MIT researchers have developed a new method to map interactions between genes and their regulators, revealing a new layer of 3D genome structure. With 100 times higher resolution than previous methods, this breakthrough enables the affordable study of genomic interactions, potentially driving advances in gene regulation.
MIT scientists have developed the highest-resolution maps of 3D genome interactions to date. Their new method, Region Capture Micro-C (RCMC), focuses on regions of interest, allowing them to generate maps 100 times richer in information than previous methods.
According to scientific estimates, over 50% of the genome is comprised of regulatory elements that are responsible for controlling genes, despite genes accounting for only 2% of the genome.
Recent genome-wide association studies have identified various genetic variants within these regulatory regions, linked to specific diseases. To gain a better understanding of how these diseases develop and potentially find treatments, researchers need to identify which genes interact with these regulatory elements.
This task requires mapping the genome’s different sections and their interactions when chromosomes are condensed in the nucleus. Chromosomes consist of nucleosomes, structural units of tightly wound DNA strands around proteins that allow them to fit inside the nucleus’s limited space.
Over a decade ago, a group of researchers from MIT, among others, created a technique known as Hi-C that uncovered the fractal globule architecture of the genome. This organization allows cells to tightly pack DNA while preventing tangles and enables easy unfolding and refolding of DNA as needed.
The Hi-C method involves using restriction enzymes to break down the genome into smaller pieces, which are then biochemically linked together based on their 3D proximity within the cell’s nucleus. After amplifying and sequencing the connected pieces, researchers can identify their interacting partners.
While Hi-C provides valuable insights into the overall 3D structure of the genome, it has limited resolution when it comes to pinpointing specific interactions between regulatory elements like enhancers and genes. Enhancers are short DNA sequences that can activate gene transcription by binding to the gene’s promoter site, where transcription begins.
The MIT team used a more contemporary technique called Micro-C, developed by scientists at the University of Massachusetts Medical School under the direction of Stanley Hsieh and Oliver Rando, to reach the resolution required to discover these interactions. Researchers from the University of California at Berkeley and UMass Medical School, including Hansen, Hsieh, Rando, and others, used micro-C for the first time in budding yeast in 2015 and then transferred it to mammalian cells in three articles published in 2019 and 2020.
By fragmenting the genome with an enzyme called micrococcal nuclease, Micro-C provides better resolution than Hi-C. Hi-C’s restriction enzymes only cleave the genome at certain, randomly dispersed DNA sequences, leaving behind DNA pieces of various sizes. Contrarily, micrococcal nuclease evenly divides the genome into pieces the size of nucleosomes, each of which has 150–200 DNA base pairs. This consistency of minuscule fragments gives Micro-C a higher resolution than Hi-C.
The existing approach, Micro-C, surveys the entire genome but lacks the necessary resolution to identify specific types of interactions. For instance, to observe the interactions of 100 different genome sites with each other, Micro-C would need to sequence 10,000 times, making it impractical and expensive. Since the human genome contains around 22 million sites, this method would require more than $1 billion.
To address this issue, the researchers devised a more focused approach called Region Capture Micro-C (RCMC). By targeting regions containing genes of interest, RCMC reduces the number of possible genomic sites by a thousandfold, thereby reducing sequencing costs by a millionfold to about $1,000. The new method allows for generating genome maps that are 100 times richer in information than other published techniques, making it an affordable and practical solution.
Now, MIT researchers have discovered a new technique to map out the regulatory regions in the human genome, which control gene expression within a cell. These regions can be located up to 2 million base pairs away from the target gene.
The genome loops itself in a 3D structure to allow these distant regions to interact closely. With this innovative approach, MIT researchers were able to map these interactions with an unprecedented 100 times higher resolution than was previously possible, providing new insights into the complex workings of the human genome.
“Using this method,” as explained by senior author Anders Sejr Hansen, “we generate the highest-resolution maps of the 3D genome that have ever been generated, and what we see are a lot of interactions between enhancers and promoters that haven’t been seen previously.
“The one limitation is that you can’t get the whole genome, so you need to know approximately what region you’re interested in, but you can get very high resolution, very affordably.”
The recent study conducted by researchers focused on exploring five regions that varied in size from hundreds of thousands to about 2 million base pairs. These regions were chosen because of interesting features that were revealed by previous studies, including the well-known gene Sox2, which plays a significant role in tissue formation during embryonic development.
The researchers captured and sequenced the DNA segments of interest, and their findings revealed several enhancers that interact with Sox2, as well as previously undiscovered interactions between nearby genes and enhancers. Notably, in regions filled with genes and enhancers, some genes were found to interact with as many as 50 other DNA segments, with each interacting site contacting an average of about 25 others.
“People have seen multiple interactions from one bit of DNA before, but it’s usually on the order of two or three, so seeing this many of them was quite significant in terms of difference,” Huseyin adds.
However, the study’s technique falls short in providing insights into whether these interactions occur simultaneously or at different times, and which ones are the most critical.
During the study, the researchers observed that DNA has a tendency to coil into “microcompartments,” which help facilitate these interactions. Unfortunately, the researchers were unable to determine precisely how these microcompartments form. Despite this, they remain optimistic that further investigation into the underlying mechanisms will help answer the fundamental question of how genes are regulated.
“Even though we’re not currently aware of what may be causing these microcompartments, and we have all these open questions in front of us, we at least have a tool to really stringently ask those questions,” adds lead author Viraat Goel.
The MIT team has announced plans to collaborate with researchers at Boston Children’s Hospital and Harvard Medical School in their pursuit of understanding genomic regions linked to various disorders. Their focus is not only on addressing pertinent questions but also on applying their analysis to blood disorders that have been identified in genome-wide association studies. Additionally, they aim to study variants linked to metabolic disorders through their collaboration with Harvard Medical School researchers.
Source: 10.1038/s41588-023-01391-1
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