Saturday, May 27, 2006

What is a gene?   posted by JP @ 5/27/2006 06:41:00 AM

This weeks Nature has a news article called "What is a gene?". Here's what they have to say:
In classical genetics, a gene was an abstract concept - a unit of inheritance that ferried a characteristic from parent to child. As biochemistry came into its own, those characteristics were associated with enzymes or proteins, one for each gene. And with the advent of molecular biology, genes became real, physical things - sequences of DNA which when converted into strands of so-called messenger RNA could be used as the basis for building their associated protein piece by piece. The great coiled DNA molecules of the chromosomes were seen as long strings on which gene sequences sat like discrete beads. This picture is still the working model for many scientists. But those at the forefront of genetic research see it as increasingly old-fashioned - a crude approximation that, at best, hides fascinating new complexities and, at worst, blinds its users to useful new paths of enquiry.

The one gene, one protein idea is coming under particular assault from researchers who are comprehensively extracting and analysing the RNA messages, or transcripts, manufactured by genomes, including the human and mouse genome. Researchers led by Thomas Gingeras at the company Affymetrix in Santa Clara, California, for example, recently studied all the transcripts from ten chromosomes across eight human cell lines and worked out precisely where on the chromosomes each of the transcripts came from. The picture these studies paint is one of mind-boggling complexity. Instead of discrete genes dutifully mass- producing identical RNA transcripts, a teeming mass of transcription converts many segments of the genome into multiple RNA ribbons of differing lengths. These ribbons can be generated from both strands of DNA, rather than from just one as was conventionally thought. Some of these transcripts come from regions of DNA previously identified as holding protein-coding genes. But many do not. "It's somewhat revolutionary," says Gingeras's colleague Phillip Kapranov. "We've come to the realization that the genome is full of overlapping transcripts."

Many scientists are now starting to think that the descriptions of proteins encoded in DNA know no borders — that each sequence reaches into the next and beyond. This idea will be one of the central points to emerge from the ENCODE project when its results are published later this year.

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