Following Phylogenetic Footprints
Researchers apply computational power to their hunt for noncoding regulatory
sequences | By Jeremy L. Peirce

Scientists know that the regulatory elements that guide and control gene
expression, for the most part, lie not within coding sequences but outside
and between them. Now researchers are taking their search for these
sequences genome-wide. And with hundreds of completed genomes in hand, and
still more in the works, a full comprehension of regulation at a genomic
level has become increasingly plausible.
Understanding noncoding elements is necessary to understand cellular and
developmental processes at a molecular level. "Eventually one wants maps of
the genome that show which sites are active in which cells, and how they
[the sites] change as the cells differentiate," says Ian Dunham, senior
investigator at the Wellcome Trust Sanger Institute, Cambridge, UK. For the
moment, though, these crucial snippets of genetic information remain elusive
prey.

Phylogenetic footprinting, a method that sifts functional regulatory
elements from nonfunctional DNA, has become an increasingly popular tool.
The name harkens back to DNAse footprinting, a low-throughput experimental
technique used to detect functional transcription factor binding sites
(TFBS). In DNAse footprinting, protein-bound regions are protected from
DNAse digestion, creating a "footprint" in a sequencing gel. In the
phylogenetic equivalent, regulatory elements are protected from random drift
across evolutionary time by selection. Such sequences reveal themselves by
their unexpectedly high homology when compared to orthologs, implying slower
evolution.

Before the advent of readily available genomic sequences and computational
techniques, investigators often defined regulatory regions using DNAse
footprinting and so-called promoter bashing. Promoter bashing involves
fusing a series of truncated promoter fragments to a reporter gene,
introducing the constructs into cells, and evaluating changes in expression.
Newer approaches promise to largely eliminate these laborious procedures.

According to Wyeth Wasserman, associate professor of medical genetics at the
University of British Columbia, phylogenetic footprinting is one of two
informatic approaches at researchers' disposal, the other being module
detection. Phylogenetic footprinting, he says, "can eliminate about 90% of
false predictions while keeping most of the true ones." But module detection
is even better, he adds. "If you know which transcription factors you're
interested in, and you have enough data to know what they bind to, there are
now good methods to look at clusters of binding sites [modules] and tell
which ones are most likely to be real. We can eliminate about 99% of false
positives this way."

Though studying combinations of binding sites generally is preferable to
phylogenetic footprinting, Wasserman says, it's not always tractable. "The
challenge is that we seldom have enough data to make those models."
Phylogenetic footprinting, on the other hand, can be applied in the absence
of any knowledge of the biology involved, so it is more widely applicable.

Full Text at TheScientist
http://www.the-scientist.com/yr2004/sep/tech_040927.html

Posted by
Robert Karl Stonjek
---
þ RIMEGate(tm)/RGXPost V1.14 at BBSWORLD * Info{at}bbsworld.com

---
 * RIMEGate(tm)V10.2áÿ* RelayNet(tm) NNTP Gateway * MoonDog BBS
 * RgateImp.MoonDog.BBS at 9/27/04 5:58:24 AM