A laboratory at the Washington University School of Medicine has linked mutation of a newly discovered gene to blindness.

The study from the lab of Joseph Corbo, assistant professor of pathology and immunology, has determined that the transcription factor CRX is necessary for regulation of hundreds of retina related genes, including the gene FAM161A.

Corbo’s lab and collaborator Thomas Langmann, of the Institute of Human Genetics in Regensburg, Germany, used analysis of DNA regions binding to CRX to isolate the FAM161A gene as a cause of retinitis pigmentosa, a heritable form of blindness. The study found that a German family with previously unexplained onset of blindness expressed a mutated form of FAM161A. The mutation prematurely ended transcription of the gene by insertion of a stop codon, known in biology as a nonsense mutation. While the function of the gene is unknown, the gene must be present in the retina for proper development of the retina.

Affecting over 1 million individuals, retinitis pigmentosa manifests in the second to third decade of life, leading to severe visual impairment by the fifth decade and legal blindness in the sixth decade.

Additionally, the research discovered a different nonsense mutation of FAM161A in three unrelated individuals, suggesting a common founder who allowed for widespread dispersal of the mutation among the German population.

“Knowing which gene has a mutation in a given patient is very important for establishing prognosis and for devising novel therapies to treat their particular form of blindness,” Corbo said. “Not only does this research project lead to significant strides in disease diagnosis and treatment, it also sheds light on the fundamental biology of gene regulation because it identifies previously unknown players in the process.”

The lab group identified FAM161A due to high binding affinity of the transcription factor CRX to a DNA region near the FAM161A gene.

Transcription factors are relatively small proteins that bind to non-coding regions of DNA, leading to transcription or down-regulation of the genes they regulate. CRX promotes transcription of genes critical to the successful differentiation and survival of photoreceptors in the retina.

Photoreceptors are the light-sensitive cells that line the back of the eye. They process visual stimuli in the form of light energy and convert them into electrical impulses, which the brain translates into images.

The mechanism of photoreceptor synthesis functions most of the time. However, mutations in many of the genes involved in the formation and function the photoreceptors can lead to varying degrees of blindness.

“If cell types were cars, photoreceptors would be a high-performance vehicle like a Ferrari or a Maserati,” Corbo said. “They function wonderfully when things are going OK, but they break down easily and are very costly to repair.”

Knowing the importance of CRX, researchers hypothesized that regions of DNA with dense CRX-binding might be important in vision. To isolate such regions, they used a technique called chromatin immunoprecipitation (ChIP) to identify the regions of interest and used massively parallel sequencing (ChIP-seq) to determine the sequence of the bound regions.

A commonly used procedure in biomedical research, ChIP uses DNA binding proteins to cross link DNA regions of interest before shearing the DNA strands by sonication. The small strands then bind to a specific antibody and can be amplified, sequenced, or used in a microarray to assess if the DNA interacts with other DNA, RNA, or proteins.

From microarray and sequencing data on a mouse genome, researchers identified more than 10,000 regions bound by CRX. By using the density of CRX-binding, researchers can prioritize which genes are likely to have more important roles in blindness.

The identification of CRX and FAM161A has shed light on the onset of blindness, but many questions still remain. Many genes that express high affinity for CRX are yet to be understood, and even the exact function of FAM161A remains unclear.