New technique provides insights into gene regulation

Researchers at the University of Toronto have developed a new technique that enables them to examine the genetic material of cells in greater detail than ever before, a finding that could lead to better ways to study and diagnose diseases.
The U of T research is published in the Dec. 22 issue of Molecular Cell. The new technique developed by the investigators uses a modified type of “gene chip” and a computer program to accurately monitor alternative splicing, a cellular process through which basic genetic material becomes more complex and acquires the ability to control genetic messages (mRNAs) that are required for the development of complex organisms.

“Now that we can look at mRNA in more detail, it has opened the door to understanding more about some diseases,” explains lead investigator Professor Benjamin Blencowe of U of T’s Banting and Best Department of Medical Research (BBDMR) and the Department of Medical Genetics and Microbiology, who notes out-of-control RNA splicing is involved in many human diseases, including cancers and birth defects. “The new information we can now obtain could also provide insights into new treatments.”

Each cell in the human body contains about 25,000 genes. Although human tissues and organs all have the same genes, some of the genes are “turned on” and others “off”. The complete set of genes in humans is only several times that of budding yeast and close to the number found in the significantly less complex nematode worm, C.elegans, a microscopic ringworm.

How very different organisms develop from comparable numbers and types of genes has been a major question since the genetic similarity was discovered. Scientists are trying to understand what turns a gene “off” or “on”, or alters its activity when “on” – in other words, the process of gene regulation.

The answer may lie in the coding segments (exons) of human genes, which are separated by long, non-coding segments (introns). The exons can be spliced in different combinations to generate different genetic messages, or mRNAs, and corresponding protein products. This process, known as alternative splicing, is analogous to the editing of a film sequence, where different combinations of editing can lead to different messages being created.

Presently scientists rely on DNA microarrays, also know as gene chips, to measure the levels of mRNAs. An array is an orderly arrangement of samples of DNA. An experiment with a single DNA microarray can provide researchers information on thousands of genes simultaneously – a dramatic increase in throughput from the era when only one gene could be studied at a time.

The new system developed by the U of T team enables accurate measurements of the levels of individual exons that make up different mRNAs to be attained, which current gene chips are unable to do. These differences found in the individual exons may account for how very similar genetic material can result in marked differences between organisms.

Blencowe developed the system in collaboration with U of T professors Brendan Frey of the Department of Electrical and Computer Engineering and Timothy Hughes of the BBDMR and the Department of Medical Genetics and Microbiology. The research team also included Quaid Morris and Ofer Shai of the Department of Electrical and Computer Engineering and Qun Pan, Christine Misquitta, Wen Zhang, Naveed Mohammad, Tomas Babak, Arneet Saltzman and Henry Siu of the BBDMR.