( es it very clear that they really are i...)Scientists reveal structure of gateways to gene control

The study also revealed that the nucleosomes at the transcription-promoter control centers occupy several overlapping positions on the DNA molecule, typically 10 base pairs apart, which exactly matches the periodic rotation of the DNA double helix. "It is striking how well these positions match with the architecture of the DNA as it wraps around the nucleosome's protein core," Pugh said.

This result powerfully simplifies previous theories about the possible architecture of gene packaging. "There is a certain DNA sequence that shapes the gene's architecture in the same way, producing the same structure in every gene," Pugh said. The overall sequence of DNA building blocks is different in each gene, but the underlying architecture is the same."

To obtain their high-resolution map, the researchers first isolated 322,000 nucleosomes from the 6,000 regions that control gene transcription in the DNA of baker's yeast, S.cerevisiae, an organism widely studied as a model of how human cells work. These promoter nucleosomes are the only ones in the yeast DNA that contain in their core a histone protein called H2A.Z. Led by Pugh and Stephan Schuster, associate professor of biochemistry and molecular biology, the Penn State research team then used antibodies that bind only to this H2A.Z protein as a tool for separating all these promoter nucleosomes from the other parts of the yeast's DNA. Next, the team used a state-of-the-art DNA-sequencing machine to identify, or "read," the sequence of base-pair building blocks along the DNA of each of the H2A.Z nucleosomes. The scientists then pinpointed the original location of the H2A.Z nucleosomes by matching the sequence of each one with the identical sequence on the previously published yeast genome. "Obtaining the exact DNA sequences for all these nucleosomes allows us to prec
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Source:Penn State