In 2004, John Hogenesch and his colleagues at the drug company Novartis created an atlas of gene expression in humans and mice, a sketch of which DNA snippets were busiest in certain areas of the body—in the thyroid, the retina, the blood, the tongue, and scores of other tissues. Though virtually all of a person’s cells contain the same genes, some are expressed (that is, used as blueprints for making proteins) more often in particular places. The so-called housekeeping genes, for instance, which regulate basic cell function, are active throughout the body, but the gene that encodes insulin is most active in the pancreas, where insulin is manufactured. Hogenesch’s atlas quickly became an important resource for molecular biologists, but he was troubled that it failed to account for an important dimension of gene expression. “Biology is kinetic, it’s dynamic,” he recently told me. He wanted his maps to account for time.

Many aspects of our physiology fluctuate in a twenty-four-hour rhythm. We sleep and wake; our blood pressure, body temperature, and hormonal secretions oscillate; even the composition of breast milk changes from morning to evening. It wasn’t until the early nineteen-seventies, however, that a group of biologists discovered the circadian pacemaker in mammals—the body’s master clock. It is located just above the brain stem, in the hypothalamus, and is called the suprachiasmatic nucleus. This tiny group of neurons, which is connected to the retina, oversees the cyclical response to darkness and light, directing the nearby pineal gland, for example, to make the hormone melatonin, which causes sleepiness. By the early two-thousands, scientists had worked out much of the complex interplay that keeps mammals on a stable twenty-four-hour loop. Initially, Hogenesch told me, it was assumed that this clockwork was limited to the brain. But it soon became clear that time-observing genes exist throughout the body, turning on and off in regular, repeating cycles.

Hogenesch has taken a key step toward merging the atlas with the clock, with a study that explores the mouse genome in time as well as space. Published last month in the Proceedings of the National Academy of Sciences, it covers twelve tissues, including the heart, lung, liver, kidney, and thyroid. For each, it shows whether—and at what time of day or night—particular genes are active. To draw up this new atlas, Hogenesch and his colleagues at the University of Pennsylvania, where he now works, took DNA samples from their lab mice every two hours and RNA samples every six. (RNA is produced from DNA and then translated into protein.) Some tissues showed a flurry of activity in many genes once a day—what the researchers referred to as “rush hour.” In the liver, rush hour occurred soon after the animals ate, when the organ was helping the body to metabolize food. In other areas, there were two rush hours. The adrenal glands, for instance, registered traffic spikes as the mice were waking up and as they were preparing for sleep. (Hogenesch noted that “booting up the restorative functions of sleep” may be more complicated than it seems. “It’s not simply an absence of activity,” he said.)

According to Joseph Takahashi, a neuroscientist at the Howard Hughes Medical Institute, in Dallas, and the editor of Hogenesch’s study, this is the first time that scientists have profiled daily patterns of gene expression in numerous areas of a mammal’s body at once. The work suggests that many more genes than had been assumed are regulated by the clock. Previously, Takahashi said, only around ten per cent of genes were thought to work this way; Hogenesch and his colleagues arrived at a figure of forty-three per cent. And that estimate may be low, because Hogenesch did not account for all of the body’s regions and subregions in his work. From the brain, for instance, he included only the cerebellum, the brain stem, and the hypothalamus. Essentially, his work “sets a floor for how many genes might be clock-regulated,” Nicholas Stavropoulos, a researcher at New York University’s Neuroscience Institute, told me. Although the details of timed gene expression are likely to differ between mice and humans—mice are active at night rather than during the day—it could be that the majority of human genes fall into this category. As Stavropoulos noted, there seem to be “few biological processes that are not influenced by the clock.”

Time may be an especially important consideration when it comes to developing new medications or revising the usage instructions for existing ones. Researchers have long observed that a drug’s toxicity or effectiveness can vary with the hour at which it is taken. Short-acting statins, for example, which inhibit cholesterol synthesis, work better when taken at night than in the morning, since most cholesterol is manufactured at night. In his study, Hogenesch shows that a majority of best-selling drugs, including treatments for asthma, diabetes, influenza, A.D.H.D., and heart failure, work on targets that follow a circadian cycle. “People are going to pay attention to that,” Takahashi told me. By changing the time at which an existing drug is administered, said Hogenesch, physicians could get “big benefits practically for free.”

Further gains may also come in the course of drug development. “The pharmaceutical industry tends to be wary of compounds that do not persist for long in the body,” Takahashi said. But if there were data on when exactly certain drug targets are most active, the developers might broaden their criteria. This could yield real benefits for patients, in part because compounds that are cleared more rapidly from the body tend to have fewer side effects. The latest atlas, said Hogenesch, is a way of getting such research started. “Biologists, physicians, patients—we need to start thinking about time.”