healthzone.ca
Some interesting basic research published in Nature. However, is the "language" for selecting and assembling exons really that significant a discovery? i.e. - wasn't the process already well known and understood even though the underlying chemistry may not have been?
LEAD In and a brief extract:
U of T team decodes secret messages of our genes
May 5, 2010
Joseph Hall
HEALTH REPORTER
In a groundbreaking study, University of Toronto researchers have unveiled an “Enigma machine” program that can decode the messages of our very genes.
Like the German decoding device captured by the Allies during WW II, the U of T program can unlock the meaning of a garbled language – in this case, the cryptic orders that direct our genetic machinery.
“We are the first people to actually make predictions about which genetic message will be produced in different tissues,” said Brendan Frey, one of the paper’s senior authors.
“Prior to this, there was no way to predict that actually,” said Frey, who has a joint appointment in engineering and medicine at the school.
The paper was featured Wednesday on the cover of Nature ...
...
Here’s how it works:
Genes reside within the nucleus of a cell and do their work by acting as a template, throwing open their encoding DNA sequences as an assembly point for strands of messenger RNA.
This messenger strand then goes out into the cell and creates a protein, plucking out the correct, amino acid ingredients and stitching them together according to its genetically encoded instructions.
The resulting protein will then help to build an organ or direct a bodily function.
Scientists had long thought that this messenger RNA building would occur along a continuous segment of a gene.
And if this had been the case, discovering what message a gene would make would be relatively simple.
“But it turns out that that view is actually wrong for over 95 per cent of genes,” Frey said.
What genes do instead, he says, is use different segments of their encoding surfaces to build separate segments of messenger RNA. Then they “splice” those segments together.
Different segments of the same gene would be spliced in different patterns in accordance to the needs of each different tissue.
These “alternative splicing” activities are directed by “code words” – short DNA sequences embedded along other parts of the gene – that dictate which segments will be used and how the messenger strand will be arranged.
Using about 400 code words, most of which they discovered themselves, the U of T team built up a computational algorithm that would determine which of those words would be used in any given tissue.
More importantly, the program was able to predict what message those code words would create in the form of the messenger RNA for each of the different tissues.
Frey says the code can be adapted to include all the body’s tissues once the relevant code words are found for them.
“Now that we have that framework in place, people can take that framework and they can expand it,” he said.
“Then they will be able to make predictions about what’s going to happen in terms of splicing in those other tissues.”
The code as it stands can only predict what the messenger RNA will look like, and the study does not look at the protein products those strands will actually assemble.
And while the code allows a deep understanding of a fundamental aspect of human biology – alternative splicing – its real value will come from the insight it can give into gene products.
“Now that we have the splicing code, doctors can actually dig in there and find out what’s going on with the actual proteins,” Frey said.
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