HSE Researchers Create Genome-Wide Map of Quadruplexes
An international team, including researchers from HSE University, has created the first comprehensive map of quadruplexes—unstable DNA structures involved in gene regulation. For the first time, scientists have shown that these structures function in pairs: one is located in a DNA region that initiates gene transcription, while the other lies in a nearby region that enhances this process. In healthy tissues, quadruplexes regulate tissue-specific genes, whereas in cancerous tissues they influence genes responsible for cell growth and division. These findings may contribute to the development of new anticancer drugs that target quadruplexes. The study has been published in Nucleic Acids Research.
The word 'DNA' usually brings to mind a double helix, but this molecule can adopt other forms as well. In some regions, the DNA strand can unwind, bend, and form a small knot. If such a fragment is rich in guanine (denoted by the letter G in the DNA sequence), it can fold into a quadruplex—a three-dimensional structure in which several layers of guanine are stacked on top of one another. For proteins that regulate gene activity, these structures serve as prominent landmarks, helping them locate the correct regions of DNA.
Quadruplexes are short-lived structures: they form rapidly, perform their function, and then disappear, meaning that experiments can capture only a fraction of them. Moreover, different experimental methods detect different types of quadruplexes. As a result, it has not been possible to create a genome-wide map that includes all DNA regions where quadruplexes can form.
To address this problem, the team of HSE researchers further trained the genomic language model DNABERT on quadruplex data and used its predictions to reconstruct where these structures arise across the genome.
Maria Poptsova
'In our study, we trained DNABERT on EndoQuad, the world’s largest database of experimentally validated quadruplexes, resulting in the GQ-DNABERT model. This model evaluates DNA sequences to predict where a quadruplex is likely to form,' comments Maria Poptsova, Director of the Centre for Biomedical Research and Technology at the HSE Faculty of Computer Science.
Unlike simple algorithms that search only for sequences capable of forming a quadruplex, GQ-DNABERT also considers the surrounding DNA context, which determines whether a region actually folds into a quadruplex. As a result, the model was able to predict about 360,000 quadruplexes—far more than have been identified by individual experimental methods.
The model confirmed the well-known fact that quadruplexes frequently occur in promoters—DNA regions upstream of genes where transcription is initiated. Unexpectedly, many quadruplexes were also found in nearby enhancers, genomic elements that boost gene transcription and influence how much protein is produced. The researchers discovered that quadruplexes often form simultaneously in both the promoter and the enhancer, creating pairs that jointly regulate gene activity.
To investigate the role of these pairs in cells, the researchers used single-cell sequencing data from experiments. In such datasets, the DNA regions that are statistically associated with the activity of specific genes are pre-identified. By overlaying the GQ-DNABERT map for six tissue types onto these data, the scientists found that promoter–enhancer pairs are more often associated with genes responsible for tissue-specific functions: in the brain, for neuronal development and function; in the blood, for immune cell activity; and in the intestine, for epithelial functions. The researchers then examined these pairs in tumour tissues and compared them with those in healthy tissues. While the number of promoter–enhancer pairs containing quadruplexes was similar, the functions of the associated genes differed dramatically.
'In normal cells, these pairs are associated with tissue-specific programmes, whereas in cancer cells they are linked to universal processes of cell division and growth that drive tumour proliferation regardless of the tissue of origin,' explains Poptsova. 'In other words, in healthy cells, these pairs support tissue specialisation, while in cancer they become part of general programmes for rapid cell division.'
The resulting map of quadruplexes provides a clearer understanding of how these structures regulate gene activity in both normal and tumour cells. In the future, this information could be used to develop new anticancer drugs that selectively target quadruplexes.
The study was supported by a grant from the HSE AI Research Centre.
See also:
HSE and Yandex Propose Method to Speed Up Neural Networks for Image Generation
A team of scientists at HSE FCS and Yandex Research has proposed a method that reduces computational costs and accelerates text-to-image generation in diffusion models without compromising quality. These models currently set the standard for text-to-image generation, but their use is limited by high computational loads, the company said in a statement.
HSE Scientists Identify Effective Models for Training Research Personnel for Industry
Experts from the HSE Institute for Statistical Studies and Economics of Knowledge have examined industrial PhD programmes across 19 countries worldwide. The analysis shows that the key components of an effective model include co-funding by universities, industry, and government; dual academic supervision; and flexible intellectual property arrangements. The findings have been published in Foresight and STI Governance.
HSE Biologists Identify Factors That Accelerate Breast Cancer Recurrence
Scientists at HSE University have identified a molecular mechanism underlying aggressive breast cancer. They found that the signals supporting tumour growth originate not from the tumour itself but from its microenvironment. The researchers also demonstrated that reduced levels of the IGFBP6 protein in the tumour microenvironment lead to the accumulation of macrophages—immune cells associated with a higher risk of cancer recurrence. These findings already make it possible to assess patient risk more accurately and may, in the future, enable the development of drugs that target cells of the tumour microenvironment. The study has been published in Current Drug Therapy.
HSE University and Moscow DIT Partner to Advance 5G and 6G Networks
The Moscow Department of Information Technology and HSE University have signed a cooperation agreement in the field of innovative development of the capital’s IT infrastructure. The parties agreed on joint research into modern and promising communication technologies, including 5G and 6G, as well as AI, the Internet of Things, and other smart city technologies.
HSE University Presents Research Results at AI Conference in Oman
In April 2026, the International Conference on Intelligent Systems and Artificial Intelligence Applications (ISAA 2026) was held at the University of Nizwa in the Sultanate of Oman. The event was co-organised by HSE University, the University of Nizwa, and the University of Technology and Applied Sciences–Ibri. Researchers from HSE University were among the key speakers at the conference.
Russian Scientists Propose Method to Speed Up Microwave Filter Design
Researchers at HSE MIEM, in collaboration with colleagues from the Moscow Technical University of Communications and Informatics (MTUCI), have implemented a novel approach to designing microwave filters—generative synthesis using machine learning tools. The proposed method reduces the filter development cycle from several days to just a few minutes and in the future could be applied to the design of other microwave electronic devices. The results were presented at the IEEE International Conference '2026 Systems of Signals Generating and Processing in the Field of on Board Communications.'
Scientists Find That Only Technological Innovations Consistently Advance Environmental Sustainability
Renewable energy and labour productivity do not always contribute to environmental sustainability. Technological innovation is the only factor that consistently has a positive effect. This is the conclusion reached by an international team of researchers, including Natalia Veselitskaya, Leading Research Fellow at the HSE ISSEK Foresight Centre. The study has been published in Sustainable Development.
HSE’s CardioLife Test Among Winners of Data Fusion Awards 2026
The CardioLife genetic test—a development by the Centre for Biomedical Research and Technologies of the AI and Digital Science Institute at HSE University’s Faculty of Computer Science—has won the All-Russian cross-industry Data Fusion Awards, which recognise achievements in data and AI technologies. The project took first place in the Science–Business Partnership category, demonstrating a successful model for transferring technology from university research into the real healthcare sector.
HSE Researchers Train Neural Network to Predict Protein–Protein Interactions More Accurately
Scientists at the AI and Digital Science Institute of the HSE Faculty of Computer Science have developed a model capable of predicting protein–protein interactions with 95% accuracy. GSMFormer-PPI integrates three types of protein data (including information about protein surface properties) to analyse relationships between proteins, rather than simply combining datasets as in previous models. The solution could accelerate the discovery of disease molecular mechanisms, biomarkers, and potential therapeutic targets. The paper has been published in Scientific Reports.
HSE University Installs Geoscan Station at IIT Bombay
A Russian ground station for receiving SONIKS satellite data has been installed on the campus of the Indian Institute of Technology Bombay (IIT Bombay). Developed by Geoscan, the system will become part of a mirror laboratory project run jointly by HSE University and one of India’s leading universities.