If I asked you, dear reader, to come up with a shortlist of the most monumental scientific achievements of the last century, chances are the Human Genome Project (HGP) would appear somewhere on that list. While many know of this herculean effort—which in 2003 produced the first draft sequence of our genetic blueprints—the detail-oriented among us may be quick to point out that, technically speaking, the HGP didn’t sequence the entirety of the human genome! Certain complex regions of our genome evaded the genome sequencing technologies available at the time, such that the ‘completed’ draft human genome announced in 2003 more accurately represented roughly 92% of the entire human genome. To be sure, this was still a monumental result, especially considering that the portion that was sequenced contains virtually all of our protein-coding genes.
If you’re Dr. Andrew Stergachis—an associate professor in the Division of Medical Genetics at the University of Washington who is dedicated to studying how changes in noncoding genomic regions contribute to human disease—that 8% isn’t just ‘leftover.’ In a recent publication in Cell Genomics, Stergachis and colleagues combined a powerful chromatin profiling technique with new, complete genome sequencing data to discover exotic chromatin biology hiding in the most difficult-to-reach portions of our genomes. Their results have potentially far-reaching implications for our understanding of how our genomes are maintained, regulated, and replicated.
“This work was actually one of the first projects we started when I opened the lab around five years ago,” begins Stergachis. “At its core, it revolves around two technologies: one was a sequencing-based approach that we developed called Fiber-seq, which lets us determine the landscape of genome accessibility on a single DNA strand-level. The other was the advent of truly complete genome sequences produced by the Telomere-to-Telomere (T2T) Consortium, which for the first time gave us a look at the entire human genome, including those parts which previously evaded accurate sequencing.”
One might assume that the ~8% of ‘gaps’ left by the HGP are randomly dispersed throughout the genome and relatively unimportant, but nothing could be further from the truth. In fact, one major constituent of these gaps were centromeres—the regions smack dab in the middle of each of our chromosomes, which cells use as ‘handles’ to portion the replicated genome into each daughter cell during cell division. “Once the first complete human genome (called CHM13) was available, we applied our Fiber-seq technique to the same cell line, mapped the resulting genome accessibility to CHM13, and immediately noticed something very strange happening at the centromeres,” notes Stergachis.
What Stergachis and colleagues noticed was a strange pattern of genome accessibility that challenged the dogma of how genomes work. Classically, chromatin is thought to exist in one of two distinct states: euchromatin, which is accessible to genome-interacting proteins and generally transcriptionally active, and heterochromatin, which is dense, inaccessible, and generally not transcriptionally active. At single centromeric DNA strands, the team saw something in between: regions of ultra-dense, inaccessible chromatin punctuated with patches of open and accessible chromatin. Because this chromatin had features of both traditional chromatin types, they named it ‘dichromatin.’ Beyond being of mixed type, dichromatin was also heterogenous: different DNA strands (from the same genomic locus) showed different patterns of accessible and inaccessible chromatin, though the patches of accessible DNA clustered non-randomly within each individual DNA strand.
As Stergachis notes, “The first thing we did when we got this result was get skeptical and wait for another complete genome sequence to be available, so that we could rule out some artifact of our sample or approach.” Reassuringly, once reference genomes for two other human cell lines were available, the team applied Fiber-seq to centromeric regions and again found this conspicuous dichromatin feature.
To ascertain whether centromeric dichromatin was evolutionarily conserved, Stergachis and collaborators sequenced and assembled complete centromeres from an eastern hoolock gibbon, revealing centromeric dichromatin as a feature likely conserved in all primates! Finding centromeric dichromatin in the gibbon genome also gave the researchers an important mechanistic clue concerning this exotic DNA architecture. Specifically, the gibbon genome has recently evolved to deactivate old centromeres and form new ones, which lack two DNA sequence features characterizing human centromeres (CENP-B boxes and alpha-satellite repeats, for the aficionados). The fact that gibbon centromeres had dichromatin indicates that these two highly conserved genomic features aren’t necessary for dichromatin formation.
How far back in evolution does dichromatin go? To tackle this question, Stergachis and colleagues collaborated with Dr. Sue Biggins of the Basic Sciences Division at Fred Hutch, whose lab are experts in centromere biology. From Dr. Biggins, the team obtained and applied Fiber-seq to full genomes from the budding yeast, Saccharomyces cerevisiae. Unlike primates, whose centromeres belong to a class known as regional centromeres, yeast have a distinct centromere architecture called point centromeres. “Interestingly, and perhaps reassuringly, we found a notable absence of dichromatin in centromeres from yeast,” Stergachis notes. Instead, Fiber-seq on yeast DNA revealed a near-homogenous patch of inaccessible chromatin fitting neatly with the described binding sites of the yeast kinetochore (the large protein complex responsible for pulling chromosomes apart during cell division). Thus, it appears that centromeric dichromatin may be one biological feature that distinguishes point centromeres from regional centromeres.
To Stergachis, this work highlights the utility of sequencing genomes end-to-end and the potential perils of generalizing the biology we know to uncharted territory. “If I had to choose one takeaway from this work, it would be that there is fascinating and wholly distinct chromatin biology going on in these hard-to-reach portions of our genomes—we can’t always take what we know about the rest of the genome and simply apply it to these portions as well,” he says. Looking forward, the team is excited to figure out how dichromatin is established in the first place and how it changes over time in different biological contexts—including in some human diseases that feature expansion and misplacement of centromeres. “Of course, this work couldn’t be possible without collaborations within and beyond Seattle; we’re grateful to the T2T Consortium for the complete genomes, the Biggins lab at the Hutch for the yeast work, our collaborators at UConn for the primate work, and many others that truly enabled this discovery.”
The spotlighted work was funded by the National Institutes of Health, a 2021 Catalytic Collaborations pilot grant from the Brotman Baty Institute for Precision Medicine, and the Howard Hughes Medical Institute.
Dubocanin, D., Hartley, G. A., Sedeño Cortés, A. E., Mao, Y., Hedouin, S., Ranchalis, J., Agarwal, A., Logsdon, G. A., Munson, K. M., Real, T., Mallory, B. J., Eichler, E. E., Biggins, S., O’Neill, R. J., & Stergachis, A. B. (2025). Conservation of dichromatin organization along regional centromeres. Cell Genomics, 5(4), 100819. https://doi.org/10.1016/j.xgen.2025.100819
Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium member Dr. Sue Biggins contributed to this research.
Science Spotlight writer David Sokolov is a graduate student in the Sullivan Lab at the Fred Hutch. He studies how cancer cells modify their metabolism to facilitate rapid proliferation and accommodate tumor-driving mitochondrial defects. He's originally from the east coast and has bachelors' and masters' degrees from West Virginia University. Outside of the lab, you'll find him enjoying the outdoors, playing music, or raising composting worms in his front yard.
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