Yale's cellular spray paint highlights "dark matter" of the genome
While science continues to identify and unravel the role of the thousands of proteins in the human body, many of them are too small to be picked up with current techniques. These ghost microproteins live in what scientists refer to as the "dark matter" of our genome and may play important roles in the progression of disease. A team at Yale University has now claimed a breakthrough with a technology they liken to "spray paint" for cells, which they've now demonstrated by mapping previously unknown proteins for the first time.
This idea of "dark matter" of the human genome can be traced back to the completion of the Human Genome Project in 2003, which still left some sizable blanks to fill in. In search of the unknown elements that remained, some scientists began using cutting-edge techniques to identify proteins in biological samples that measured less than 100 amino acid units.
Among the scientists was Sarah Slavoff, now an Associate Professor of Chemistry, Molecular Biophysics and Biochemistry at Yale University. Her earlier work involved discovering large classes of previously unknown microproteins using a form of mass spectrometry, which laid the foundation for the identification of thousands more in the years since.
Despite these advances, there remains many more microproteins to discover. Based on preliminary research, scientists like Slavoff suspect these may be connected to human disease, helping melanoma and other types of cancers evade current treatments, for example.
One of the more promising techniques for discovering microproteins today is called proximity biotinylation, which is based on the premise that by fixing enzymes to certain proteins, other proteins they interact with can be revealed by affixing a chemical tag for easy identification. There are a few variations of this technology, and Yale scientists including Slavoff have been working with a form they call MicroID.
“Our technique is like spray painting various areas of a cell with a tag that allowed us to ‘grab’ and identify all of the microproteins in that cellular region,” said Slavoff.
The researchers have now used this technique to map previously unannotated microproteins in live cells for the first time. This, the researchers write, validates the MicroID technique for use in live cells and establishes it "for discovery of microproteins and alt-proteins in vivo."
“Combining chemical biology tools with modern gene-editing methods helps us to move beyond a list of microprotein sequences to figure out which ones might actually be doing something in our biology,” said Zhenkun Na, study author. “In the future it’s not going to take us another hundred years to figure out which of these novel genes are involved in important biological processes.”
The research was published in the journal Molecular Cell.
Source: Yale University