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| This illustrative rendering of a 2.1 Mb region on chromosome 20 shows eight domains, six of which are demarcated by loops between convergent CTCF-binding sites located at the domain boundaries. The research team identified approximately 10,000 of these loops in the human genome. |
In a triumph for cell biology, researchers have assembled the first
high-resolution, 3D maps of entire folded genomes and found a structural
basis for gene regulation -- a kind of "genomic origami" that allows
the same genome to produce different types of cells. The research
appears online today in Cell.
A central goal of the five-year project, a collaboration between
researchers at Harvard University, Baylor College of Medicine, Rice
University, and the Broad Institute of Harvard and MIT, was to identify
the loops in the human genome. 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 analyzed 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 realizing that folding is regulation," said
study co-first author Suhas Rao, a researcher at Baylor's Center for
Genome Architecture and a 2012 graduate of Harvard College. "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."
Co-first author Miriam Huntley, a doctoral student at the Harvard
School of Engineering and Applied Sciences (SEAS), said, "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."
Senior author Erez Lieberman Aiden, Ph.D. '10, formerly a junior
fellow in the Harvard Society of Fellows, is now assistant professor of
genetics at Baylor and of computer science and computational and applied
mathematics at Rice. Aiden said the work began five years ago, shortly
after he and colleagues at the Broad Institute published a
groundbreaking study introducing the Hi-C methodology for sequencing
genomes in 3-D.
"The 2009 study was a great proof of principle, but when we looked at
the actual maps, we couldn't see fine details," Aiden said. "It took us
a few years to get the resolution to a biologically usable level. The
new maps allow us to really see, for the first time, what folding looks
like at the level of individual genes."
The work to refine Hi-C and produce full-genome maps with gene-level
resolution continued when Aiden moved to Houston in 2013, established
the Center for Genome Architecture at Baylor and joined the Center for
Theoretical Biological Physics at Rice. Aiden, who earned his master's
degree in applied physics and Ph.D. in applied mathematics at Harvard
SEAS, credited Huntley and Rao with leading the research effort.
In addition to the challenge of overhauling the Hi-C experimental design, the team faced significant computational hurdles.
"In 2009, we were dividing the genome into 1-million-base blocks, and
here we are dividing it into 1,000-base blocks," said Huntley, who is a
student of Aiden's. "Since any block can collide with any other block,
we end up with a problem that is a millionfold more complicated. The
overall database is simply vast."
Identifying the loops themselves was yet another challenge.
"Ordinary computer CPUs (central processing units) are not
well-adapted for the task of loop detection," Rao said. "To find the
loops, we had to use GPUs, processors that are typically used for
producing computer graphics."
Huntley said new methods were also developed to speed the data
processing and reduce experimental "noise," irregular fluctuations that
tend to obscure weak signals in the data.
"We faced a real challenge because we were asking, 'How do each of
the millions of pieces of DNA in the database interact with each of the
other millions of pieces?'" Huntley said. "Most of the tools that we
used for this paper we had to create from scratch because the scale at
which these experiments are performed is so unusual."
The big-data tools created for the study included parallelized
pipelines for high-performance computer clusters, dynamic programming
algorithms, and custom data structures. Rao said the group also relied
heavily on data visualization tools created by co-authors Neva Durand
and James Robinson.
"When studying big data, there can be a tendency to try to solve
problems by relying purely on statistical analyses to see what comes
out, but our group has a different mentality," Rao said. "Even though
there was so much data, we still wanted to be able to look at it,
visualize it and make sense of it. I would say that almost every
phenomenon we observed was first seen with the naked eye."
Through these methods, the team discovered a series of rules about how and where loops can form in the genome.
"If DNA were a shoestring, you could make a loop anywhere. But within
the cell, the formation of loops is highly constrained," said Rao. "The
loops we see almost all span fewer than 2 million genetic letters; they
rarely overlap; and they are almost always associated with a single
protein, called CTCF." CTCF is known to be involved in the regulation of
the 3D structure of chromatin, the building block of chromosomes.
"The most stunning discovery was about how CTCF proteins form a loop"
said Eric Lander, a corresponding author on the paper. "Even when they
are far apart, the CTCF elements that form a loop must be pointing at
each other -- forming a genomic yin and yang." Lander is director of the
Broad Institute, professor of biology at MIT, and professor of systems
biology at Harvard Medical School.
Interestingly, the team found that the largest loops in the genome
are only present in women. Huntley pointed out that "the copy of the X
chromosome that is off in females contains gigantic loops that are up to
30 times the size of anything we see in males."
They also found that many of the loops present in humans are also
present in mice, implying that these specific folds have been preserved
over nearly one hundred million years of evolution.
"Our findings suggest that mammals share not only similar 1D genome
sequences, but also similar 3D genome folding patterns," said Aiden.
Additional co-authors include Elena Stamenova, Ivan Bochkov, Adrian
Sanborn, Ido Machol, and Arina Omer at Baylor. The research was
supported by the National Science Foundation, the National Institutes of
Health, the National Human Genome Research Institute, NVIDIA, IBM,
Google, the Cancer Prevention and Research Institute of Texas and the
McNair Medical Institute.
This release was adapted from materials produced by Rice University and Baylor College of Medicine.
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