Even as cells split, the genome quietly holds on to its structure and its memory.
Before a cell can split into two, it must first copy all of its chromosomes so that each daughter cell receives a complete set of genetic instructions. For a long time, scientists believed that during this process, the genome temporarily lost its characteristic three-dimensional organization.
Once division finished, researchers thought the DNA slowly rebuilt that rounded, folded structure, which is critical for determining which genes are active inside a cell.
New findings from MIT now show that this long-standing view is incomplete. By applying a much more detailed genome mapping approach, the researchers discovered that small three-dimensional loops linking genes with their regulatory elements remain in place even as cells divide during mitosis.
“This study really helps to clarify how we should think about mitosis. In the past, mitosis was thought of as a blank slate, with no transcription and no structure related to gene activity. And we now know that that’s not quite the case,” says Anders Sejr Hansen, an associate professor of biological engineering at MIT. “What we see is that there’s always structure. It never goes away.”
DNA Loops Grow Stronger During Chromosome Compaction
The team also found that these regulatory loops become more pronounced as chromosomes tighten in preparation for division. As DNA packs more densely, regulatory elements are pushed closer together, making it easier for them to connect. According to the researchers, this process may allow cells to carry forward important gene interactions from one division cycle to the next.
“The findings help to bridge the structure of the genome to its function in managing how genes are turned on and off, which has been an outstanding challenge in the field for decades,” says Viraat Goel PhD ’25, the study’s lead author.
Hansen and Edward Banigan, a research scientist at MIT’s Institute for Medical Engineering and Science, are the paper’s senior authors. The study was published in Nature Structural and Molecular Biology. Additional authors include Leonid Mirny of MIT’s Institute for Medical Engineering and Science and Department of Physics, and Gerd Blobel of the Perelman School of Medicine at the University of Pennsylvania.
How Scientists Map the Genome in Three Dimensions
Over the past two decades, researchers have learned that DNA inside the cell nucleus naturally folds into a network of three-dimensional loops. Some of these loops allow genes to interact with distant regulatory regions that can be separated by millions of base pairs, while others help compact chromosomes during cell division.
Much of this work has relied on a method called Hi-C, which was developed by a team that included MIT researchers and was led by Job Dekker at the University of Massachusetts Chan Medical School. Hi-C involves cutting DNA into many fragments, chemically linking pieces that sit close together in three-dimensional space inside the nucleus, and then sequencing those fragments to identify interacting regions.
While useful, Hi-C lacks the resolution needed to detect many precise interactions between genes and regulatory elements such as enhancers. Enhancers are short stretches of DNA that activate gene transcription by binding to a gene’s promoter — the site where transcription begins.
A Sharper Tool Reveals Hidden Genome Structures
In 2023, Hansen and his colleagues introduced a new method capable of examining genome architecture at dramatically higher resolution. Called Region-Capture Micro-C (RC-MC), the technique uses a different enzyme to cut DNA into evenly sized pieces and focuses on specific regions of the genome, allowing for highly detailed three-dimensional mapping.
With RC-MC, the researchers identified a previously unseen type of genome organization they named “microcompartments.” These are small, tightly connected loops that form when nearby enhancers and promoters bind together.
Earlier experiments showed that microcompartments did not arise through the same processes that create larger genome structures, but how they formed remained unclear. To investigate further, the researchers turned their attention to cells undergoing division. During mitosis, chromosomes become highly compact so they can be copied, organized, and evenly distributed between two daughter cells. As this happens, larger genome features such as A/B compartments and topologically associating domains (TADs) vanish.
Unexpected Persistence During Mitosis
The team initially assumed that microcompartments would also disappear during mitosis. By following cells throughout the entire division process, they aimed to observe how these structures reappeared once division ended.
“During mitosis, it has been thought that almost all gene transcription is shut off. And before our paper, it was also thought that all 3D structure related to gene regulation was lost and replaced by compaction. It’s a complete reset every cell cycle,” Hansen says.
Instead, the researchers were surprised to find that microcompartments remain visible throughout mitosis and actually become stronger as division progresses.
“We went into this study thinking, well, the one thing we know for sure is that there’s no regulatory structure in mitosis, and then we accidentally found structure in mitosis,” Hansen says.
The RC-MC data also confirmed earlier findings that larger features like A/B compartments and TADs still disappear during mitosis.
Effie Apostolou, an associate professor of molecular biology in medicine at Weill Cornell Medicine who was not involved in the research, says, “This study leverages the unprecedented genomic resolution of the RC-MC assay to reveal new and surprising aspects of mitotic chromatin organization, which we have overlooked in the past using traditional 3C-based assays. The authors reveal that, contrary to the well-described dramatic loss of TADs and compartmentalization during mitosis, fine-scale “microcompartments” — nested interactions between active regulatory elements — are maintained or even transiently strengthened.”
Why Gene Activity Briefly Surges During Division
The findings may also help explain a long-observed burst of gene activity near the end of mitosis. Since the 1960s, scientists believed that gene transcription stopped completely during cell division. Studies published in 2016 and 2017 challenged that view, showing a short-lived spike in transcription that is quickly suppressed until division is complete.
In the MIT study, microcompartments were frequently located near genes that show this brief surge in activity. The researchers also found that these loops form as chromosomes compact during mitosis, bringing enhancers and promoters close enough to bind together.
Once established, microcompartments may unintentionally trigger gene transcription. The cell then rapidly shuts this activity down. After division ends and the cell enters G1, many of these loops weaken or disappear.
“It almost seems like this transcriptional spiking in mitosis is an undesirable accident that arises from generating a uniquely favorable environment for microcompartments to form during mitosis,” Hansen says. “Then, the cell quickly prunes and filters many of those loops out when it enters G1.”
New Questions About Cell Shape and Genome Control
Chromosome compaction can also be influenced by a cell’s size and shape, prompting the team to explore how physical changes to cells affect genome organization and gene regulation.
“We are thinking about some natural biological settings where cells change shape and size, and whether we can perhaps explain some 3D genome changes that previously lack an explanation,” Hansen says. “Another key question is how does the cell then pick what are the microcompartments to keep and what are the microcompartments to remove when you enter G1, to ensure fidelity of gene expression?”
Reference: “Dynamics of microcompartment formation at the mitosis-to-G1 transition” by Viraat Y. Goel, Nicholas G. Aboreden, James M. Jusuf, Haoyue Zhang, Luisa P. Mori, Leonid A. Mirny, Gerd A. Blobel, Edward J. Banigan and Anders S. Hansen, 17 October 2025, Nature Structural & Molecular Biology.
DOI: 10.1038/s41594-025-01687-2
The research received funding from the National Institutes of Health, a National Science Foundation CAREER Award, the Gene Regulation Observatory of the Broad Institute, a Pew-Steward Scholar Award for Cancer Research, the Mathers Foundation, the MIT Westaway Fund, the Bridge Project of the Koch Institute and Dana-Farber/Harvard Cancer Center, and the Koch Institute Support (core) Grant from the National Cancer Institute.