Mining mammalian genes

Credit: Courtesy of Piero Carninci" /> Credit: Courtesy of Piero Carninci The paper: The FANTOM Consortium and RIKEN, "The transcriptional landscape of the mammalian genome," Science, 309:1559-63, 2005. (Cited in 251 papers) The finding: Techniques such as cap-analysis gene-expression and gene-identification signature technology allowed a group led by Yoshihide Hayashizaki at the RIKEN Institute in Wako, Japan, to look more in-depth at the mouse tran

Nov 1, 2007
Kelly Rae Chi
<figcaption> Credit: Courtesy of Piero Carninci</figcaption>
Credit: Courtesy of Piero Carninci

The paper:
The FANTOM Consortium and RIKEN, "The transcriptional landscape of the mammalian genome," Science, 309:1559-63, 2005. (Cited in 251 papers)

The finding:
Techniques such as cap-analysis gene-expression and gene-identification signature technology allowed a group led by Yoshihide Hayashizaki at the RIKEN Institute in Wako, Japan, to look more in-depth at the mouse transcriptome. The team identified more than 180,000 RNA transcripts, which varied extensively based on alternative splicing and other modifications. Grouping these sequences into 44,000 transcript groups, they found that more than half did not code for proteins.

The significance:
The large variation in transcript modifications suggests that "mammalian genome RNA output is much more complex that previously thought," writes coauthor Piero Carninci in an E-mail. The study was "really the first" to start explaining how such complex mammalian systems can be encoded by so few genes, says Merete Fredholm of the University of Copenhagen.

The companion study:
In the same issue of Science, the same group showed that perturbing antisense RNA in mice could alter the expression of sense mRNAs (Science, 309:1564-6, 2005).

The questions:
"It's not exactly clear" how alternative splicing leads to proteins with different functions, says Mark Gerstein from Yale University. It will be a challenge to do the functional studies, because "there's not that many genes we know the full function of," Fredholm says.

The numbers:

The mouse transcriptome:
181,047 transcripts identified
16,247 transcripts encoding mouse proteins
5,154 transcripts encoding previously unidentified proteins