GENES & CELLS
Turning on genes requires teamwork
Flipping genetic switches isn’t a job for solo proteins, studies find
BY TINA HESMAN SAEY
Turning on genes may work like forming
a flash mob.
Inside a cell’s nucleus, fast-moving
groups of floppy proteins crowd together
around genetic switches and coalesce
into droplets to turn on genes, biological physicist Ibrahim Cissé of MIT and
colleagues report online June 21 in two
papers in Science.
Researchers have previously demonstrated that proteins form such droplets
in the cytoplasm, the cell’s jellylike guts.
Some scientists, including Cissé’s MIT
colleagues Richard Young and Phillip
Sharp, have proposed that this process — called phase separation — could
also happen in the nucleus when cellular machinery turns genes on, which
involves copying DNA instructions into
If confirmed, the discovery challenges earlier ideas that gene activity is
controlled by single molecules of stable
protein complexes that remain stuck to
DNA for long periods.
Cissé and colleagues used super-
resolution microscopy to view single
protein molecules in live mouse embry-
onic stem cells. In particular, the team
was interested in RNA polymerase II, the
enzyme that copies DNA into RNA, and
parts of the Mediator complex, a group
of proteins that helps kick-start that
copying process, called transcription.
The researchers tagged the proteins with
a fluorescent protein and watched what
RNA polymerase II and Mediator
proteins both formed large clusters,
each with about 200 to 400 molecules.
Those clusters had properties of phase-separated droplets: The clusters formed
distinct dots when viewed through the
microscope. Those dots could fuse
together, like oil droplets merging in
water. And the droplets could be dispersed with alcohol. That’s convincing
evidence that Cissé’s group sees phase-separated condensates, says Anthony
Hyman, a biologist at the Max Planck
Institute of Molecular Cell Biology and
Genetics in Dresden, Germany.
While these clusters seem stable, individual polymerase or Mediator proteins
were constantly darting in or out of the
cluster. About 90 percent of polymerase
molecules and 60 percent of Mediator
molecules spent only about 10 seconds
in the clusters, the team found.
That’s in contrast to previous studies suggesting that RNA polymerase II
stays at a gene for minutes to hours, says
single-cell biochemist Robert Tjian, a
Howard Hughes Medical Institute investigator at the University of California,
Berkeley. “The biggest surprise is how
fast these things are happening,” he says.
In a study also reported online June 21
in Science, he and colleagues found that
these proteins interact only briefly, most
for just five to 20 seconds.
These protein mobs are drawn
together by their floppy bits, called low
complexity or intrinsically disordered
regions, Tjian’s team found. Floppy,
In this microscope image of mouse embryonic
stem cells, molecules of the enzyme that
copies DNA instructions into RNA messages
cluster (white and blue spots) within nuclei.
intrinsically disordered proteins are
needed for a wide variety of cellular processes (SN: 2/9/13, p. 26).
In Cissé’s studies, Mediator proteins
clustered with groups of genetic switches
called super-enhancers. Typically, super-enhancers are located far from the genes
they regulate and may control several
genes, sometimes simultaneously. Droplets containing Mediator proteins and
super-enhancers may interact with droplets containing RNA polymerase II to
spur transcription, the findings suggest.
Sudden coalescence of proteins into
droplets could help explain why genes
turn on in a flash, Hyman says. Bubbles
of enhancers might interact with multiple bubbles of RNA polymerase II to
turn on several genes at once, something
that could be hard to explain if single
protein molecules were responsible.
Tjian doesn’t call what he sees phase
separation, even though his results are
similar to Cissé’s. It’s not necessary to
concentrate proteins so densely that
they will form droplets to get transcription started, he says. Instead, proteins
clustered in hubs can spur transcription
at a range of concentrations, he found.
Julie Forman-Kay, a biophysical
chemist at the Hospital for Sick Children
in Toronto, contends that Tjian is making a semantic argument. “What he calls
a hub is, in my book, evidence for phase
separation,” she says. All of the studies
show the same thing, she says: Clusters
of floppy proteins concentrate in particular locations to turn on genes.
But the association between phase
separation and transcription hasn’t
been proven yet, says Danny Reinberg,
a biochemist at New York University
Langone Health. He agrees with Tjian’s
findings that weak interactions between
proteins can add up to a strong push to
do something, in this case to copy DNA
into RNA. But he needs more evidence
that transcription is spurred by phase
separation into droplets, as Cissé and
colleagues describe. “I’m not saying it’s
not happening,” Reinberg says. “I’m saying it can happen, it might be happening, but there’s no proof of that in these
two papers.” s