The five-year project to identify the loops in the human genome was a collaboration between researchers at Harvard University, Baylor College of Medicine, Rice University and the Broad Institute of Harvard and MIT.
Loops form when two bits of DNA that are far apart in the genome sequence end up in close contact in the folded version of the genome in a cell's nucleus.
Researchers used a technology called "in situ Hi-C" to collect billions of snippets of DNA that were later analysed for signs of loops. The team found that loops and other genome folding patterns are an essential part of genetic regulation.
"More and more, we're realising that folding is regulation," said study co-first author Suhas Rao, a researcher at Baylor's Centre for Genome Architecture.
"When you see genes turn on or off, what lies behind that is a change in folding. It's a different way of thinking about how cells work," said Rao.
"Our maps of looping have revealed thousands of hidden switches that scientists didn't know about before. In the case of genes that can cause cancer or other diseases, knowing where these switches are is vital," co-first author Miriam Huntley, a doctoral student at Harvard's School of Engineering and Applied Sciences, said.
"The new maps allow us to really see, for the first time, what folding looks like at the level of individual genes," said senior author Erez Lieberman Aiden, assistant professor of genetics at Baylor.
The research appears in the journal Cell.