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Grouping like with like

Copied at similar times, active genes may be clustered on nearby 'shelves' in the nuclear closet, says study by Basic Sciences postdoc Dirk Sch?beler
Dr. Dirk Sch?ebler
Dr. Dirk Schubeler pipets DNA samples in Dr. Mark Groudine's laboratory. "People think that a sequenced genome is a book that can be read to predict gene expression, but that's not true at all," he said. "Many other factors are at play." Photo by Todd Mcnaught

Tomorrow morning, you'll rifle through your overstuffed sweater drawers and hunt for shoes under your bed. It'll take you an agonizing 35 minutes. And as each minute goes by, you'll curse the closet-organizing consultants who claim that coordinating your outfit shouldn't make you late for work.

But your quandary over your attire will pale compared to the challenge faced by your body's cells. They have to coordinate a molecular wardrobe of thousands of genes with precision or risk death or disease.

How much order a cell needs to function with maximum efficiency has long been a source of scientific dispute. But new insights from the Basic Sciences Division suggest that complex cells heed the same advice offered by the closet consultants: It pays to group like with like.

Dr. Dirk Schubeler, a postdoctoral fellow in Dr. Mark Groudine's laboratory, and colleagues have found that, unlike the relatively simple, single-celled baker's yeast, cells of more complex organisms coordinate two fundamental genetic processes:

  • Gene expression, or the switching on or off of genes as their products are needed.
  • The timing of replication, the act of duplicating DNA in preparation for cell division.

The findings will help scientists develop detailed genetic blueprints of normal development and disease states.

Fred Hutchinson collaborators on the study, published in the November edition of Nature Genetics, include David Scalzo, a research technician in the Groudine lab; Dr. Charles Kooperberg, a mathematician in the Public Health Sciences Division; and Dr. Jeffrey Delrow, head of the Genomics facility. Dr. Bas van Steensel, an investigator at the Netherlands Cancer Institute and a former postdoctoral fellow in Dr. Steven Henikoff's laboratory, also contributed.

Based on the analysis of only a handful of genes in higher organisms, it has long been thought that active (expressed) genes are replicated early and inactive genes late. In contrast, a genome-wide analysis of replication timing in baker's yeast revealed no such correlation.

Using fruit flies as their model and DNA array as their tool, Schubeler and colleagues analyzed the replication timing and expression of thousands of genes and found that active genes are the first to be duplicated as a cell readies itself to divide into two, whereas genes that are rarely used are copied late during the duplication portion of the cell cycle. Although not yet known, other animals, including humans, likely exhibit similar behavior.

This synchrony of tasks likely reflects a high degree of order in the nuclei of complex cells, akin to shelving wool sweaters to the back of the closet as spring sets in while keeping shorts within easy reach. Such order may be essential for the myriad genetic wardrobe changes that occur as animals move through a succession of developmental stages.

Gene expression and DNA duplication tend to be thought of as distinct processes. The observation that these events are linked, at least in some organisms, implies that the control of gene expression may involve factors that govern the timing of duplication, making gene regulation much more complex than previously suspected.

More detailed map

Identifying each factor that influences control of gene expression would let scientists draw a much more detailed map of an organism's genetic program, Schubeler said. Such a map, dubbed an "epi-genome" because it relies on information that goes beyond DNA sequence, would aid understanding of normal development as well as provide clues to the causes of diseases, including cancer.

"Creating these maps would be extremely informative," he said. "People think that a sequenced genome is a book that can be read to predict gene expression, but that's not true at all. Many other factors are at play."

Groudine labeled Schubeler's work a first step toward completion of such a multifaceted genetic map, an effort under way in his laboratory.

"Dirk's study has given us the first detailed insight into the relationship between replication timing and gene expression in higher organisms," he said. "Our long-term goal is to determine the interplay between those process, chromosome modifications (such as DNA methylation and chromatin structure) and the three-dimensional position of genes in the nucleus. This would provide important insights into the regulation of gene expression during cellular differentiation."

Only a subset of the thousands of fruit-fly genes is needed at any one time during the fly's development. Similarly, the start times at which each gene is duplicated are staggered over the eight hours required to copy an entire fly genome.

The discovery that active genes are copied at similar times suggests they are clustered on nearby "shelves" in the nuclear closet. The wardrobe arrangement might differ among cells from distinct parts of the body. For example, some genes active in eye cells would not be needed in wing cells.

To look for a link between gene expression and timing of DNA replication, Schubeler and colleagues took a global approach afforded by DNA-array technology. Also known as gene chips, DNA arrays let researchers examine simultaneously the expression of every cellular gene.

In their experiments, they took advantage of a gene chip that was designed and assembled at the center's Genomics facility and that allowed them to determine the time at which thousands of fruit-fly genes are duplicated. Kooperberg, a biostatistician, processed the enormous volume of data generated by the experiments. His analysis revealed that genes located near one another on a chromosome tend to be replicated at similar times.

Next, they used the gene chip to determine the relationship between the timing of replication and gene activity. The later a gene was replicated during the portion of the cell cycle in which DNA is duplicated, the less likely it is to be expressed.

The study could not have been completed without a team effort, Groudine said.

"Each person brought a different expertise that was essential to both the experimental design and data interpretation," he said.

Complex organization

The team's discovery of co-regulation may reflect a complex organization of genes in the nucleus that is needed for tissue-specific gene regulation.

"We'd next like to study this in mammalian cells with distinct patterns of gene expression," said Schubeler, who leaves the center next February to establish his own laboratory at the Friedrich Miescher Institute in Basel, Switzerland. "For example, we can compare red and white blood cells to see whether gene activity, which is different between the two types of cells, correlates with replication timing."

The technique could also be applied to study the most dramatic cellular costume change of all: the development of cancer.

In some cancers, chromosomes are broken, relocating genes from their normal position and potentially affecting their replication timing and expression. While the consequences of abnormal replication timing are unknown, Schubeler noted that disruptions to the normal procession of molecular events often cause dire outcomes for cells.

"Anything that is important for normal cell division is also a candidate to be important in the establishment of cancer," Schubeler said.

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Last Modified, October 28, 2019