In a groundbreaking advance that reshapes our understanding of genomic architecture, researchers at Penn State have unveiled a comprehensive map of non-canonical DNA structures—known as non-B DNA—in the complete, gapless genomes of great apes. This study leverages the revolutionary telomere-to-telomere (T2T) sequencing technology, which for the first time allows scientists to explore regions of DNA previously hidden due to their highly repetitive and complex nature. The work not only broadens our insight into the evolution and function of these enigmatic DNA conformations, but it also sets the stage for future discoveries into their roles in genetic diseases and cancer.
Since the first draft of the human genome was published in 2001, genomics has faced the formidable challenge of resolving highly repetitive DNA sequences. These regions, which often form unusual secondary structures, eluded complete characterization because short-read sequencing technologies could not reliably assemble them. Traditional methods fragmented the genome into countless small pieces, making it virtually impossible to reconstruct repetitive stretches. As a result, approximately 8% of the human genome remained unresolved for nearly two decades, veiling crucial parts of the genome—including telomeres and centromeres—from genetic scrutiny.
The advent of T2T sequencing marks a turning point. This long-read technology reads uninterrupted DNA segments spanning hundreds of thousands of base pairs, bypassing the confounding puzzle of identical repeat units imposed by previous approaches. The Telomere-to-Telomere Consortium successfully completed the human genome sequence in 2022 and 2023, and more recently, the complete genomes of all great apes, including chimpanzee, bonobo, gorilla, orangutans, and siamang, have been fully elucidated at this level of detail. This monumental achievement provides an unprecedented window into repetitive DNA landscapes and the curious non-B DNA structures they harbor.
Non-B DNA refers to DNA conformations deviating from the classic right-handed Watson-Crick double helix. These structures include bent DNA, hairpins, G-quadruplexes (G4s), and Z-DNA, each formed by specific sequence motifs frequently found in repetitive regions. They have been implicated in regulating critical cellular functions, such as initiating DNA replication, modulating gene expression, and maintaining chromosome integrity through telomeres and centromeres. However, until now, the full extent and distribution of these motifs in primate genomes had not been systematically surveyed.
The study, led by Kateryna Makova, Professor of Biology and Verne M. Willaman Chair of Life Sciences at Penn State, deployed computational and experimental approaches to chart these motifs across the newly assembled T2T genomes of six great ape species and the siamang as an outgroup. Their findings reveal non-B DNA motifs are significantly enriched in the recently resolved segments of the genomes, notably within the telomeric and centromeric regions which play pivotal roles during cell division.
Importantly, patterns of non-B DNA accumulation were remarkably conserved across the apes, highlighting a shared evolutionary blueprint amidst species diversity. The gorilla genome stands out with a notably higher load of repetitive DNA and correspondingly more non-B DNA motifs, suggesting species-specific nuances that may inform the understanding of genomic stability and adaptation. The enrichment of these motifs within complex repetitive sequences underscores their potential functional significance and evolutionary relevance.
Beyond their structural intrigue, non-B DNA conformations are prone to higher mutation rates and genomic instability, phenomena that can precipitate chromosomal rearrangements. Such rearrangements have profound implications, sometimes underpinning genetic disorders and cancer. The researchers pinpointed Z-DNA motifs as strikingly overrepresented—up to 97-fold—in satellite DNA regions corresponding to known chromosomal breakpoints, for instance in the translocation event associated with Down Syndrome on chromosome 21. This correlation hints at a mechanistic link between non-B DNA structures and chromosomal fragility.
While only a subset of non-B DNA motifs have been experimentally validated in this study, these findings ignite vital questions about the context-dependent formation of these structures in living cells. Factors such as cell type, developmental stage, and epigenetic modifications (e.g., DNA methylation) are likely to influence their stability and biological roles. This nuanced view shifts the paradigm from thinking of the genome as a static sequence to appreciating it as a dynamic, structurally complex entity.
The researchers emphasize that harnessing the power of complete genomes to characterize non-B DNA landscapes offers a powerful springboard for future inquiries. Integrating genome-wide structural predictions with experimental validation will be key to uncovering how these DNA structures participate in gene regulation, genome stability, and evolutionary innovation. The tangible link to diseases underscores the urgency of this line of research within biomedicine.
Interdisciplinary collaboration was pivotal to this project. Alongside Makova and first author Linnea Smeds, the team included experts in computer science, statistics, and biophysics from Penn State and the Czech Academy of Sciences. Such a blend of computational prowess and experimental biology sets a new standard for genomic research, especially when tackling complex, repetitive sequences long regarded as genomic “dark matter.”
This pioneering work, published in the journal Nucleic Acids Research, propels the frontier of genomics into uncharted territory by exposing the intricate dance between DNA sequence, structure, and function in primates. As researchers continue to unravel the roles of non-B DNA, these insights promise to illuminate fundamental mechanisms of genome evolution and open novel avenues for diagnosing and treating human diseases linked to genomic instability.
The journey from fragmented puzzles to complete genomic portraits of great apes underscores the transformative impact of technological innovation on biological discovery. In unlocking the mysteries of non-B DNA, the field moves closer to decoding the full complexity of the genome and harnessing its potential for human health and evolutionary understanding.
Subject of Research: Animals
Article Title: Non-canonical DNA in human and other ape telomere-to-telomere genomes
News Publication Date: 14-Apr-2025
Web References: http://dx.doi.org/10.1093/nar/gkaf298
Image Credits: Dani Zemba and Makova laboratory, Penn State
Keywords: non-B DNA, genome assembly, telomere-to-telomere sequencing, great apes, repetitive DNA, DNA secondary structures, genome evolution, chromosomal rearrangements, genetic diseases, G-quadruplex, Z-DNA, genome instability
Tags: alternative DNA conformationscancer research and DNA structuresDNA diversity in ape genomesevolutionary biology and genomicsgenetic disease implicationsgenomic architecture of great apeslong-read sequencing advancementsnon-B DNA researchnon-canonical DNA structuresrepetitive DNA sequences characterizationresolving complex genome regionstelomere-to-telomere sequencing technology