The original plan was to repeat the sequencing more times

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  1. Correct errors and proofread. The original plan was to repeat the sequencing up to 12 times to prune away the mistakes that inevitably accompany a project involving 3.1 billion pieces of datum. In the rush to make the joint announcement, the privately funded Celera Genomics and the publicly funded international consortium Human Genome Project settled temporarily for less than half that goal. Proofreading will probably take another year or two from the date of the announcement.
  2.  Fill tens of thousands of gaps in the sequence. These holes amounted to about 15 percent of the genome on June 26, 2000. Most gaps lie in stretches of short sequences repeated hundreds or thousands of times, which makes them enormously difficult to get right.
  3.  Sequence the seven percent of the Homo sapiens genome that was originally excluded by design. This region is heterochromatin, highly condensed DNA long believed to contain no genes. But in March 2000, analysis revealed that fruit fly heterochromatin (about one third of the fly’s genome) appears to contain about 50 genesso Homo sapiens heterochromatin probably contains a few genes, too.
  4.  Finish finding all the genes that make proteins. This step takes place after the sequence is cleaned up and deemed 99.99 percent accurate. About 38,000 protein-coding genes have been confirmed so far. Recent estimates have tended to fall below 60,000.
  5.  Find the non-protein-making genes. There are, for instance, genes that make RNA rather than protein. They tend to fall below the threshold of today’s gene-finding software, so new ways of discovering them will have to be devised.
  6.  Discover the regulatory sequences that activate a gene and that govern how much of its product to make.
  7.  Untangle the genes’ intricate interactions with other molecules.
  8.  Identify gene functions. Because a gene may make several proteins, and each protein may perform more than one job, the task will be stupendous.

As they check each item off the list, researchers will be generating the information that will make it possible to attack and even prevent a vast array of Homo sapiens ills. But how long will it take to get through the checklist? If anyone knows, it should be Celera president J. Craig Venter. On announcement day Venter predicted that the analysis will take most of this century.

Finding the Genome’s Master Switches

Once the Human Genome Project delivers a list of all of our genes, the next trick will be figuring out just what those genes do. Making the job a little easier, though, is a new DNA microarray technique developed by scientists at the Whitehead Institute at the Massachusetts Institute of Technology and Corning, Inc. Reporting in the December 2000 issue of Science, Richard Young and his colleagues unveil a method that identifies in about a week which cellular circuits are controlled by which master switches in the genomea task that ordinarily takes years. “We are very excited by these results because they suggest that our technique can be used to create a ‘user’s manual’ for the cell’s master controls, a articlelet that matches the master switches to the circuits they control in the genome,” Young says.

The master switches are in fact proteins, called gene activators, that bind to specific regions of DNA, or genes, and in doing so, initiate series of steps that control everything from cell growth and development to seeding disease. Young’s group built their method around DNA microarrays because these devices make it possible to take a kind of snapshot of a cell, and see which genes are turned on and which are turned off. For biologists, knowing which genes are active as a cell performs some function is incredibly useful information, much like being able to match the individual notes in a chord with the sound they produce. But it doesn’t reveal which master switchor handplayed the notes, and the Homo sapiens genome contains about 1,000 master switches. To date, scientists know the activity of only a quarter of them, such as the p53 protein, which plays a role in cancer.

The first step in the new technique is fixing the master switch proteins in living cells to their DNA binding sites using chemical crosslinking methodssort of like gluing the hands to the keys they are striking. The scientists then open the cells, creating a soup of protein-DNA complexes. They use antibodies with magnetic beads to draw out interesting fragments of DNA, with the master switch protein still attached. Next they isolate the DNA fragments, label them with fluorescent dye and hybridize them to a DNA array containing genomic DNA from yeast, which identifies what they are. As a test of the method, Young and his colleagues demonstrated that it can successfully pick out the cellular circuits controlled by two known master switches. “Our goal is to use this technique to find the circuits controlled by the 200 or so master switches in yeast,” Young adds, “and then develop analogous techniques in Homo sapienss.”

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