New technique captures view of 10,000 genes' activity in the moment

June 7, 2018

Researchers have developed a new technique that allows them to view the activity of more than 10,000 genes at once in single cells. Unlike other single-cell sequencing technologies, the new method captures changes in these thousands of genes at - or close to - the moment they turn on.

That distinction, a timescale of minutes versus a few hours, enables a completely new view of how genes and chromosomes are behaving inside cells, said Dr. Long Cai, a biologist at the California Institute of Technology and senior author on a study describing his team's findings, published today in the journal Cell. 

"You see what the cell is trying to do at that moment in time," said Cai, who is also part of the team at the Allen Discovery Center at UW Medicine

undefinedIn a study published in the journal Cell, Caltech biologist Dr. Long Cai and his colleagues demonstrated a scaled up version of their technique, seqFISH, that let them view close to real-time activity of 10,000 genes in a single cell at once. In this 3D reconstruction of a mouse cell, chromosomes are stained blue and all the active genes in the cell are labeled with different colored dots that correspond to their native chromosome.

The technique, which the researchers dubbed seqFISH, detects a very transient form of RNA, the go-between molecule that bridges the gap between a gene and its protein product. Other RNA sequencing techniques look at a mature, longer-lived form of the molecule.

There's a lot you can learn from those sturdier bits of RNA, Cai said, but because they last for three to four hours, you can't get a glimpse of gene activity when - and where - it's happening. The transient version their technique analyzes only lasts about five minutes.

New discoveries made possible

undefinedIn the study, the researchers captured images of more than 10,000 genes' RNA within minutes of its birth in mouse stem cells and connective tissue cells. The resulting images revealed a few surprises about the nature of genome-wide activity, Cai said. The first was that the genes' activity seemed to be synchronized in each cell - but not cell to cell - on a two-hour biological clock. The cells turn on and off in concert, they found. 

Cai and his team don't understand why gene activity cycles like this, but they want to probe the mystery further. A similar two-hour biological clock acts in embryo development, Cai said, so one possibility is that same clock persists to adulthood but hadn't previously been detected.

The researchers also found that each chromosome takes up its own little ball of space inside the cell, with the active genes clustered around the outside of each chromosome. 

"It's almost like a ball of yarn that's packed in the middle and more fuzzy on the surface," Cai said. The active genes tend to reside on the outside of chromosomes and appear more intertwined with neighboring chromosomes, they found.

Next, the scientists want to apply the technique to cells in their native environs, both looking at how cells change during animal development and mapping the differences between human cells - and maybe eventually looking at how cells' gene activity goes awry in different diseases.

Getting seqFISH to work at the genome scale was a four-year road with a lot of bumps, Cai said. The flexible funding through The Paul G. Allen Frontiers Group, which partially supported the technology development, was essential along the way, he said.

"It took a lot of tries to get this to work. The funding through the Allen Discovery Center gave us the freedom to try a lot of things," Cai said.