PRESS RELEASE

The research group of Dr Claudia Keller Valsecchi (Institute of Molecular Biology, Mainz, Germany) and their collaborators have discovered the master regulator responsible for balancing the expression of X chromosome genes between males and females in the malaria mosquito. This discovery helps scientists to better understand the evolution of the epigenetic mechanisms responsible for equalising gene expression between the sexes. The findings may contribute to the development of new ways to prevent the spread of malaria.

Most people would agree that mosquitoes are among the most annoying species on the planet. They keep us up all night with their whining, whirring wings, all while seeking a way to bite us and suck our blood. Yet mosquitoes are more than just a nuisance – they can also carry a whole host of serious, sometimes deadly diseases.

One of the most dangerous diseases that mosquitoes can carry is malaria, a disease that affects millions of people and causes hundreds of thousands of deaths every year, primarily in African countries. Malaria is caused by Plasmodium parasites, which are spread through mosquito bites – specifically those of marsh mosquitoes (Anopheles).

Importantly, only female mosquitoes bite, as they need the nutrients from blood to produce eggs. Scientists are therefore interested in understanding the mechanisms responsible for the molecular differences between male and female mosquitoes, as it could help us develop new ways to combat malaria.

Just like humans, the sex of a mosquito is determined by the sex chromosomes: females have two X chromosomes (XX), while males have an X and a Y chromosome (XY). This can be problematic, as males have only half the number of X chromosome genes as females, and hence would have only half the amount of proteins from the X chromosome. To compensate for this, there must be a way to increase the expression of X chromosome genes in males. However, no one knew what this mechanism could be in mosquitoes.

Agata Kalita from Claudia’s group, who is the first author of the study and funded by a fellowship from the Boehringer Ingelheim Fonds (BIF), spearheaded the research. They collaborated with the groups of Dr M. Felicia Basilicata (University Medical Center Mainz), Dr Eric Marois (University of Strasbourg, France) and Prof. Franjo Weissing (University of Groningen, The Netherlands). Together, the researchers discovered that the protein SOA (sex chromosome activation) is the key regulator that balances X chromosome gene expression in male mosquitoes. They found that SOA works by binding to X chromosome genes and increasing their expression, but only in males. Female mosquitoes, on the other hand, only produce a small amount of very short, non-functional SOA.

Agata comments on the study: “Balancing gene expression on sex chromosomes is essential for development in some species. However, others do not have such a mechanism at all. Unexpectedly, we discovered that in mosquitoes, balancing X chromosome expression by SOA is not necessary for development, but it does give males a head start”. Claudia says, “This is an important clue as to how the mechanisms that balance gene expression on sex chromosomes may have evolved in the first place”. M. Felicia Basilicata, a joint senior author, adds “Understanding the molecular principles acting on sex chromosomes will help us to understand differences between males and females in various human pathologies”.

The groups’ findings, which were published in the journal Nature, mark a major step forward in our understanding of how gene expression is balanced on the sex chromosomes. The researchers speculate that manipulating genes that exclusively affect one sex could be a useful strategy for reducing the number of blood-sucking female mosquitoes, which would be a huge boon in the fight against malaria.

For her part in the study, Agata was given an honourable mention for the International Birnstiel Award for Doctoral Research in Molecular Life Sciences 2023.

_{Further details}

_{Further information can be found at www.nature.com/articles/s41586-023-06641-0}

_{www.bifonds.de/fellowships-grants/phd-fellowships.html}

_{www.imp.ac.at/achievements/birnstiel-award}

_{Claudia Keller Valsecchi is a Group Leader at the Institute of Molecular Biology (IMB). Further information about research in the Keller Valsecchi lab can be found at www.imb.de/keller-valsecchi.}

_{About the Institute of Molecular Biology gGmbH}

_{The Institute of Molecular Biology gGmbH (IMB) is a centre of excellence in the life sciences that was established in 2011 on the campus of Johannes Gutenberg University Mainz (JGU). Research at IMB focuses on the cutting-edge fields of epigenetics, genome stability, ageing and RNA biology. The institute is a prime example of successful collaboration between a private foundation and government: The Boehringer Ingelheim Foundation has committed 154 million euros to be disbursed from 2009 until 2027 to cover the operating costs of research at IMB. The State of Rhineland-Palatinate has provided approximately 50 million euros for the construction of a state-of-the-art building and is giving a further 52 million in core funding from 2020 until 2027. For more information about IMB, please visit: www.imb.de.}

_{About the University Medical Center of the Johannes Gutenberg University Mainz}

_{The University Medical Center of the Johannes Gutenberg University Mainz is the only medical institution of supra-maximum supply in the German state of Rhineland-Palatinate and an internationally recognized science location. Medical and scientific specialists at more than 60 clinics, institutes and departments work interdisciplinarily to treat more than 345,000 patients per year. Highly specialized patient care, research and teaching are inseparably intertwined. More than 3,500 medicine and dentistry students as well as around 670 future medical, commercial and technical professionals are trained in Mainz. With a workforce of approximately 8,700 colleagues the University Medical Center Mainz is one of the largest employers in the region and an important driver of growth and innovation. Find more information online at www.unimedizin-mainz.de/?L=1}

_{Boehringer Ingelheim Foundation}

_{The Boehringer Ingelheim Foundation is an independent, non-profit organization that is committed to the promotion of the medical, biological, chemical, and pharmaceutical sciences. It was established in 1977 by Hubertus Liebrecht (1931–1991), a member of the shareholder family of the Boehringer Ingelheim company. Through its funding programmes Plus 3, Exploration Grants and Rise up!, the Foundation supports excellent scientists during critical stages of their careers. It also endows the international Heinrich Wieland Prize, as well as awards for up-and-coming scientists in Germany. In addition, the Foundation funds institutional projects in Germany, such as the Institute of Molecular Biology (IMB) and the European Molecular Biology Laboratory (EMBL) in Heidelberg. www.boehringer-ingelheim-stiftung.de/en}

_{Press contact for further information}

_{Dr Ralf Dahm, Director of Scientific Management}

_{Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany}

_{Phone: +49 (0) 6131 39 21455, Email: press@imb.de}

PRESS RELEASE

The research team of René Ketting at the Institute of Molecular Biology (IMB) in Mainz, Germany, has identified a new enzyme called PUCH, which plays a key role in preventing the spread of parasitic DNA in our genomes. These findings may also reveal new insights into how our bodies detect and fight bacteria and viruses to prevent infections.

Our cells are under constant attack from millions of foreign intruders, such as viruses and bacteria. To keep us from getting sick, our bodies have an immune system – a whole army of cells that specialises in detecting and destroying these invaders. However, our cells face threats not only from external enemies but also from within.

An amazing 45% of our genome is comprised of thousands of “genomic parasites” – repetitive DNA sequences called transposable elements (TEs). TEs are found in all organisms but have no specific function. They can, however, be dangerous; TEs are also called “jumping genes” because they can copy and paste themselves into new locations in our DNA. This is a major problem because it can lead to mutations that cause our cells to stop working normally or to become cancerous. As such, almost half of our genome is engaged in a constant guerrilla war with the other half: TEs seek to multiply, while our cells try to prevent them from spreading.

How do our cells combat these internal enemies? Fortunately, our cells have evolved a genomic defence system of specialised proteins whose job is to hunt down TEs and prevent them from replicating. In a new paper published in the journal Nature, René Ketting and Sebastian Falk (Max Perutz Labs, Vienna, Austria) and their research teams report their discovery of PUCH – a completely new, previously unknown type of enzyme, which is key to this genomic defence system. They found that PUCH plays a crucial role in producing small molecules called piRNAs, which detect TEs when they attempt to “jump” and activate the genomic defence system to stop them before they paste themselves into new locations in our DNA.

The researchers discovered PUCH in the cells of the roundworm (C. elegans) – a simple invertebrate often used in biological research. However, the findings may also shed light on how our own immune system works. PUCH is characterised by unique molecular structures called Schlafen folds. Enzymes with Schlafen folds are also found in mice and humans, where they appear to play a role in innate immunity – the body’s first line of defence against viruses and bacteria. For example, some Schlafen proteins interfere with the replication of viruses in humans. On the other hand, some viruses (e.g. monkeypox viruses) may also use Schlafen proteins to attack the cell’s defence system. René suspects that Schlafen proteins may have a wider, conserved role in immunity in many species, including humans.

“Schlafen proteins may represent a previously unknown molecular link between immune responses in mammals and deeply conserved RNA-based mechanisms that control TEs”, he says. If so, Schlafen proteins may represent a common defence mechanism against both external enemies (viruses and bacteria) and internal ones (TEs). Sebastian continues: “It’s conceivable that Schlafen proteins have been repurposed into enzymes that protect cells from infectious DNA sequences, such as TEs. This discovery may profoundly impact our understanding of innate immune biology”.

_{Further details}

_{Further information can be found at www.nature.com/articles/s41586-023-06588-2}

_{René Ketting is a Scientific Director at the Institute of Molecular Biology (IMB) and a Professor of Biology at Johannes Gutenberg University (JGU) Mainz. Further information about research in the Ketting lab can be found at www.imb.de/ketting.}

_{About the Institute of Molecular Biology gGmbH}

_{The Institute of Molecular Biology gGmbH (IMB) is a centre of excellence in the life sciences that was established in 2011 on the campus of Johannes Gutenberg University Mainz (JGU). Research at IMB focuses on the cutting-edge fields of epigenetics, genome stability, ageing and RNA biology. The institute is a prime example of successful collaboration between a private foundation and government: The Boehringer Ingelheim Foundation has committed 154 million euros to be disbursed from 2009 until 2027 to cover the operating costs of research at IMB. The State of Rhineland-Palatinate has provided approximately 50 million euros for the construction of a state-of-the-art building and is giving a further 52 million in core funding from 2020 until 2027. For more information about IMB, please visit: www.imb.de}

_{Boehringer Ingelheim Foundation}

_{The Boehringer Ingelheim Foundation is an independent, non-profit organization that is committed to the promotion of the medical, biological, chemical, and pharmaceutical sciences. It was established in 1977 by Hubertus Liebrecht (1931–1991), a member of the shareholder family of the Boehringer Ingelheim company. Through its funding programmes Plus 3, Exploration Grants and Rise up!, the Foundation supports excellent scientists during critical stages of their careers. It also endows the international Heinrich Wieland Prize, as well as awards for up-and-coming scientists in Germany. In addition, the Foundation funds institutional projects in Germany, such as the Institute of Molecular Biology (IMB) and the European Molecular Biology Laboratory (EMBL) in Heidelberg. www.boehringer-ingelheim-stiftung.de/en}

_{Press contact for further information}

_{Dr Ralf Dahm, Director of Scientific Management}

_{Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany}

_{Phone: +49 (0) 6131 39 21455, Email: press@imb.de}

RESEARCH HIGHLIGHTS

The research groups of Julian König and Katja Luck (Institute of Molecular Biology, IMB, Mainz, Germany), together with the group of Michael Sattler (Institute of Structural Biology and Technical University of Munich, Germany) have discovered that the proto-oncogene FUBP1 has a previously unknown function as a core splicing component at long introns. They find that FUBP1 is responsible for stabilising the binding of other splicing factors to the 3’ splice site. Additionally, FUBP1 helps promote pairing of splice sites across introns, thereby encouraging spliceosome formation. These findings can help researchers better understand the complex and dynamic splicing processes. Furthermore, it can lead to the design of new and improved anticancer treatments to target disrupted splicing in cancer cells.

Splicing is an essential step of mRNA maturation in eukaryotes, during which the non-coding introns are cut out of the pre-mRNA and the coding exons are joined together, creating a mature mRNA. This process is often disrupted in cancer cells, resulting in exon skipping and/or intron inclusion. Studies show that up to 30% of cancers have more alternative splicing than normal cells. Such disruption of splicing can promote cancer growth by upregulating genes that increase cell survival, growth and resistance to anticancer treatments, as well as downregulating genes that promote apoptosis.

A common cause of these splicing disruptions is loss-of-function mutations in the proteins that catalyse splicing. Splicing is a complex, multistep process involving hundreds of proteins: some are responsible for recognising the splice sites, while others stabilise the binding of the spliceosome to the mRNA or cut out the introns and join the exons. However, our understanding of the proteins and interactions involved is still incomplete. To better understand how mRNAs are spliced in normal cells and how this is disrupted in cancer, Julian and his colleagues Katja and Michael set out to study FUBP1 (far upstream binding protein 1), which is known to be frequently mutated in gliomas, and to determine whether it has a role in splicing.

Through careful molecular and computational analysis, the researchers discovered that FUBP1 has two key roles in regulating the splicing of long introns. First, FUBP1 stabilises the binding of other splicing proteins to the 3’ splice site, helping the cell to recognise the correct exon-intron boundary. Second, FUBP1 helps promote the pairing of splice sites on either side of long introns, bridging them to facilitate the subsequent catalytic steps of cutting out the introns and joining exons. Indeed, when the researchers analysed sequencing data from glioma patients, they found that patients with FUBP1 loss-of-function mutations had more skipping of exons with long adjacent introns than patients with mutations in other splicing factors.

Julian says, “Long introns comprise over 80% of the introns in the human genome, but they are particularly difficult to splice and require more complex regulation. Our findings now reveal that FUBP1 plays a key role in this regulation. By gaining a better understanding of the proteins that regulate splicing, we can contribute to the design of new anticancer drugs that target the splicing machinery, creating new therapies to help people live longer and stay healthy in old age.”

The results of their study were published in the journal Molecular Cell.

^{Further details}

^{Further information can be found at https://doi.org/10.1016/j.molcel.2023.07.002}

^{Julian is a Group Leader at the Institute of Molecular Biology (IMB) Mainz. Further information about research in the König lab can be found at www.imb.de/koenig.}

^{Katja Luck is a Group Leader at the Institute of Molecular Biology (IMB) Mainz. Further information about research in the Luck lab can be found at www.imb.de/luck.}

^{About the Institute of Molecular Biology gGmbH}

^{The Institute of Molecular Biology gGmbH (IMB) is a centre of excellence in the life sciences that was established in 2011 on the campus of Johannes Gutenberg University Mainz (JGU). Research at IMB focuses on the cutting-edge fields of epigenetics, genome stability, ageing and RNA biology. The institute is a prime example of successful collaboration between a private foundation and government: The Boehringer Ingelheim Foundation has committed 154 million euros to be disbursed from 2009 until 2027 to cover the operating costs of research at IMB. The State of Rhineland-Palatinate has provided approximately 50 million euros for the construction of a state-of-the-art building and is giving a further 52 million in core funding from 2020 until 2027. For more information about IMB, please visit: www.imb.de.}

^{Boehringer Ingelheim Foundation}

^{The Boehringer Ingelheim Foundation is an independent, non-profit organization that is committed to the promotion of the medical, biological, chemical, and pharmaceutical sciences. It was established in 1977 by Hubertus Liebrecht (1931–1991), a member of the shareholder family of the Boehringer Ingelheim company. Through its funding programmes Plus 3, Exploration Grants and Rise up!, the Foundation supports excellent scientists during critical stages of their careers. It also endows the international Heinrich Wieland Prize, as well as awards for up-and-coming scientists in Germany. In addition, the Foundation funds institutional projects in Germany, such as the Institute of Molecular Biology (IMB) and the European Molecular Biology Laboratory (EMBL) in Heidelberg. www.boehringer-ingelheim-stiftung.de/en}

^{Press contact for further information}

^{Dr Ralf Dahm, Director of Scientific Management}

^{Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany}

^{Phone: +49 (0) 6131 39 21455, Email: press@imb.de}

RESEARCH HIGHLIGHTS

14 June – The research groups of Prof. Christof Niehrs (Institute of Molecular Biology, IMB, Mainz, Germany) and Prof. Steve Horvath (University of California Los Angeles, USA) have created a DNA methylation-based “clock” that can be used to measure ageing in frogs—an important model organism used to study many fundamental aspects of biology. They discovered that despite the many biological differences between humans and frogs, both have surprisingly similar changes in DNA methylation with age. This “clock” will provide a useful tool to help researchers better understand the causes of ageing and develop new treatments for age-related diseases.

Ageing occurs in almost all organisms, from humans and mice to frogs and insects. To better understand why we age and to test new treatments against age-related diseases such as cardiovascular disease and cancer, scientists often study animals like mice, frogs and worms. These animals age much faster than humans, allowing studies to be completed in a few months or years, rather than decades. But is ageing in humans really the same as ageing in a frog?

One way to determine if ageing is similar across different species is to see whether the same molecular changes occur during ageing. In mammals, one of the most important age-related changes occurs in how our DNA is methylated. DNA methylation refers to small chemical groups (methyl groups) that are enzymatically attached to the bases of DNA. These methyl groups act like switches to turn genes on or off. Scientists have found that the on/off pattern of these “methylation switches” on the DNA naturally changes in a predictable way as we grow and age. Indeed, by analysing the on/off patterns of these methylation switches, scientists can determine the age of an individual with high accuracy. This pattern of changes in DNA methylation is known as the “epigenetic clock”.

But do these DNA methylation changes occur in other species as well, or are they unique to mammals? To investigate this, Prof. Niehrs and his colleagues analysed the DNA methylation patterns of African clawed frogs and western clawed frogs—both important model organisms used worldwide to study basic aspects of biology—ranging in age from 2 days to 19 years. The researchers discovered that DNA methylation in frogs also changes in a predictable way with age, just as it does in humans. In other words, frogs also have an “epigenetic clock”. Most interestingly, many of these age-related DNA methylation changes overlapped with those known to occur in humans. This indicates that despite the many biological differences between frogs and humans, the underlying DNA methylation changes that take place during ageing are remarkably similar in both species.

Based on this similarity, the researchers were able to construct the first epigenetic clock to measure age in frogs, as well as a combined epigenetic clock that measures age in both frogs and humans. Prof. Niehrs says, “The fact that age-related epigenetic changes in frogs and humans are so similar is highly significant because it suggests that the basic molecular processes that underlie ageing are the same. This means that any treatments that are found to be effective against age-related diseases in frogs may also be effective in humans.” The new frog epigenetic clock will also allow researchers who study ageing in frogs to more accurately test whether anti-ageing treatments are effective in slowing down ageing or preventing age-related diseases. This will be a key step towards designing new therapies that can help humans live longer and stay healthy into old age.

^{Further details}

^{Further information can be found at https://link.springer.com/article/10.1007/s11357-023-00840-3}

^{Christof Niehrs is a Scientific and Founding Director at the Institute of Molecular Biology (IMB). Further information about research in the Niehrs lab can be found at www.imb.de/niehrs.}

^{About the Institute of Molecular Biology gGmbH}

^{The Institute of Molecular Biology gGmbH (IMB) is a centre of excellence in the life sciences that was established in 2011 on the campus of Johannes Gutenberg University Mainz (JGU). Research at IMB focuses on the cutting-edge fields of epigenetics, genome stability, ageing and RNA biology. The institute is a prime example of successful collaboration between a private foundation and government: The Boehringer Ingelheim Foundation has committed 154 million euros to be disbursed from 2009 until 2027 to cover the operating costs of research at IMB. The State of Rhineland-Palatinate has provided approximately 50 million euros for the construction of a state-of-the-art building and is giving a further 52 million in core funding from 2020 until 2027. For more information about IMB, please visit: www.imb.de.}

^{About the Centre for Healthy Ageing}

^{The Centre for Healthy Ageing (CHA) is a virtual research centre launched in 2021 that brings together scientists in basic and clinical research from across Mainz that focus on ageing and age-related diseases. These findings should be used to promote healthy ageing and to find treatments that could prevent or cure age-related disease. For more information, please visit: www.cha-mainz.de.}

^{Boehringer Ingelheim Foundation}

^{The Boehringer Ingelheim Foundation is an independent, non-profit organization that is committed to the promotion of the medical, biological, chemical, and pharmaceutical sciences. It was established in 1977 by Hubertus Liebrecht (1931–1991), a member of the shareholder family of the Boehringer Ingelheim company. Through its Perspectives Programme Plus 3 and its Exploration Grants, the Foundation supports independent junior group leaders. It also endows the international Heinrich Wieland Prize, as well as awards for up-and-coming scientists in Germany. In addition, the Foundation funds institutional projects in Germany, such as the Institute of Molecular Biology (IMB), the department of life sciences at the University of Mainz, and the European Molecular Biology Laboratory (EMBL) in Heidelberg. www.bistiftung.de}

^{Press contact for further information}

^{Dr Ralf Dahm, Director of Scientific Management}

^{Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany}

^{Phone: +49 (0) 6131 39 21455, Email: press@imb.de}

PRESS RELEASE

01 June – The Institute of Molecular Biology (IMB) is pleased to announce that Siyao Wang is joining IMB as a new group leader. Siyao joins us from the Institute for Genome Stability in Ageing and Disease (IGSAD) in Cologne, Germany, where she worked as a group leader. Her research focuses on how DNA damage and repair affects epigenetic regulation in the model organism C. elegans, and whether this could have long-term effects on the health and longevity of their offspring.

Siyao’s lab works to understand how cells repair their DNA and how this repair process influences histone modifications in the genome. DNA is a fragile molecule that is frequently damaged by UV radiation or chemicals from the environment. Such damage must be regularly repaired, or they will lead to mutations that prevent the cell from functioning normally.

During the DNA repair process, the cell makes alterations to its histone modifications. These histone modifications play an important role in opening the chromatin to make it more accessible for DNA repair proteins, as well as recruiting them to the site of damage.

Importantly, changes in histone modifications can also affect gene expression, and previous studies have shown that these changes may even be inherited by offspring. Such inherited epigenetic changes can affect the health and longevity of the offspring. Siyao is particularly interested in finding out whether the histone modification changes during DNA repair might also cause long-term effects that are inherited in subsequent generations. Her lab will also investigate whether somatic and reproductive ageing causes histone modification changes that are inherited in offspring, as ageing is not only associated with more mutations due to a lifetime of exposure to DNA-damaging factors, but also reduced DNA repair.

By studying how DNA repair causes long-term or transgenerational epigenetic alterations, Siyao’s research can help us better understand the heritable effects of somatic and reproductive ageing, and identify therapeutic approaches to prevent congenital diseases caused by parental DNA damage.

_{Further details}

_{Siyao Wang is a Group Leader at the Institute of Molecular Biology (IMB). Further information about research in the Wang lab can be found at www.imb.de/wang.}

_{About the Institute of Molecular Biology gGmbH}

_{The Institute of Molecular Biology gGmbH (IMB) is a centre of excellence in the life sciences that was established in 2011 on the campus of Johannes Gutenberg University Mainz (JGU). Research at IMB focuses on the cutting-edge fields of epigenetics, genome stability, ageing and RNA biology. The institute is a prime example of successful collaboration between a private foundation and government: The Boehringer Ingelheim Foundation has committed 154 million euros to be disbursed from 2009 until 2027 to cover the operating costs of research at IMB. The State of Rhineland-Palatinate has provided approximately 50 million euros for the construction of a state-of-the-art building and is giving a further 52 million in core funding from 2020 until 2027. For more information about IMB, please visit: www.imb.de.}

_{Boehringer Ingelheim Foundation}

_{The Boehringer Ingelheim Foundation is an independent, non-profit organization that is committed to the promotion of the medical, biological, chemical, and pharmaceutical sciences. It was established in 1977 by Hubertus Liebrecht (1931–1991), a member of the shareholder family of the Boehringer Ingelheim company. Through its Perspectives Programme Plus 3 and its Exploration Grants, the Foundation supports independent junior group leaders. It also endows the international Heinrich Wieland Prize, as well as awards for up-and-coming scientists in Germany. In addition, the Foundation funds institutional projects in Germany, such as the Institute of Molecular Biology (IMB), the department of life sciences at the University of Mainz, and the European Molecular Biology Laboratory (EMBL) in Heidelberg. www.bistiftung.de}

_{Press contact for further information}

_{Dr Ralf Dahm, Director of Scientific Management}

_{Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany}

_{Phone: +49 (0) 6131 39 21455, Email: press@imb.de}

RESEARCH HIGHLIGHTS

19 May – Researchers at the Institute of Molecular Biology (IMB) in Mainz, Germany, have discovered how mammals balance the expression of genes on the X chromosome with those on other chromosomes (known as autosomes). The key to this balancing act lies in methylating bases on mRNAs from autosomes, but not those from the X chromosome. This reduces the stability of autosome mRNAs such that they are kept at a precisely 1:1 ratio with X chromosome mRNAs. Maintaining this balance in expression is extremely important for the normal development and function of organisms.

Mammals inherit two copies of each chromosome, one from the father and one from the mother. The exception is the sex chromosomes: females have two copies of the X chromosome, while males have a single X and a Y chromosome. In females, one of the X chromosome copies is inactivated. This means that genes on the X chromosome are always expressed from only a single copy in both males and females, while genes on all other chromosomes (known as autosomes) are expressed from two copies.

Having an unequal gene copy number can be extremely detrimental to organismal function, as genes present in only one copy would be expressed at only half the level of those present in two copies. This would be like having only one X chromosome factory producing mRNAs, while all the autosomes have two factories, resulting in twice as many autosome mRNAs. Such imbalances typically cause genetic diseases such as Down’s syndrome in humans. So how is it that mammals function normally with only one active X chromosome?

Scientists reasoned that mammals must have some compensatory mechanism to balance the expression of X chromosome and autosome genes. However, this mechanism had remained elusive until now. In a new study published in the journal Nature Structural & Molecular Biology, Julian König and his group, together with the group of his colleague Claudia Keller Valsecchi (both at IMB), have shown that mammals use RNA modifications to help achieve this balance.

RNAs can be post-transcriptionally modified to regulate their translation, processing and stability. Scientists know of over 100 RNA modifications, but the most common is adenosine methylation (m⁶A), which destabilises RNAs so that they are more rapidly degraded and recycled.

By manipulating the levels of m⁶A in mouse embryonic stem cells, Julian and his colleagues discovered that m⁶A mostly affects the stability of mRNAs from the autosomes but not those from the X chromosome. In agreement with this, they found that X chromosome mRNAs have significantly less m⁶A than autosome mRNAs. In other words, the autosomes may have two factories producing twice as many mRNAs, but because the autosome mRNAs are modified with m⁶A they break down and are removed from the cell faster than X chromosome mRNAs. The researchers propose that the cell uses this mechanism to keep mRNAs from the X chromosome and autosomes present in equal amounts, even though the X chromosome only has one active ‘factory’. These observations also hold true for human cell lines, suggesting that this mechanism may be common to all mammals.

Based on these results, the researchers hypothesise that mammalian X chromosome genes have evolved to produce mRNAs with less m⁶A so they can be more highly expressed, despite being present in only one active copy.

Nadine Körtel and Cornelia Rücklé, the two first authors of the study, say “We are so excited to have unlocked a key piece of the puzzle of how mammals ensure a balanced expression of genes in the unique case of the X chromosome.” By studying how mammals naturally balance the expression of X chromosome genes, the researchers also hope to gain a better understanding of how gene expression is balanced (or unbalanced) in other situations of unequal gene copy number during embryonic development and ageing, as well as in genetic diseases.

_{Further details}

_{Further information can be found at www.nature.com/articles/s41594-023-00997-7.}

_{Julian König is a Group Leader at the Institute of Molecular Biology (IMB). Further information about research in the König lab can be found at www.imb.de/koenig.}

_{Claudia Keller-Valsecchi is a Group Leader at the Institute of Molecular Biology (IMB). Further information about research in the König lab can be found at www.imb.de/keller-valsecchi.}

_{About the Institute of Molecular Biology gGmbH}

_{The Institute of Molecular Biology gGmbH (IMB) is a centre of excellence in the life sciences that was established in 2011 on the campus of Johannes Gutenberg University Mainz (JGU). Research at IMB focuses on the cutting-edge fields of epigenetics, genome stability, ageing and RNA biology. The institute is a prime example of successful collaboration between a private foundation and government: The Boehringer Ingelheim Foundation has committed 154 million euros to be disbursed from 2009 until 2027 to cover the operating costs of research at IMB. The State of Rhineland-Palatinate has provided approximately 50 million euros for the construction of a state-of-the-art building and is giving a further 52 million in core funding from 2020 until 2027. For more information about IMB, please visit: www.imb.de.}

_{Boehringer Ingelheim Foundation}

_{The Boehringer Ingelheim Foundation is an independent, non-profit organization that is committed to the promotion of the medical, biological, chemical, and pharmaceutical sciences. It was established in 1977 by Hubertus Liebrecht (1931–1991), a member of the shareholder family of the Boehringer Ingelheim company. Through its Perspectives Programme Plus 3 and its Exploration Grants, the Foundation supports independent junior group leaders. It also endows the international Heinrich Wieland Prize, as well as awards for up-and-coming scientists in Germany. In addition, the Foundation funds institutional projects in Germany, such as the Institute of Molecular Biology (IMB), the department of life sciences at the University of Mainz, and the European Molecular Biology Laboratory (EMBL) in Heidelberg. www.bistiftung.de}

_{Press contact for further information}

_{Dr Ralf Dahm, Director of Scientific Management}

_{Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany}

_{Phone: +49 (0) 6131 39 21455, Email: press@imb.de}

PRESS RELEASE

08 May – The DFG (German Research Foundation) has approved a new Research Training Group (RTG) on “R-loop Regulation in Robustness and Resilience” (4R). This research initiative was applied for by Johannes Gutenberg University Mainz (JGU) in close cooperation with the Institute of Molecular Biology (IMB), Mainz, and focuses on R-loops, which are a highly topical subject in the field of genome biology research.

The new RTG will investigate “R-loops”, which are a specific type of RNA-DNA hybrid with both positive and negative effects in cells. From autumn 2023, 12 PhD students will begin their research projects in this field as part of 4R. “It’s a rapidly evolving research field, with many successful and ground-breaking findings over the past five years. We are delighted to be able to start intensive research on the subject with this Research Training Group”, says the speaker of the new research training group, Prof. Brian Luke, who is also a Professor at JGU and an Adjunct Director at IMB. The DFG will support the project with approximately €6.8 million during the first 5 years, with an additional €1.49 million for overheads.

The 4R RTG will investigate open questions on the benefits and risks of R-Loops

RNA-DNA hybrids form when RNA and single-stranded DNA, which are structurally similar molecules, bind to each other. One particularly interesting type of RNA-DNA hybrid is R-loops, which contain three strands: two DNA and one RNA, with one of the DNA strands being displaced to form a loop. “Previously, R-loops were considered to be a byproduct of RNA biosynthesis: RNA was thought to get caught on a DNA strand, causing breaks in the DNA and damaging the chromosomes”, Brian explains. This could, in turn, promote inflammatory diseases and cancer, as well as accelerate ageing. More recent discoveries indicate that it is not the formation of the R-loops per se that causes these problems, but rather their faulty removal, which leaves them “in the wrong place at the wrong time, because they were not removed in time”, says Brian. He points out that R-loops, which occur in animals, plants and bacteria as well as humans, play a significant role in important processes such as DNA repair, telomere elongation and gene regulation.

An RTG based in Mainz with interdisciplinary participants

The 4R RTG integrates 12 research groups, allowing the PhD students to explore a diverse range of biochemical processes in addition to the specific focus on the regulation of R-loops. This includes groups from JGU’s Faculty of Biology and IMB, as well as two groups from JGU’s University Medical Center, to encourage the development of translational applications. “This is the first RTG with a direct focus on the biology of R-loops”, says IMB’s Executive Director Prof. René Ketting, who is also deputy speaker of the RTG. “R-loops have recently become a focal point of intense interest in genome biology, and we hope that this research will help us to understand their mechanisms of action in the cell more precisely”.

To achieve this, the 4R RTG will develop molecular tools and methods to characterise the function of R-loops throughout the genome and decipher the difference between planned and unplanned R-loops. “There is a distinct lack of knowledge when it comes to the question of why R-loops can sometimes be beneficial and sometimes do harm”, says Brian. “It appears that the regulation of these structures is crucial but complicated. We have many highly topical and relevant research questions ahead of us”.

4R is the second collaborative RTG between JGU and IMB

4R is the second RTG jointly organised by JGU’s Faculty of Biology and IMB that has been successfully funded by the DFG. The first RTG on “Gene Regulation in Evolution: From Molecular to Extended Phenotypes” (GenEvo) was approved in 2019 and aims to improve our understanding of the evolution of complex and multilayered gene regulatory systems through a structured, high-quality research and training programme for PhD students.

^{Further details}

^{Further information can be found at www.dfg.de/service/presse/pressemitteilungen/2023/pressemitteilung_nr_12/index.html.}

^{Brian Luke is an Adjunct Director at the Institute of Molecular Biology (IMB) and a Professor at Johannes Gutenberg University Mainz. Further information about research in the Luke lab can be found at www.imb.de/luke.}

^{René Ketting is the Executive Director of the Institute of Molecular Biology (IMB). Further information about research in the Ketting lab can be found at www.imb.de/ketting.}

^{About the Institute of Molecular Biology gGmbH}

^{The Institute of Molecular Biology gGmbH (IMB) is a centre of excellence in the life sciences that was established in 2011 on the campus of Johannes Gutenberg University Mainz (JGU). Research at IMB focuses on the cutting-edge fields of epigenetics, genome stability, ageing and RNA biology. The institute is a prime example of successful collaboration between a private foundation and government: The Boehringer Ingelheim Foundation has committed 154 million euros to be disbursed from 2009 until 2027 to cover the operating costs of research at IMB. The State of Rhineland-Palatinate has provided approximately 50 million euros for the construction of a state-of-the-art building and is giving a further 52 million in core funding from 2020 until 2027. For more information about IMB, please visit: www.imb.de.}

^{About Johannes Gutenberg University Mainz}

^{Johannes Gutenberg University Mainz (JGU) is a globally recognized research-driven university with around 31,000 students from over 120 nations. Its core research areas are in particle and hadron physics, the materials sciences, and translational medicine. JGU's success in Germany's Excellence Strategy program has confirmed its academic excellence: In 2018, the research network PRISMA+ (Precision Physics, Fundamental Interactions and Structure of Matter) was recognized as a Cluster of Excellence – building on its forerunner, PRISMA. Moreover, excellent placings in national and international rankings as well as numerous honors and awards demonstrate the research and teaching quality of Mainz-based researchers and academics. Further information at www.uni-mainz.de/eng}

^{Boehringer Ingelheim Foundation}

^{The Boehringer Ingelheim Foundation is an independent, non-profit organization that is committed to the promotion of the medical, biological, chemical, and pharmaceutical sciences. It was established in 1977 by Hubertus Liebrecht (1931–1991), a member of the shareholder family of the Boehringer Ingelheim company. Through its Perspectives Programme Plus 3 and its Exploration Grants, the Foundation supports independent junior group leaders. It also endows the international Heinrich Wieland Prize, as well as awards for up-and-coming scientists in Germany. In addition, the Foundation funds institutional projects in Germany, such as the Institute of Molecular Biology (IMB), the department of life sciences at the University of Mainz, and the European Molecular Biology Laboratory (EMBL) in Heidelberg. www.bistiftung.de}

^{Press contact for further information}

^{Dr Ralf Dahm, Director of Scientific Management}

^{Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany}

^{Phone: +49 (0) 6131 39 21455, Email: press@imb.de}

RESEARCH HIGHLIGHTS

26 April – Tiny pores in the cell nucleus play an essential role in healthy ageing by protecting the DNA from viruses and DNA-damaging substances. A team of scientists in Germany from the Institute of Molecular Biology Mainz, Johannes Gutenberg University Mainz and the Max Planck Institute of Biophysics in Frankfurt am Main has now filled a hole in our understanding of the structure and function of these nuclear pores. The scientists showed how intrinsically disordered proteins in the centre of the pore can form a spaghetti-like mobile barrier that permits important cellular factors to pass, but blocks viruses and other organisms and molecules that can cause disease.

Our DNA is protected within the cell nucleus, which is shielded by a barrier called the nuclear membrane. As the cell’s control centre, the nucleus must be able to exchange important messenger molecules, metabolites or proteins with the rest of the cell. To facilitate this, the nuclear membrane has about 2,000 built-in pores, each consisting of about 1,000 proteins.

For decades, researchers have been fascinated by the 3D structure and function of these nuclear pores, which act as guardians of the genome; substances that are required for controlling the cell are allowed to pass in and out, while viruses and other DNA-damaging substances are blocked from entry. The nuclear pores can therefore be thought of as molecular bouncers, each checking many thousands of visitors per second. Only those who have an entrance ticket are allowed to pass.

How do the nuclear pores manage this enormous task? About 300 of the proteins that make up the pore protrude deep into the central opening, like tentacles. Until now, researchers did not know how these tentacles are arranged and how they repel intruders. This is because these proteins are intrinsically disordered – that is, they lack a defined 3D structure – instead, they are flexible and continuously moving, like spaghetti in boiling water.

Combination of microscopy and computer simulations

As these intrinsically disordered proteins (IDPs) are constantly changing their structure, it is very difficult for scientists to decipher their 3D structure and function. Most experimental techniques that researchers use to visualise proteins only work with a defined 3D structure. Because of this, until now the central region of the nuclear pore has just been represented as a simple hole because it was not possible to determine the structure of the IDPs within the opening.

Now, a team of scientists led by Edward Lemke (Professor of Synthetic Biophysics at Johannes Gutenberg University Mainz and Adjunct Director at the Institute of Molecular Biology Mainz) and Gerhard Hummer (Director of the Max Planck Institute of Biophysics) has used a novel combination of synthetic biology, multidimensional fluorescence microscopy and computer-based simulations to study nuclear pore IDPs in living cells.

“We used modern precision tools to mark several points of the spaghetti-like proteins with fluorescent dyes, which we then excite using light and visualise under the microscope,” Lemke explains. “Based on the glow patterns and duration, we were able to deduce how the proteins must be arranged.” Hummer adds, “We then used molecular dynamics simulations to calculate how the IDPs are spatially organised in the pore, how they interact with each other and how they move. For the first time, we could visualise the gateway into the control centre of human cells.”

A dynamic protein network as a transport barrier

Using the techniques above, the scientists discovered that the protein ‘tentacles’ in the pore behave completely differently from what was previously thought, because they interact with each other and with the molecules attempting to enter, moving perpetually like the aforementioned spaghetti in boiling water. This means that in the centre of the pore, there is no hole, but instead a shield of wiggly, spaghetti-like molecules. Viruses or bacteria are too big to get in through this sieve. However, other large molecules needed in the nucleus can pass, as they carry very specific signals. Such molecules have an entry ticket, whereas others, such as viruses and DNA-damaging molecules, usually do not. “By disentangling the nuclear pore filling, we enter a new phase in nuclear transport research,” adds Martin Beck, collaborator and colleague at the Max Planck Institute of Biophysics. Their findings were published today in the journal Nature.

"Understanding how the pores transport or block cargo will help us to identify how errors occur. After all, some viruses manage to enter the cell nucleus despite the barrier," Hummer sums up. “With our combination of methods, we can now study IDPs in more detail to find why they are indispensable for certain cellular functions, despite being error-prone. In fact, IDPs are found in almost all species, even though they carry the risk of forming aggregates during the ageing process, which can lead to neurodegenerative diseases such as Alzheimer's,” Lemke says. By learning how IDPs function, the researchers aim to develop new drugs or vaccines that can prevent viral infections and help promote healthy ageing.

^{Further details}

^{The image shows an artistic impression of the rocky scaffold structure of the nuclear pore complex, filled with intrinsically disordered nucleoporins in the central channel, which are depicted as seaweed. In this work, we “dived” into the dark hole of the nuclear pore complex to shine light on the disordered nucleoporins. Image credit: Sara Mingu.}

^{Further information can be found at www.nature.com/articles/s41586-023-05990-0.}

^{Edward Lemke is an Adjunct Director at IMB and a Professor of Synthetic Biophysics at Johannes Gutenberg University Mainz. Further information about research in the Lemke lab can be found at www.imb.de/lemke.}

^{About the Institute of Molecular Biology gGmbH}

^{The Institute of Molecular Biology gGmbH (IMB) is a centre of excellence in the life sciences that was established in 2011 on the campus of Johannes Gutenberg University Mainz (JGU). Research at IMB focuses on the cutting-edge fields of epigenetics, genome stability, ageing and RNA biology. The institute is a prime example of successful collaboration between a private foundation and government: The Boehringer Ingelheim Foundation has committed 154 million euros to be disbursed from 2009 until 2027 to cover the operating costs of research at IMB. The State of Rhineland-Palatinate has provided approximately 50 million euros for the construction of a state-of-the-art building and is giving a further 52 million in core funding from 2020 until 2027. For more information about IMB, please visit: www.imb.de.}

^{About Johannes Gutenberg University Mainz}

^{Johannes Gutenberg University Mainz (JGU) is a globally recognized research-driven university with around 31,000 students from over 120 nations. Its core research areas are in particle and hadron physics, the materials sciences, and translational medicine. JGU's success in Germany's Excellence Strategy program has confirmed its academic excellence: In 2018, the research network PRISMA+ (Precision Physics, Fundamental Interactions and Structure of Matter) was recognized as a Cluster of Excellence – building on its forerunner, PRISMA. Moreover, excellent placings in national and international rankings as well as numerous honors and awards demonstrate the research and teaching quality of Mainz-based researchers and academics. Further information at www.uni-mainz.de/eng}

^{Boehringer Ingelheim Foundation}

^{The Boehringer Ingelheim Foundation is an independent, non-profit organization that is committed to the promotion of the medical, biological, chemical, and pharmaceutical sciences. It was established in 1977 by Hubertus Liebrecht (1931–1991), a member of the shareholder family of the Boehringer Ingelheim company. Through its Perspectives Programme Plus 3 and its Exploration Grants, the Foundation supports independent junior group leaders. It also endows the international Heinrich Wieland Prize, as well as awards for up-and-coming scientists in Germany. In addition, the Foundation funds institutional projects in Germany, such as the Institute of Molecular Biology (IMB), the department of life sciences at the University of Mainz, and the European Molecular Biology Laboratory (EMBL) in Heidelberg. www.bistiftung.de}

^{Press contact for further information}

^{Dr Ralf Dahm, Director of Scientific Management}

^{Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany}

^{Phone: +49 (0) 6131 39 21455, Email: press@imb.de}