Molecule crucial for processing non-coding RNA identified

Long-standing scientific question resolved

The discovery in 1977 that the coding regions of a gene could appear in separate segments along the DNA won the 1993 Nobel Prize in Physiology or Medicine for Richard J. Roberts and Phillip A. Sharp. The active segments of a gene were termed exons, separated from each other within the gene by inactive introns.

The research suggested the necessary existence of a number of biological processes and active entities, many of which have since been tracked down by other scientists. Some, however, have resisted intensive inquiry. Now, researchers at The Wistar Institute and colleagues have resolved one of the important biological questions to which this earlier research pointed. A report on their findings appears in the October 21 issue of Cell.

Researchers who followed Roberts and Sharp discovered a molecular machine called a spliceosome, which was responsible for processing messenger RNA, or mRNA, the gene transcript from which proteins are produced. The spliceosome does this by snipping out the introns from the mRNA and then stitching together the exons into the finished mRNA. The activity takes place in the nucleus of the cell.

The spliceosome itself is composed of proteins and so-called small nuclear RNAs, or snRNAs. These snRNAs, as is the case with other forms of non-coding RNA in the nucleus, never produce proteins but play important roles in facilitating and regulating genetic activity. How these snRNAs were processed, however, remained a mystery for over twenty years. And because the spliceosome underlies the successful transcription of every single gene in the body, the question has been a vital one to answer.

In the new study, the Wistar-led research team identifies an entirely novel multi-protein complex called the Integrator that plays a central role in the processing of snRNAs. The Integrator appears to perform two important duties simultaneously. It binds a molecule called CTD, which is a component of the polymerase enzyme that transcribes snRNA genes, and it also binds to the specific genes that code for the snRNAs. With CTD as a platform, the Integrator forms a bridge between the genes and the polymerase components that transcribe them. Then, as the polymerase transcribes the genes into RNA, the Integrator processes the RNA into finished snRNAs ready for transport into the cytoplasm and incorporation into the spliceosome.

Interestingly, the Integrator contains at least 12 subunits, all of which were previously unknown to scientists. The Integrator also appears to be an evolutionarily conserved complex, appearing in animals as diverse as humans, worms, and flies.

“The Integrator complex appears to be completely new, previously undefined in any way, which is surprising in this era of the Human Genome Project,” says Ramin Shiekhattar, Ph.D., a professor at Wistar and senior author on the Cell study. “People had hypothesized that a complex of this kind must exist and had looked for it for many years, but until now it had eluded them.”

The lead author on the Cell study is David Baillat, Ph.D. Mohamed-Ali Hakimi, Anders M. Naar, Ali Shilatifard, and Neil Cooch are coauthors. Baillat and Cooch are both members of the Shiekhattar laboratory at Wistar. Hakimi is at the CNRS in France, Naar is affiliated with Harvard Medical School and the Massachusetts General Hospital Cancer Center, and Shilatifard is at the St. Louis University Health Sciences Center. Senior author Shiekhattar is a professor in two programs at Wistar, the Gene Expression and Regulation program and the Molecular and Cellular Oncogenesis program. Support for the research was provided by the National Institutes of Health.