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Genome study reveals centromeres as one of the fastest-changing regions in human DNA
A centromere is a specific region on a chromosome that ensures that, when a cell divides, the chromosome separates accurately so each new cell receives the correct amount of genetic material. Despite their essential role, centromeres remain one of the last major blind spots in the human genome.
A recent study published in Nature set out to reveal what had been hidden inside human centromeres, using advanced long-read sequencing and custom-built computational tools to piece together 2,110 complete centromeres. The researchers sampled individuals from 28 population groups across five continents, then compared their centromeres with 5,747 assembled by the Human Pangenome Reference Consortium to trace how these regions differ and evolve.
They discovered 226 major centromere haplotypes—distinct genetic patterns—and 1,870 new genetic variants. By studying a four-generation family, they were able to follow centromeres as they changed from parent to child, tracking genetic changes across generations.
They discovered that centromeres mutated faster than any other part of the human genome, with certain chromosomes accumulating changes at up to 20 times the rate of others.
The kinetochore attachment site, the anchor point where the chromosome attaches to the cell machinery during division, mutated faster than any other part.
Mapping minute changes
Centromeres have often been overlooked in studies of human genetic variation because they consist of long stretches of nearly identical repeated DNA called α-satellites. That similarity makes it difficult for standard methods to distinguish one sequence from another and detect the differences between them.
As a result, standard genome references captured very little of the diversity hidden in centromeres across individuals and populations, leaving scientists with no clear idea of how centromere DNA, structure and kinetochore placement vary around the world. They are also in the dark about how quickly these regions mutate or whether their rapid change contributes to chromosomal errors.
New tools open the region
Recent advances in DNA sequencing, particularly long-read sequencing technologies that can finally make sense of complex repetitive regions and structural variants, enabled this study to overcome those old technical barriers. In this study, the researchers took advantage of this new technique to explore centromeres and answer some of their questions.
They began by assembling DNA from 65 diverse individuals using a tool the team created called AssemblyRepairer. They successfully assembled 2,110 centromeres and verified that they were more than 99.9999% accurate.
To watch how centromere mutations occur in real time across generations, the team turned to a four-generation, 28-member family, resolving 483 centromeres and comparing parents directly with children. This allowed them to spot brand-new, spontaneous mutations that appeared in just one generation.
Unexpected structures and ancient traces
The results revealed that centromeres have far more genetic and structural diversity than previously appreciated. When a cell divides, it attaches each chromosome to a protein handle called a kinetochore. For years, scientists assumed there was only one handle per chromosome.
This sequencing found that some centromeres break that rule: Around 6% have two kinetochores, and about 1% have three. Even more importantly, these multi-handled centromeres run in families, passing from parents to children across generations.
While mapping centromeres, the researchers noticed something remarkable: On chromosomes 10 and 21, some people carried centromeres that were separated by more than a million years of evolution from the other modern versions.
Comparing these sequences with ancient genomes indicated that modern humans outside Africa might have inherited these unique centromeres from ancient human relatives through interbreeding with Neanderthals and Denisovans.
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Evidence of potential introgression from archaic hominins within centromeres. Credit: Nature (2026). DOI: 10.1038/s41586-026-10841-9 -
Accelerated mutation rates within the putative kinetochore site results in changes in its position, distribution and sequence composition across generations. Credit: Nature (2026). DOI: 10.1038/s41586-026-10841-9
A fast-moving evolutionary contest
Based on the findings, the researchers proposed a kind of evolutionary tug-of-war between centromere DNA and its binding proteins. The anchor point mutates so often that they keep changing both the DNA sequence and the chemical markers that control how it's used, driving rapid evolution in these critical regions of our genome.
This study brings much-needed clarity to one of the genome's last blind spots. With better centromere maps, doctors may be able to interpret genetic tests that detect chromosomal abnormalities more accurately.
Written for you by our author Sanjukta Mondal, edited by Sadie Harley, and fact-checked and reviewed by Robert Egan—this article is the result of careful human work. We rely on readers like you to keep independent science journalism alive. If this reporting matters to you, please consider a donation (especially monthly). You'll get an ad-free account as a thank-you.
Publication details
Shenghan Gao et al, A global view of human centromere variation and evolution, Nature (2026). DOI: 10.1038/s41586-026-10841-9
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Citation: Genome study reveals centromeres as one of the fastest-changing regions in human DNA (2026, August 11) retrieved 12 August 2026 from https://phys.org/news/2026-08-genome-reveals-centromeres-fastest-regions.html
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