chris Sander from the Computational Biology Center at Memorial Sloan-Kettering Cancer Center in New York, New York all contributed to this paper. The research was supported by funds from Rockefeller University.
Journal
Cell