Researchers at the Karolinska Institutet’s SciLifeLab in Stockholm recently found almost a hundred new protein-coding regions in parts of the human genome that previously seemed to lack any purpose and were referred to as junk DNA. Some of these genes are so-called pseudogenes, which may be linked to cancer.
“Our study challenges the old theory that pseudogenes don’t code for proteins,” said Janne Lehtiö, associate professor at the institute and study leader. “We had to develop both new experimental and bioinformatics methods to allow protein based gene detection, but when we had everything in place it felt like participating in a Jules Verne adventure inside the genome,” Lehtiö said.
The methods used by Lehtiö’s team included a new DNA-mapping technology that is being developed by GE Healthcare’s Life Sciences unit.
Scientists have found about 21,000 human genes since they first decoded the complete human genome in 2000. These snippets of DNA are blueprints for large biological molecules called proteins.
Since proteins help regulate all living things – from viruses and bacteria to large organisms like humans – defective genes can lead to cancer, anemia, cystic fibrosis and many other serious diseases.
Genes make up just a few percent of the human genome. Most of the rest, which includes pseudogenes, lacks any known purpose. Scientists think that pseudogenes could be remnants of genes that lost their functions during evolution.
How proteins are made: DNA in the nucleus of this eukaryote cell is “read” by RNA polymerase. The process generates amino acids, the building blocks of proteins. Ribosomes in the cytoplasm, the stuff that fills the cell, link amino acids into a strand. The strand then folds into a functional protein. Credit: Nicolle Rager, National Science Foundation
But Lehtiö’s team found evidence for close to 100 new protein-coding regions in the DNA junkyard. Many of the new proteins encoded by pseudogenes also could be traced in cancer cell lines. The scientists now plan to see whether these genes play a role in cancer and other diseases.
The Karolinska team used a prototype version of Immobiline DryStrip gels developed by GE Healthcare Life Sciences for their research. The technology allowed them to create detailed maps of gene expressions. “It’s like having a new high-resolution digital camera,” says Lotta Ljungqvist, head of research and development for bioprocess at GE’s Life Sciences unit.
The strips look like thin transparent plastic ribbons, about 10 inches long. Their surfaces are covered with proprietary high-resolution gel. “We can use this technology to detect the function on the junk DNA, observe the difference between healthy and diseased samples, and eventually find a way to treat diseases,” Ljungqvist says.
“Everybody was looking for genes, but now we are looking at what these genes actually mean. It gives us new understanding.”
Photo illustrations: Winning and short-listed entries from GE Healthcare Life Sciences’ annual cell imaging competition.