The University of California, Santa Cruz (UCSC) genome browsers (see http://genome.ucsc.edu) absorb mountains of data from genome sequencing and analysis projects around the world, including projects at ucsc itself, with the goal of creating coherent genome views. Or, as Haussler puts it, "We want an interactive, Web-based 'microscope' for each model animal genome."

With this versatile microscope, a user can zero in on a requested portion of the genome (and zoom out for a longer view) while simultaneously displaying information in annotation tracks (see chart). Users can also add their own tracks with proprietary data that will flash into place only on their own Web browsers or be shared only with close collaborators.

"Wherever you look in the genome," Haussler says, "you can bring up tracks of data that no one else has ever looked at before and also notice new correlations between different types of data previously studied only in isolation. The experience is like looking through a microscope. It is live discovery." Says Haussler: "We're happy to be feeding hypotheses to the world."

A GENETIC SNAPSHOT
This sample chart from the UCSC Human Genome Browser yields a rich lode of data about the evolution and operations of two specific genes on human chromosome 22, CHEK2 and HSC20. CHEK2, a "checkpoint" gene, senses when there has been DNA damage or a problem with DNA replication and sends a signal to halt the cell cycle while the damage is repaired. Mutations in CHEK2 can make one susceptible to many types of common cancers.

The lines in blue at the top of the chart show the location of three known splice variants of the CHEK2 gene. Splice variants are naturally occurring variations that give rise to different protein products from a single gene; some have little or no effect, but others are associated with human disease. Knowledge of specific splice variants can help those who are researching diseases and searching for therapies.

Most of our direct evidence for many human genes comes from the vast collection of copies of short segments of RNA transcripts known as expressed sequence tags, or ESTs (black lines in center of chart). By joining overlapping ESTs, one can assemble possible splice variants for a gene. The data here suggest that there may be more splice variants for CHEK2 beyond the three known variants displayed in blue above.

The next three lines are snapshots of evolution. The blue track marked "Fugu Blat" in the margin shows regions of the human genome where the DNA is similar to certain segments in the genome of the pufferfish Takifugu rubripes, despite the fact that these two species are separated by several hundred million years of evolution.

The next track (brown) shows similarities of the human genes to a region on the reverse strand of mouse chromosome 5 that evolved from the same part of the genome of our common mammalian ancestor.

The orange line that follows further analyzes our common ancestry with rodents. The hatched lines indicate parts that are unique to the human (primate) lineage.

The penultimate track shows the locations of single nucelotide polymorphisms (SNPs) in the human genome. SNPs are positions in the human genome where a single base shows a significant level of variation from person to person in the human population. Having a particular version, or "allele," of a SNP in a key functional region may be linked to susceptibility or resistance to disease.

The last track shows the locations of certain repetitive elements in the human genome. These are primarily transposons, a form of selfish DNA that repeatedly copies itself to new locations in the genome, eventually dying out and leaving the copies behind to accumulate mutations.

—Jeff Miller

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Reprinted from the HHMI Bulletin,
June 2003, pages 28-31.
©2003 Howard Hughes Medical Institute