A new study has found that CLAMP, a protein previously identified as the linchpin in the process by which cells in males doubly express their single X chromosome to achieve genetic parity with females, is also responsible for coordinating the process by which the DNA in newly replicating cells of an embryo becomes properly wound up and structured.
"It's really exciting because now we have these two separate chromosomes on which CLAMP does vital jobs," said Erica Larschan, assistant professor of biology at Brown University and senior author of the study published in Genes and Development. "That sets us up for a compare-and-contrast strategy where we can understand how one protein can function differently in context-specific ways."
That matters, added co-lead author Leila Rieder, a postdoctoral researcher at Brown, because in order for clinical interventions that target key proteins to do more good than harm, they need to be tailored to a specific context. It may be tempting to block or amplify a gene or protein to treat a disease, but without confining the intervention to that one process, it could upset the entirely healthy actions of the same gene or protein in an unrelated process.
"One of the biggest fears about using genetics in people is that there are off-target effects," Rieder said. "You don't know when you manipulate a gene if it's going to have a single effect or if it's going to have many effects. We don't understand all the roles that that one manipulation is going to have."
In a series of experiments, a team from Brown, the University of North Carolina (UNC), and Massachusetts General Hospital found that in fruit flies, CLAMP is the protein that launches the process of gene regulation that produces histones by recruiting other known regulators. It is among the very first proteins on the scene of the histone locus in a newly fertilized egg and opens up the histone locus for expression by the cell. Experiments in which the team interfered with CLAMP led almost universally to fly eggs failing to hatch.
Foiling CLAMP proved to be so lethal, in fact, that studying its function at all required an experimental ploy that would allow the scientists to manipulate CLAMP while keeping the flies alive. To understand, for example, how CLAMP lures the other histone-related proteins to the histone locus, the Brown team worked with the UNC collaborators, including co-lead author Kaitlin Koreski, to generate CLAMP mimics that wouldn't interfere with natural CLAMP's DNA binding, but could still attract the other key regulatory proteins that control histone gene regulation.
CLAMP (glowing green) is found all over these fly chromosomes, but it's particularly concentrated at the histone locus (red) at the bottom center.