Tiny, transient loops of genetic material, detected and
studied by the hundreds for the first time at Brown University, are providing
new insights into how the body transcribes DNA and splices (or missplices)
those transcripts into the instructions needed for making proteins.
genetic snippets—they are called lariats—that the Brown team reports studying
in Nature Structural & Molecular Biology are byproducts of gene transcription.
Until now scientists had found fewer than 100 lariats, mostly by poring over
very small selections of introns, which are sections of genetic code that do
not directly code for proteins, but contain important signals that direct the
way protein-coding regions are assembled. In the new study, Brown biologists report
that they found more than 800 lariats in a publicly available set of billions
of RNA reads derived from human tissues.
“We used modern
genomic methods, deep sequencers, to detect these rare intermediates of
splicing,” said William Fairbrother, associate professor of biology and senior
author of the study. “It’s the first ever report of these things being
discovered at a genome scale in living cells, and it tells us a lot about this
step of gene processing.”
step is known as RNA splicing. Like film editors splicing together movie
scenes, enzymes cut away the introns to assemble exons that instruct a cell’s
ribosome to make proteins. The body often has a choice of ways and places to
make those cuts. Most of what is known about splicing has come from studying
these spliced instructions, said Allison Taggart, a graduate student who is
lead author of the study. What’s been missing is the data hidden in the
lariats, which fall apart shortly after being spliced out, but turn out to
predict the body’s splicing choices.
The key information
uncovered in the study, Taggart said, is the location of so-called “branchpoints” on the lariats. Physically, the branchpoint is where the lariat
closes on itself to form a loop during the first step of splicing, but its
position and proximity to possible splice sites, the researchers learned,
reliably relate to where splicing will occur.
the sites of these branchpoints and their relationship to splice sites, the
researchers created an algorithmic model that could predict splice sites 95.6%
of the time. The value of the model is not in identifying splice sites—those
are already well known, Fairbrother said. Instead, the model’s accuracy shows
that, with the new data from the lariats, scientists have gained a more general
understanding of how the body chooses among alternative splicing sites.
“What it does
tell us is sets of rules defining the relationship between branchpoints and the
chosen splice sites, which gives clues about how the splicing machinery makes
decisions,” Taggart said. “Certain branchpoint locations can enforce specific
Connections to disease
In addition to
ferreting out the mechanisms of alternative splicing, the team also studied the
connection between branchpoints and disease. They looked through the Human Gene
Mutation Database for disease-causing mutations found in introns and compared
their newly found branchpoint sequences to those mutations. They found that
many relate specifically to branchpoints.
“We saw a
sequence motif that looked exactly like a branchpoint sequence motif,” she
said. “What this tells us is that these mutations are forming at branchpoints
and are leading to disease, presumably through causing aberrant splicing by interfering
with lariat formation.”
In other words,
Fairbrother said, it could well be that a consequence of mutations in
branchpoints could be disease.
Source: Brown University