A team of researchers led by University of Virginia Health System geneticists has uncovered a major secret in the mystery of how the DNA helix replicates itself time after time.
It turns out that it is not just the sequence of the bases (building blocks) in the DNA, but also how loosely or tightly the chromatin (the material that makes up chromosomes) is packed at different points of the chromosome that is critical.
Where chromatin is packed more loosely, the genes are replicated earlier than other genes and are expressed at high levels. Where chromatin is dense, these genes are replicated later and are not expressed.
"Our work showed that by looking at time of replication, we could predict which genes are in an environment that could be expressed and the potential that cell has of going down different paths of differentiation," says Anindya Dutta, M.D., UVa professor of biochemistry and molecular genetics, who headed the replication portion of the major ENCODE project published in Nature journal (June 14). "The time of replication of different parts of our genome is very nicely correlated with the chromatin packaging."
This finding held true for both cell lines studied, the HeLa cervical cancer cell line and a normal cell line (lymphocytic cells). "To our surprise, what the HeLa cells were predicting in terms of chromatin packaging held true in the lymphocytes, even though the HeLa cells are cancer cells with scrambled genes," Dutta said. "The chromatin packaging predictions were approximately comparable."
Chromosomes, then, are not just a framework of DNA but also are influenced by the proteins that pack the DNA, particularly histones. This packaging determines how the cell's enzymes get access to the DNA to read off the DNA and replicate, ultimately to create all of the proteins needed by a given cell.
Several other researchers around the country were part of this larger project, the Encyclopedia of DNA Elements (ENCODE) project, using two preset cell lines. Overall, the consortium looked at just 1 percent of the human genome, using HeLa and lymphocytic cells for the study. Groups that were performing other experiments found that their data about genetic expression perfectly correlated with what the Dutta lab would have predicted, in terms of gene expression timing. In the ENCODE study, the next project is to examine the remaining 99 percent of the genome, using at least 10 more cell lines, Dutta says.
One of the very intriguing questions that comes from the findings is: what determines the boundaries between the actively expressing domains of a chromosome and the inactive portions"
"The length that is active in each chromosome is likely to be different between different types of cells because different genes are expressing," Dutta said. "How does that boundary shift so that something that was inactive in one cell is now active in another cell line?"
Future research will help to tell this story, but one possibility is that special proteins come and bind with the chromosome elements. Their job may be to grab on to a site on the chromosome and define the boundary element.
"There is nothing in the DNA sequence of bases that sets up the boundary areas between active and inactive portions, but clearly the chromosome is set up to have these domains," Dutta explains.