Surprising Molecule Tied to Rare Disease

The U4atac minor spliceosomal RNA.The Rfam database.

Researchers have found that defects in a molecule called a small nuclear RNA (snRNA) are responsible for a rare genetic disease. The finding represents the first time that snRNAs have been linked to disease.

Microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1) is a genetic condition characterized by small head size, abnormal bone growth and dwarfism (disproportionate short stature). The symptoms begin in the womb. Most babies born with the condition don’t live past the age of 3.

A team led by Dr. Albert de la Chapelle at Ohio State University was studying a cluster of 7 MOPD1 cases among a small community of Amish people in Ohio. The scientists suspected that the disease was caused by a single founder mutation. To pinpoint the mutation in such a small number of patients, they turned to a technique called homozygosity mapping. This approach hinges on the idea that disease-causing recessive mutations would be flanked by genetic regions that are homozygous (2 identical copies) in children but heterozygous (2 different copies) in parents. Once the researchers found such regions, sequencing would uncover the disease-causing mutations.

The researchers pinpointed an area of interest on chromosome 2. They then used a method called deep sequencing to identify a single mutation in the RNU4ATAC gene that was homozygous in all 7 patients and heterozygous in their 13 Amish parents. The study, which was partly supported by NIH’s National Institute of General Medical Sciences (NIGMS) and National Cancer Institute (NCI), appeared in Science on April 8, 2011, along with another paper by researchers in France identifying the same gene.

Surprisingly, RNU4ATAC doesn’t code for a protein. It codes for an snRNA called U4atac. U4atac is a component of what’s called the minor U12-dependent spliceosome. After genes are transcribed from DNA into messenger RNA (mRNA), spliceosomes remove portions of the mRNA (called introns) to make a functional mRNA to be read by the cell’s protein-making machinery. The U12-dependent spliceosome recognizes and removes a small subset of introns called U12-type introns.

The researchers found other U4atac mutations in 2 German families with MOPD1. Experiments confirmed that the mutations associated with MOPDI cause defective U12-dependent splicing. As expected, adding wild-type U4atac snRNA into cells taken from the patients enhanced U12-dependent splicing.

“Individuals who have inherited 2 defective copies of the gene for this critical component of the minor spliceosome cannot efficiently splice out minor-class introns, and this leads to the developmental defects seen in MOPD1,” explains de la Chapelle.

An estimated 700-800 genes in the human genome have U12-type introns. The researchers now plan to explore the downstream affected genes in MOPDI patients. “We are now asking clinicians around the world for samples we can test from children and their families who are suspected of suffering from MOPD1 or similar conditions,” de la Chapelle says. “This research may help us determine which family members may unknowingly carry a copy of the harmful mutation, and to understand how these mutations can have such severe developmental consequences.”

Future research will be needed to address the question of whether defects in spliceosomes can contribute to later onset diseases such as cancer.

— by Harrison Wein, Ph.D.