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December 15, 2014

Gene-Level Loop-ome Ties Up Regulatory Loose Ends

A 2.1 Mb region on chromosome 20 shows eight domains, six of which are demarcated by loops between convergent CTCF-binding sites. About 10,000 of these loops have been identified in the human genome. [Miriam Huntley and Cell]

  • In the genome, folding is tantamount to regulation, say researchers who have catalogued 10,000 loops in what has been jocularly called the loop-ome. Drollery aside, the catalogue reveals structures that correlate with gene activation and show conservation across cell types. Essentially, the loops reveal a new kind of genetic regulation that can help explain how a single genome can produce different types of cells.

    The loop-ome is the culmination of a five-year project undertaken by researchers at Harvard University, Baylor College of Medicine, Rice University, and the Broad Institute. These researchers presented their findings December 11 in the journal Cell, in an article entitled, “A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping.”

    “We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments,” wrote the authors, who added that the loops they found “frequently link promoters and enhancers.” The loops, moreover, are demarcated by loop anchors that “typically occur at domain boundaries and bind CTCF.”

    To arrive at these results, the researchers used a technology called in situ Hi-C to collect billions of snippets of DNA that were alter analyzed for signs of loops. Hi-C, introduced five years ago by researchers at the Broad Institute, was refined during the length of the current study so that it could attain the necessary resolution.

    “The 2009 study was a great proof of principle, but when we looked at the actual maps, we couldn't see fine details,” said senior author Erez Lieberman Aiden, Ph.D., an assistant professor of genetics at Baylor and of computer science and computational and applied mathematics at Rice. “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.”

    Besides overhauling Hi-C, the researchers had to overcome significant computational hurdles. "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?'" said co-first author Miriam Huntley, a doctoral student at the Harvard School of Engineering and Applied Sciences. "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."

    By combining their revamped Hi-C technology and their “big data” visualization tools, the researchers 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," remarked first author Suhas Rao, Ph.D., a researcher at Baylor's Center for Genome Architecture. "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," emphasized Eric Lander, Ph.D., a corresponding author on the paper and director of the Broad Institute, professor of biology at MIT, and professor of systems biology at Harvard Medical School. "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."

    Interestingly, the team found that the largest loops in the genome are present only 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."

    The researchers 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," noted Dr. Aiden.

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