Simultaneously Determining Chromosome Structures and Methylations Patterns

Salk Institute researchers have developed a method to simultaneously analyze how chromosomes, along with their epigenetic features, are compacted inside of single human brain cells. The team combined two different analysis techniques into one method, which enabled them to identify gene regulatory elements in distinct cell types.

"We've taken this new and better approach to analyzing the genomes of single cells and applied it to healthy brain tissue," says Joseph Ecker, co-corresponding author of a paper published today in Nature Methods. "The next step is to compare normal and disease tissue."

In the past, researchers have had to use separate methods to determine chromosome structures and methylation patterns of individual cells. In their new method, called single-nucleus methyl-3C sequencing (sn-m3C-seq), the Salk team "double dips" from each single cell, collecting data on both chromosome structure and methylation at the same time. While doing the process manually would be slow and cumbersome, the team automated sn-m3C-seq, letting them easily study thousands of cells. The development of new approaches to handle cells, coupled with new computational methods to handle data, enabled this new technique.

The team says developing a method that examines these features in single cells allows scientists to use certain "analytical tricks" to directly study tissue samples and resolve chromosome structure and DNA methylation in all the different cell types in the tissue. "We know these features can vary a lot between cell types and there's value in having both types of information together from the same cells," says Jesse Dixon, co-corresponding author. "It really opens up our ability to understand what regulatory sequences are affecting which genes across a wide variety of cell types and tissues."

To test out sn-m3C-seq, the team applied the method to more than 4,200 human brain prefrontal cortex cells. While using data from chromosome structure alone allowed only the crude separation of neurons from non-neurons, combining the approaches let the researchers identify gene regulatory elements in distinct cell types and then further study the chromosome structures present in each cell type. Moreover, the team noticed relationships between the two levels of regulation that they plan to study more in the future. Now that the method is established, they'd like to begin applying it to more types of both healthy and diseased tissues.