Those of us with messy desks or bench spaces know how difficult it can be to get organized. But don’t feel bad–a new paper in Science suggests that nucleosomes need help from “professional organizers” to form nice, evenly spaced arrays in gene promoters.
For decades now, researchers have been trying to figure out how nucleosomes get positioned in regular arrays near the 5’ ends of eukaryotic genes. The three most popular hypotheses (which are not mutually exclusive):
- Statistical positioning. Nucleosomes passively align at regular intervals from a genomic barrier that prevents nucleosome formation, such as a poly(dA:dT) tract.
- DNA-encoded positioning. The sequence of the DNA specifies where nucleosomes sit.
- Transcription initiation. Some aspect of transcription promotes nucleosome organization.
To study this perplexing issue on a genome-wide scale, a team of researchers in the U.S. and Germany reconstituted nucleosomes on genomic yeast DNA. Then, they added whole-cell extracts, with or without extra ATP, to the reconstituted nucleosomes. When they studied the patterns of nucleosomes that formed around transcriptional start sites, they found evidence for a fourth hypothesis:
- ATP-dependent factors. Enzymes use ATP to actively pack nucleosomes against barriers at the 5’ ends of genes.
The ATP-dependent packing activity seemed to peter out after about four nucleosomes, so other mechanisms for nucleosome positioning may predominate at regions distant from the barrier, the researchers say.
Don’t let this paper get lost in the shuffle; read it today at Science, May 2011.