Knot-like “i-motifs” make the genetic code more complex
The knot-like i-motif structure, which protrudes from the double helix of DNA, has been mapped to 50,000 locations in the human genome, concentrated in key functional areas, including regions that control gene activity. (Source: Garvan Institute)
DARLINGHURST, Australia — The human genome holds a secret: it is full of knots. A new study has mapped over 50,000 regions where DNA folds into complex structures called i-motifs, potentially revealing a new dimension of genetic regulation. This discovery could revolutionize our understanding of gene regulation and potentially lead to new approaches to treating disease.
For decades, scientists have known that DNA normally exists as a double helix, the typical twisted ladder structure that Watson and Crick so famously described. But this new research shows that certain sections of our genetic code can take on a more exotic shape, folding in on themselves to form four-stranded knots.
These i-motif structures, named for their unusual folding pattern, were once thought to be laboratory curiosities that could not exist in living cells. The general belief was that they required acidic conditions incompatible with life. However, recent advances have shown that i-motifs can form under physiological conditions, and this study now shows how widespread they are throughout the human genome.
Led by researchers at the Garvan Institute of Medical Research in Australia, the team developed a novel method to map i-motif structures across the human genome. They used a specially designed antibody that specifically recognizes and binds to i-motifs, allowing them to fish out these structures from purified human DNA.
The results, published in The EMBO Journalwere remarkable. The researchers identified over 50,000 regions capable of forming i-motifs in DNA samples from three different human cell lines. These structures were found throughout the genome, in different parts of the genes and in the spaces between them.
“This is a remarkably high number for a DNA structure whose existence in cells was once considered controversial,” said lead author Daniel Christ, head of the Antibody Therapeutics Lab and director of the Centre for Targeted Therapy at Garvan, in a statement. “Our results confirm that i-motifs are not just laboratory curiosities, but are widespread – and likely play a key role in genome function.”
What do these mysterious DNA origami structures actually do?
The study provides compelling evidence that i-motifs play an important role in regulating gene activity. They are usually located near the start points of genes and are particularly abundant in genes that become active in the early stages of the cell cycle when cells prepare to divide.
Further supporting this link to gene regulation is the fact that i-motifs often overlap with other known regulatory elements in the genome. For example, they often occur near another type of unusual DNA structure called G-quadruplexes, which have already been implicated in the control of gene expression.
Understanding how i-motifs contribute to gene regulation could provide new insights into fundamental biological processes and disease mechanisms. It could also open new avenues for drug development, as molecules that target or manipulate i-motifs could potentially be used to control gene activity in therapeutic contexts.
“The widespread occurrence of i-motifs near these ‘holy grail’ sequences involved in difficult-to-treat cancers opens up new opportunities for new diagnostic and therapeutic approaches,” says study co-author Sarah Kummerfeld, Chief Scientific Officer at Garvan. “It may be possible to develop drugs that target i-motifs to influence gene expression, which could expand current treatment options.”
The research also highlights the dynamic nature of our genetic material. Far from being a static blueprint, DNA appears to be a shape-shifting molecule capable of adopting different conformations to optimize its function. This adds another layer of complexity to the already intricate dance of genes and proteins that orchestrate life.
Like any major scientific advance, this discovery raises as many questions as it answers. How exactly do i-motifs form and dissolve in living cells? What proteins interact with them? How do they change in different cell types or disease states? These questions will undoubtedly drive future research in this exciting new field. The discovery of widespread i-motifs in human DNA opens a new chapter in our understanding of genetics and could ultimately lead to new approaches to diagnosing and treating a wide range of diseases.
Summary of the paper
methodology
The researchers used a sophisticated technique to map i-motifs throughout the human genome. They started with DNA extracted from three different human cell lines and broke it into small fragments. They then used a special antibody (called an iMab) that specifically recognizes i-motif structures. This antibody acted like a fishhook, allowing them to pull out DNA fragments containing i-motifs.
These fragments were then sequenced to determine their exact location in the genome. To confirm their results, the team synthesized some of the identified DNA sequences and used biophysical techniques to confirm that they did indeed form i-motifs under different conditions.
Key findings
The study identified over 50,000 regions capable of forming i-motifs in the genomes of three different cell lines. These structures were found throughout the genome, including in gene regulatory regions, introns (non-coding regions within genes), and intergenic spaces.
Importantly, i-motifs were often located near the start sites of genes and were particularly common in genes that become active in the early stages of the cell cycle. The researchers also observed considerable overlap between i-motif positions and other known regulatory elements such as G-quadruplexes.
Limitations of the study
While this study is groundbreaking, it does have some limitations. The experiments were performed on purified DNA outside of living cells, so it is not certain how accurately this reflects the formation of the i-motif in the complex environment of a living cell.
In addition, the study focused on only three cell lines, which may not capture the full diversity of i-motif patterns across different cell types or physiological states. The researchers also note that their method may not detect all possible i-motif structures, particularly those that are less stable or form under different conditions.
Discussion & Insights
This research provides strong evidence that i-motif structures are a common and likely important feature of the human genome. The widespread distribution of i-motifs and their association with gene regulatory regions suggest that they play a significant role in controlling gene expression. This could have far-reaching implications for our understanding of gene regulation, cellular processes and disease mechanisms.
The study also highlights the dynamic nature of DNA, demonstrating that our genetic material is capable of adopting complex three-dimensional structures beyond the classic double helix. These findings open new avenues for studying the structure and function of DNA and could ultimately lead to new therapeutic approaches that specifically target or manipulate i-motifs to control gene activity.
Financing and Disclosures
The study was funded by the National Health and Medical Research Council. The researchers declared that there were no conflicts of interest related to this work. The work acknowledges the use of services and facilities of the Australian Genome Research Facility and the Children’s Medical Research Institute.
