Tag Archives: #dna

New Discovery Shows Human Cells Can Write RNA Sequences Into DNA (Biology)

In a discovery that challenges long-held dogma in biology, researchers show that mammalian cells can convert RNA sequences back into DNA, a feat more common in viruses than eukaryotic cells

Cells contain machinery that duplicates DNA into a new set that goes into a newly formed cell. That same class of machines, called polymerases, also build RNA messages, which are like notes copied from the central DNA repository of recipes, so they can be read more efficiently into proteins. But polymerases were thought to only work in one direction DNA into DNA or RNA. This prevents RNA messages from being rewritten back into the master recipe book of genomic DNA. Now, Thomas Jefferson University researchers provide the first evidence that RNA segments can be written back into DNA, which potentially challenges the central dogma in biology and could have wide implications affecting many fields of biology.

“This work opens the door to many other studies that will help us understand the significance of having a mechanism for converting RNA messages into DNA in our own cells,” says Richard Pomerantz, PhD, associate professor of biochemistry and molecular biology at Thomas Jefferson University. “The reality that a human polymerase can do this with high efficiency, raises many questions.” For example, this finding suggests that RNA messages can be used as templates for repairing or re-writing genomic DNA.

The work was published June 11th in the journal Science Advances.

Together with first author Gurushankar Chandramouly and other collaborators, Dr. Pomerantz’s team started by investigating one very unusual polymerase, called polymerase theta. Of the 14 DNA polymerases in mammalian cells, only three do the bulk of the work of duplicating the entire genome to prepare for cell division. The remaining 11 are mostly involved in detecting and making repairs when there’s a break or error in the DNA strands. Polymerase theta repairs DNA, but is very error-prone and makes many errors or mutations. The researchers therefore noticed that some of polymerase theta’s “bad” qualities were ones it shared with another cellular machine, albeit one more common in viruses — the reverse transcriptase. Like Pol theta, HIV reverse transcriptase acts as a DNA polymerase, but can also bind RNA and read RNA back into a DNA strand.

In a series of elegant experiments, the researchers tested polymerase theta against the reverse transcriptase from HIV, which is one of the best studied of its kind. They showed that polymerase theta was capable of converting RNA messages into DNA, which it did as well as HIV reverse transcriptase, and that it actually did a better job than when duplicating DNA to DNA. Polymerase theta was more efficient and introduced fewer errors when using an RNA template to write new DNA messages, than when duplicating DNA into DNA, suggesting that this function could be its primary purpose in the cell.

The group collaborated with Dr. Xiaojiang S. Chen’s lab at USC and used x-ray crystallography to define the structure and found that this molecule was able to change shape in order to accommodate the more bulky RNA molecule – a feat unique among polymerases.

“Our research suggests that polymerase theta’s main function is to act as a reverse transcriptase,” says Dr. Pomerantz. “In healthy cells, the purpose of this molecule may be toward RNA-mediated DNA repair. In unhealthy cells, such as cancer cells, polymerase theta is highly expressed and promotes cancer cell growth and drug resistance. It will be exciting to further understand how polymerase theta’s activity on RNA contributes to DNA repair and cancer-cell proliferation.”

This research was supported by NIH grants 1R01GM130889-01 and 1R01GM137124-01, and R01CA197506 and R01CA240392. This research was also supported in part by a Tower Cancer Research Foundation grant. The authors report no conflicts of interest.


Article reference: Gurushankar Chandramouly, Jiemin Zhao, Shane McDevitt, Timur Rusanov, Trung Hoang, Nikita Borisonnik, Taylor Treddinick, Felicia Wednesday Lopezcolorado, Tatiana Kent, Labiba A. Siddique, Joseph Mallon, Jacklyn Huhn, Zainab Shoda, Ekaterina Kashkina, Alessandra Brambati, Jeremy M. Stark, Xiaojiang S. Chen, and Richard T. Pomerantz, “Pol theta reverse transcribes RNA and promotes RNA-templated DNA repair,” Science Advances, DOI: 10.1126/sciadv.abf1771, 2021.


Provided by Thomas Jefferson University

Scientists Make DNA Breakthrough Which Could Identify Why Some People Are More Affected by Covid-19 (Biology)

Scientists from the MRC Weatherall Institute of Molecular Medicine at Oxford University have developed a method that allows them to see, with far greater accuracy, how DNA forms large scale structures within a cell nucleus.

This breakthrough will improve understanding of how differences in DNA sequences can lead to increased risks of developing many different diseases.

The method, which is around 1000 times more accurate than existing techniques, enables scientists to measure the contacts between different pieces of DNA, which are a million base pairs apart to the nearest base pair. This is the equivalent of being able to measure contacts in the DNA fibre that are 1km apart to the nearest millimetre.

Put another way, if each letter of DNA was the size of a brick, each cell would contain roughly the number of bricks in a city (6 billion). Scientists are now able to work out which bricks are next to each other, and see the fine details of how DNA forms structures inside cells, when previously they could only see the DNA “architecture” on the scale of small buildings.

Associate Professor James Davies, the MRC clinician scientist at the Radcliffe Department of Medicine who led the research, explains, ‘This technique has real potential to make a significant impact on human health. For example, at the moment we know that there is a genetic variant which doubles the risk of being severely affected by COVID-19. However, we do not know how the genetic variant makes people more vulnerable to COVID-19.

‘This new breakthrough is helping us to work out how this causes severe COVID and which genes are involved. This is important because we know that drugs which are developed to targets with this type of genetic evidence have double the chance of making it past early stage clinical trials. The team is now using the technique to make the genetic identification and hopes to report on results in coming weeks.’

The technology has been licensed to the University of Oxford spinout company, Nucleome Therapeutics funded by Oxford Sciences Innovation. The company is using these 3D genome approaches to identify new drug targets by working out how variation in the genetic code causes common diseases such as rheumatoid arthritis and multiple sclerosis.

Featured image: How blood cell genetic variations impact on common diseases. Image credit: Shutterstock


Provided by University of Oxford

How DNA Opens While Wrapped Around Proteins? (Biology)

Researchers from the Hubrecht Institute in Utrecht (The Netherlands) and the Max Planck Institute for Molecular Biomedicine in Münster (Germany) used computer simulations to reveal in atomic detail how a short piece of DNA opens while it is tightly wrapped around the proteins that package our genome. These simulations provide unprecedented insights into the mechanisms that regulate gene expression. The results were published in PLoS Computational Biology on the 3rd of June.

Every cell in the body contains two meters of DNA. In order to fit all the DNA in the cell’s small nucleus, the DNA is tightly packed in a structure known as chromatin. Chromatin is an array of identical smaller structures named nucleosomes. In a single nucleosome, DNA is wrapped around 8 proteins called histones. Chromatin is not uniformly compact across the genome. The tightness of the packaging is important in regulating which genes are expressed and therefore which proteins are produced by a cell.

Transitions from tightly to loosely packed DNA – from closed to open chromatin – are essential for cells to convert to another cell type. These cell conversions are hallmarks of development and disease, but are also often used in regenerative therapies. Understanding how such transitions occur may contribute to understanding diseases and optimizing therapeutical cell type conversions.

Computational nanoscope

One step in the opening of chromatin is the motion of DNA while wrapped in nucleosomes. Like all molecular structures in our cells, nucleosomes are dynamic. They move, twist, breathe, unwrap and wrap again. Visualizing these motions using experimental methods is often very challenging. One alternative is to use the so-called “computational nanoscope”

Researchers use the term computational nanoscope to refer to a set of computer simulation methods. These methods enable them to visualize the movements of molecules over time. Over the past years, the methods have become so accurate that researchers started referring to them as a computational nanoscope; observing the molecules moving on the computer is similar to observing them under a very high resolution nanoscope.

Nucleosomes breathing

Jan Huertas and Vlad Cojocaru, supported by Hans Schöler from the Max Planck Institute for Molecular Biomedicine (Münster, Germany), generated multiple real-time movies of the movements of nucleosomes, each covering one microsecond from the nucleosome lifetime. Using these movies, they monitored how the nucleosomes open and close in a motion known as nucleosome breathing.

In their new paper, published in PLoS Computational Biology, Huertas and Cojocaru describe what causes nucleosome breathing. First, they found that the order in which the building blocks of DNA are arranged – the DNA sequence – is important for nucleosome breathing.  Second, the dynamics of histone tails are essential for this process. These histone tails are flexible regions in the histones that play a role in the regulation of gene expression. While the role of histone tails has been studied intensively, little is known about how they influence the motions of single nucleosomes. With their simulations, Huertas and Cojocaru described the relationship between histone tails and nucleosome breathing in atomic detail.

Histone modifications

“Being able to observe the breathing of nucleosomes in computer simulations is very challenging. The fact that we have now been able to visualize this represents a major step towards simulating the complete spectrum of nucleosome dynamics, from breathing to unwrapping. It also allows us to study how these motions are affected by modifications of the histones, which occur in different cells and regions of our DNA. Our simulations revealed that two histone tails are responsible for keeping the nucleosome closed. Only when these flexible tails moved away from particular regions of DNA, the nucleosome was able to open,” says research leader Cojocaru.

Huertas, first author in the publication and recent PhD-graduate, adds: “Active (open) and inactive (closed) chromatin contain different modifications of histone tails. The next step is to perform simulations with such modifications. The atomic resolution of the simulations would allow us to pinpoint how each modification affects nucleosomes and chromatin dynamics.”

Towards understanding epigenetics

All three researchers are excited about the future of the use of atomistic computer simulations in understanding gene expression mechanisms in development and disease. “With the further increase of computational power available in the world, we will soon be able to simulate milliseconds of a nucleosome lifetime with all its atoms included. Furthermore, we will be able to routinely simulate multiple nucleosomes to study the effect of different modifications of histones on gene expression. This will give unprecedented insights into the mechanisms that regulate gene expression,” Cojocaru concludes.

Featured image: This image shows three microseconds from the life time of a nucleosome. Snapshots in time were taken every 4 nanoseconds and were superimposed on the core region of the histones (white). The positions of the DNA (yellow) and the flexible histone tails (blue, green, red, orange, cyan) in all snapshots are shown. The ample motion of the DNA arms is known as nucleosome breathing motion. Remarkably, in this nucleosome, the lower arm moves more than the upper one due to the DNA sequence. Credit: Jan Huertas and Vlad Cojocaru, ©MPI for Molecular Biomedicine, ©Hubrecht Institute.


Publication

Huertas J, Schöler HR, Cojocaru V (2021) Histone tails cooperate to control the breathing of genomic nucleosomes. PLoS Comput Biol 17(6): e1009013. doi:10.1371/journal.pcbi.1009013


Provided by Hubrecht Institute

The Importance of DNA Compaction in Tissue Formation (Biology)

  • Researchers at IRB Barcelona identify that the expression of ancestral fragments of viral DNA results in a strong inflammatory response and causes breast tissue dysfunction.
  • This viral DNA accumulation has also been observed in some types of cancer, such as triple-negative breast cancer, and it may play a key role in determining metastatic potential.
  • The work has been published in the journal Cell Stem Cell.

Scientists led by Dr. Salvador Aznar-Benitah, head of the Stem Cells and Cancer laboratory at IRB Barcelona, have described the alterations that occur during mammary gland formation when heterochromatin (the part of DNA that does not actively produce proteins) is poorly regulated. The results, which have been published in the journal Cell Stem Cell, indicate that incorrect DNA packaging makes retrotransposons (a type of transposable element originated in ancestral fragments of viruses integrated into the cell genome) more accessible.

As these fragments are more accessible, they can be “read” and copied by the cellular machinery. The cell reacts to the presence of these viral fragments as if it was undergoing infection and it triggers an immune response through a cellular program called pyroptosis. As a result, the interactions between different cells are altered within the breast, leading to complete failure to performs its primary function of milk secretion.

“In many types of cancer, such as triple-negative breast cancer, we observe that there are regions of the genome that are unexpectedly unfolded and we need to understand the implications. The inflammatory response and the alterations that arise could play a key role in the ability of these cells to colonise other organs, causing what is known as metastasis,” explains Dr. Aznar-Benitah, ICREA researcher at IRB Barcelona.

The importance of DNA folding

The main function of the DNA in our cells is to coordinate the production of proteins responsible for executing cellular functions. However, some parts of the genome are tightly condensed and thus are not used for this purpose. This study and others published by the scientific community report that proper regulation of chromatin condensation is also key for the correct development of tissues.

The non-coding DNA of animals contains transposable elements, which are ancestral viruses that integrated into the genome a long time ago. If these elements are “read” and copied by the cellular machinery, it is detrimental for the cell. Therefore the cell has evolved mechanisms to protect itself. One of the mechanisms that prevents retroviral copying in healthy cells is chromatin compaction. In their recent work, Dr. Aznar-Benitah and colleagues demonstrated that disrupting this compaction and releasing these ancestral viruses is not only detrimental to the individual cell but has repercussions on the function of the whole tissue (and maybe even the organism).

Bringing research closer to clinical practice

Dr. Alexandra Avgustinova, first author of the article and IRB Barcelona Alumna, has now set up her own laboratory in the Paediatric Cancer programme at the Institut de Recerca Sant Joan de Déu (IRSD). Her group addresses the regulation of the genome at the onset of paediatric cancer and, in this context, will study the influence of transposable elements like retrotransposons in the responsiveness of paediatric cancers to immunotherapy.

“I learnt a lot during my years at IRB Barcelona and had the opportunity to meet outstanding scientists with whom I would like to collaborate in the future. Working with Salva has taught me to “think big” and really pursue the questions that intrigue me, which will be very important when it comes to heading your own group!” says Dr. Avgustinova.

Techniques developed and future lines of study

To carry out this research, scientists from IRB Barcelona’s Stem Cell and Cancer laboratory have had to develop a very complex study model: They employed computational tools capable of identifying the transposable elements that are being copied within a cell, in combination with a mouse model in which they could assess the functional consequences of disrupting chromatin compaction.

This study demonstrates that disrupting chromatin compaction can have repercussions that reach beyond the affected cell, and it paves the way for research into the metastatic processes of tumours with altered chromatin compaction and thus deregulation of transposable elements.

The laboratories of Dr. Juan M. Vaquerizas (Max Planck Institute for Molecular Biomedicine, Muenster) and Dr. Holger Heyn (CNAG-CRG, Barcelona); and scientists from other laboratories, such as Dr. Alexandra Van Keymeulen (Université Libre de Bruxelles, Bruxelles), participated in the work. The IRB Barcelona’s Histopathology Facility, led by Dr. Neus Prats, also collaborated.

This research project has been possible thanks to funding from the European Research Council (ERC), the Government of Catalonia, the Ministry of Science and Innovation of the Government of Spain, La Marató/TV3 Foundation and the Worldwide Cancer Research Foundation (WCRF). The researchers also received support from the European Commission within the framework of Marie Sklodowska-Curie Actions, the Spanish Association Against Cancer (AECC), the Barcelona Institute for Science and Technology (BIST), the Max Planck Society, the Deutsche Forschungsgemeinschaft programme, and the Medical Research Council of the United Kingdom.

Featured image: Immunofluorescence staining for mammary epithelium (red), highlighting the luminal lineage (green), showing aberrant mammary branching upon perturbed chromatin accessibility. © IRB Barcelona


Reference article: Alexandra Avgustinova, Carmelo Laudanna, Mónica Pascual-García, Quirze Rovira, Magdolna Djurec, Andres Castellanos, Uxue Urdiroz-Urricelqui, Domenica Marchese, Neus Prats, Alexandra Van Keymeulen, Holger Heyn, Juan M. Vaquerizas, Salvador Aznar Benitah, Repression of endogenous retroviruses prevents antiviral immune response and is required for mammary gland development, Cell Stem Cell, 2021, , ISSN 1934-5909, https://doi.org/10.1016/j.stem.2021.04.030. (https://www.sciencedirect.com/science/article/pii/S193459092100206X)


Provided by IRB Barcelona

Novel Method of Labeling DNA Bases For Sequencing (Biology)

An international research team headed by Michal Hocek of the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague) and Charles University and Ciara K. O’Sullivan of Universitat Rovira i Virgili (URV) in Spain have developed a novel method for labeling DNA, which in the future can be used for sequencing DNA by means of electrochemical detection. The researchers presented their results in the Journal of the American Chemical Society.

A DNA molecule comprises four basic building blocks, nucleotides. The genetic information carried within the molecule is determined by the order of the nucleotides. Knowledge of the order of these building blocks, which is known as the DNA sequence, is necessary for disease diagnostics and forensic DNA analysis, for example. Despite the great progress in recent years, the current DNA sequencing methods, typically based on fluorescent labelling, are still time-consuming and relatively expensive techniques, which have some limitations. Therefore, scientists are intensively searching for new approaches to simplify and accelerate sequencing.

One promising approach is the use of electrochemical detection and so-called redox labels, which are compounds that can be oxidized or reduced on electrodes. A multidisciplinary team of researchers from IOCB Prague, URV, the Faculty of Science of Charles University, the Polish Academy of Sciences, and the Institute of Biophysics of the Czech Academy of Sciences, with students David Kodr and Cansu Pinar Yenice as first authors, has now succeeded in designing and synthesizing artificial nucleotides with special attached redox labels that can be oxidized on a gold or carbon electrode at a specific potential to produce a measurable and analytically useful signal. These labels are carboranes, cage structures composed of boron and carbon atoms, into which other metal atoms can be incorporated, such as iron or cobalt, affecting their resulting electrochemical properties.

Artistic rendering of electrochemical coding of DNA bases. Graphic design: Tomáš Belloň / IOCB Prague

The modified nucleotides have been engineered so that the enzyme DNA polymerase, which uses available nucleotide building blocks to build DNA within a cell, can incorporate them into a newly synthesized DNA strand. Thus, the researchers have succeeded in preparing a strand of DNA comprising modified nucleotides. At the same time, each of the four types of nucleotide carries its own unique label allowing for its subsequent identification. And therein lay the primary pitfall of the project; until now, researchers had always only managed to label and measure one, at most two, types of redox-labelled nucleotides in a single strand of DNA.

Because each of the modified nucleotides carries its own label, which during electrochemical detection gives a specific oxidation signal at varying potentials, the individual types of nucleotides can be distinguished. Moreover, the size of each signal is dependent on the number of copies of the given nucleotide in the DNA, which then makes it possible to quickly determine the relative representation of individual nucleotides in the measured DNA.

The newly developed electrochemical coding of DNA bases offers a range of advantages, such as simpler and more affordable instrumentation and faster analysis. The method holds promise for DNA sequencing and diagnostic applications as well as for development of new DNA chips.

The original article

  • Kodr, D.; Yenice, C. P.; Simonova, A.; Saftić, D. P.; Pohl, R.; Sýkorová, V.; Ortiz, M.; Havran, L.; Fojta, M.; Lesnikowski, Z. J.; O’Sullivan, C. K.; Hocek, M. Carborane- or Metallacarborane-Linked Nucleotides for Redox Labeling. Orthogonal Multipotential Coding of all Four DNA Bases for Electrochemical Analysis and Sequencing. Journal of the American Chemical Society 2021, 143, 7124-7134. https://doi.org/10.1021/jacs.1c02222

Provided by Institute of Organic Chemistry and Biochemistry

New Method for Producing Synthetic DNA (Chemistry)

Chemically synthesized short DNA sequences are extremely important ingredients with countless uses in research laboratories, hospitals, and in industry, like in the method for identifying COVID-19. Phosphoramidites are necessary building blocks in the production of DNA sequences, but they are unstable, and break quickly. PhD Alexander Sandahl (Professor Kurt Gothelf’s group) has, in collaboration with a researcher in Professor Troels Skrydstrup’s group, developed a new patented way to quickly and efficiently manufacture the unstable building blocks immediately before they are to be used, and thus streamline DNA production.

The DNA sequences produced are also called oligonucleotides. These are widely used for disease identification, for the manufacture of oligonucleotide-based drugs, and for several other medical and biotechnological applications. 

The high demand for oligonucleotides therefore requires an efficient automated method for their chemical production.This process relies on phosphoramidites, which are chemical compounds that have the disadvantage of being unstable unless stored at the ideal -20 degrees Celsius.

Instruments used for DNA synthesis are not able to cool down the phosphoramidites, and consequently it is unavoidable that some of them degrade after being added to the instrument. 

Avoiding unwanted degradation of important ingredients

Professor Kurt Gothelf and Professor Troels Skrydstrup are each heading a research group in organic chemistry, which have worked together to develop a relatively simple but efficient technology where the production of phosphoramidites can be automated and integrated directly into the instrument for DNA synthesis.

This avoids both the manual synthesis of these, which normally would take up to 12 hours, as well as the problem of storing unstable phosphoramidites. Gothelf’s group has contributed with their expertise in automated DNA synthesis and Skrydstrup’s group has contributed with their know-how with chemical reactions that take place in continuously flowing liquids (flow chemistry).

Schematic overview of strategy for synthesis of phosphoramidites in a flow-based setup. (Illustration: Nature Commun 12, Artikel nr. 2760 (2021))

“It has been a very rewarding collaboration which is precisely one of the core values of iNANO”, says Kurt Gothelf, who adds “and I would also like to attribute to Alexander Sandahl a large part of the credit for this project being successful, as he has established the collaboration and has developed and realized a large part of the ideas for the project.” 

The results have just been published in the journal, Nature Communications. 

In the method of producing phosphoramidites, nucleosides (starting materials) are flushed through a solid material (resin), which can potentially be fully integrated into an automated process in the instrument for DNA synthesis. The resin ensures that the nucleosides are rapidly phosphorylated, whereby the nucleosides are converted to phosphoramidites within a few minutes. From the resin, the phosphoramidites are automatically flushed on to the part of the instrument which is responsible for the DNA synthesis.

This avoids the degradation of the phosphoramidites, as they are first produced just before they are to be used (on-demand), in a faster, more efficient flow-based way that can potentially be automated and operated by non-chemists.


The research is financially supported by the Lundbeck Foundation, the Novo Nordisk Foundation (CEMBID), the Independent Research Fund Denmark, and the Danish National Research Foundation (CADIAC).


Read more about the research results in Nature Communications:

Alexander F. Sandahl, Thuy J. D. Nguyen, Rikke A. Hansen, Martin B. Johansen, Troels Skrydstrup, and Kurt V. Gothelf. On-Demand Synthesis of Phosporamidites. Nature Commun2021. doi: /10.1038/s41467-021-22945-z. 

Patent

Phosphoramidite synthesis on-demand
Priority application EP20186197.8
Patentees: Sandahl, A. F.; Nguyen, T. J. D.; Gothelf, K. V.

Featured image: PhD Alexander Sandahl, together with Professor Kurt Gothelf, Professor Troels Skrydstrup and a number of students in the groups, has developed a method for efficient and automated production of ingredients for DNA synthesis. (Illustration: Colourbox)


Provided by Aarhus University

Cancer Cells Hijack the 3D Structure of DNA (Biology)

Scientists at EPFL and UNIL have used a novel algorithmic approach on cancer cells to understand how changes in histone marks (H3K27ac) induce repositioning of chromatin regions in the cell nucleus, and described how modifications of local contacts between regulatory elements (enhancers and promoters) influence oncogene expression.

In cancer, a lot of biology goes awry: Genes mutate, molecular processes change dramatically, and cells proliferate uncontrollably to form entirely new tissues that we call tumors. Multiple things go wrong at different levels, and this complexity is partly what makes cancer so difficult to research and treat.

So it stands to reason that cancer researchers focus their attention where all cancers begin: the genome. If we can understand what happens at the level of DNA, then we can perhaps one day not just treat but even prevent cancers altogether.

This drive has led a team of researchers from EPFL and the University of Lausanne (UNIL) to make a breakthrough discovery concerning a critical genetic aberration that occurs in cancer. Working together, the groups of Elisa Oricchio (EPFL) and Giovanni Ciriello (UNIL) have used a novel algorithm-based method to study how cancer cells re-organize the 3D structure of their DNA in order to ramp up the activity of cancer-promoting genes called “oncogenes.” The work is published in two journals, Nature Genetics and Nature Communications.

The research focuses on chromosomes, where our DNA is packaged, and how the chromosomes are organized in the tight space of the cell nucleus. Given that every single one of the billions of cells in our body contains about two meters of DNA, it’s understandable that we evolved mechanisms to store it properly. That mechanism involves winding DNA around specialized proteins called histones, like a string spooling around a yoyo.

The resulting super-packed and well-protected DNA-protein complex is called chromatin. Multiple units of chromatin make up the structures we know as chromosomes. Normally, each cell carries 23 chromosomes and two copies for each chromosome, but in cancer cells, their structure and organization change. For example, a piece of a copy of chromosome 8 can be attached to a copy of chromosome 14. Moreover, a chromosome can take on a more relaxed or compact structure, which depends on chemical modifications called “epigenetic marks”.

The researchers investigated how changes in specific epigenetic marks modify chromosome structures and the expression of genes that promote tumor growth, known as oncogenes.

Giovanni Ciriello’s team at UNIL developed a novel algorithmic approach called Calder (after the American sculptor Alexander Calder) to track how genomic regions are positioned with respect to each other in the nucleus. “We used Calder to compare the spatial organization of the genome in more than a hundred samples,” says Ciriello. “But this organization is not static and, just like Alexander Calder’s mobile sculptures, it can rearrange its pieces.” The researchers used Calder to track regions of chromatin that “moved” from one area of the nucleus to another as a result of changing epigenetic marks.

Meanwhile, Oricchio’s team at EPFL used Calder to track changes of the chromatin 3D structure in normal and B-cell lymphoma cells. They discovered that in the lymphoma cells, specific epigenetic changes cause chromatin regions to be repositioned in different areas of the nucleus, which lead to novel local interactions that over-activate the expression of oncogenes.

The also found that, when two fragments from different chromosomes are broken off and swapped, they assume a 3D structure that is distinguishable from the normal copies. Importantly, these changes of 3D structure correspond to different epigenetic marks, and induce high expression of genes that support tumor cell expansion.

“Most of the time we think of our DNA as a long, linear molecule, and it’s only recently that we started to understand how its 3D organization is altered in cancer cells,” says Oricchio. “Considering the spatial organization of DNA in the nucleus provides a new lens to understand how tumor cells originate, and how therapeutic modulation of epigenetic marks can block tumor progression.”

Funding

  • ISREC Foundation (E.O.)
  • Swiss National Science Foundation
  • Swiss Cancer League
  • Gelu Foundation
  • The Giorgi-Cavaglieri Foundation
  • French National Cancer Institute (INCa) Epigenetic and Cancer program
  • Marie Curie EPFL fellowship

Featured image credit: istock photos


References: (1) Stephanie Sungalee, Yuanlong Liu, Ruxandra A. Lambuta, Natalya Katanayeva, Maria Donaldson Collier, Daniele Tavernari, Sandrine Roulland, Giovanni Ciriello, Elisa Oricchio. Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci. Nature Genetics 10 May 2021. DOI: 10.1038/s41588-021-00842-x (2) Yuanlong Liu, Luca Nanni, Stephanie Sungalee, Marie Zufferey, Daniele Tavernari, Marco Mina, Stefano Ceri, Elisa Oricchio, Giovanni Ciriello. Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes. Nature Communications 10 May 2021. DOI: 10.1038/s41467-021-22666-3


Provided by EPFL

Do People Aged 105 and Over Live Longer Because They Have More Efficient DNA Repair? (Biology)

Whole-genome sequencing of people who live beyond 105 and 110 years reveals unique genetic signatures linked to protective processes such as DNA repair.

Researchers have found that people who live beyond 105 years tend to have a unique genetic background that makes their bodies more efficient at repairing DNA, according to a study published today in eLife.

This is the first time that people with ‘extreme longevity’ have had their genomes decoded in such detail, providing clues as to why they live so long and manage to avoid age-related diseases.

“Aging is a common risk factor for several chronic diseases and conditions,” explains Paolo Garagnani, Associate Professor at the Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy, and a first author of the study. “We chose to study the genetics of a group of people who lived beyond 105 years old and compare them with a group of younger adults from the same area in Italy, as people in this younger age group tend to avoid many age-related diseases and therefore represent the best example of healthy aging.”

Garagnani and colleagues, in collaboration with several research groups in Italy and a research team led by Patrick Descombes at Nestlé Research in Lausanne, Switzerland, recruited 81 semi-supercentenarians (those aged 105 years or older) and supercentenarians (those aged 110 years or older) from across the Italian peninsula. They compared these with 36 healthy people matched from the same region who were an average age of 68 years old.

They took blood samples from all the participants and conducted whole-genome sequencing to look for differences in the genes between the older and younger group. They then cross-checked their new results with genetic data from another previously published study which analysed 333 Italian people aged over 100 years old and 358 people aged around 60 years old.

They identified five common genetic changes that were more frequent in the 105+/110+ age groups, between two genes called COA1 and STK17A. When they cross-checked this against the published data, they found the same variants in the people aged over 100. Data acquired from computational analyses predicted that this genetic variability likely modulates the expression of three different genes.

The most frequently seen genetic changes were linked to increased activity of the STK17A gene in some tissues. This gene is involved in three areas important to the health of cells: coordinating the cell’s response to DNA damage, encouraging damaged cells to undergo programmed cell death and managing the amount of dangerous reactive oxygen species within a cell. These are important processes involved in the initiation and growth of many diseases such as cancer.

The most frequent genetic changes are also linked to reduced activity of the COA1 gene in some tissues. This gene is known to be important for the proper crosstalk between the cell nucleus and mitochondria – the energy-production factories in our cells whose dysfunction is a key factor in aging.

Additionally, the same region of the genome is linked to an increased expression of BLVRA in some tissues – a gene that is important to the health of cells due to its role in eliminating dangerous reactive oxygen species.

“Previous studies showed that DNA repair is one of the mechanisms allowing an extended lifespan across species,” says Cristina Giuliani, Senior Assistant Professor at the Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences, University of Bologna, and a senior author of the study. “We showed that this is true also within humans, and data suggest that the natural diversity in people reaching the last decades of life are, in part, linked to genetic variability that gives semi-supercentenarians the peculiar capability of efficiently managing cellular damage during their life course.”

The team also measured the number of naturally occurring mutations that people in each age group had accumulated throughout their life. They found that people aged 105+ or 110+ had a much lower burden of mutations in six out of seven genes tested. These individuals appeared to avoid the age-related increase in disruptive mutations, and this may have contributed in protecting them against diseases such as heart disease.

“This study constitutes the first whole-genome sequencing of extreme longevity at high coverage that allowed us to look at both inherited and naturally occurring genetic changes in older people,” says Massimo Delledonne, Full Professor at the University of Verona and a first author of the study.

“Our results suggest that DNA repair mechanisms and a low burden of mutations in specific genes are two central mechanisms that have protected people who have reached extreme longevity from age-related diseases, concludes senior author Claudio Franceschi, Professor Emeritus of Immunology at the University of Bologna.

This study will be published as part of ‘Aging, Geroscience and Longevity: A Special Issue’ from eLife. To view the Special Issue, see https://elifesciences.org/collections/6d673315/aging-geroscience-and-longevity-a-special-issue.

Featured image: Study design. (A) 105+/110+ (in blue) and controls (in orange) recruited in the Italian peninsula and analyzed by whole genome sequencing (discovery cohort). (B) The study design applied in the present study. (C) PCA plot for the discovery cohort (Cohort 1), in red are indicated 105+/110+ and in black the group of controls (CTRL). © Garagnani et al.


Reference: Paolo Garagnani et al., “Whole-genome sequencing analysis of semi-supercentenarians”, Genetics and Genomics, 2021. DOI: 10.7554/eLife.57849


Provided by ELife

DNA Building Blocks Regulate Inflammation (Biology)

Shortage of DNA building blocks in the cell releases mitochondrial DNA

Mitochondria are the energy suppliers of our body cells. These tiny cell components have their own genetic material, which triggers an inflammatory response when released into the interior of the cell. The reasons for the release are not yet known, but some cardiac and neurodegenerative diseases as well as the ageing process are linked to the mitochondrial genome. Researchers at the Max Planck Institute for Biology of Ageing and the CECAD Cluster of Excellence in Ageing research have investigated the reasons for the release of mitochondrial genetic material and found a direct link to cellular metabolism: when the cell’s DNA building blocks are in short supply, mitochondria release their genetic material and trigger inflammation. The researchers hope to find new therapeutic approaches by influencing this metabolic pathway.

Our body needs energy – for every metabolic process, every movement and for breathing. This energy is produced in tiny components of our body cells, the so-called mitochondria. Unlike other cell components, mitochondria have their own genetic material, mitochondrial DNA. However, in certain situations, mitochondria release their DNA into the interior of the cell, causing a reaction from the cell’s own immune system and being associated with various diseases as well as the ageing process. The reasons for the release of mitochondrial DNA are not yet known.

Shortage of DNA building blocks triggers inflammatory reaction

To answer the question of when mitochondria release their DNA, researchers at the Max Planck Institute for Biology of Ageing have focused on the mitochondrial protein YME1L, which owes its name to yeast mutants that release their mitochondrial DNA – yeast mitochondrial escape 1. “In cells lacking YME1L, we observed the release of mitochondrial DNA into the cell interior and a related immune response in the cells”, said Thomas MacVicar, one of the study’s two first authors. Closer examination revealed a direct link to the building blocks of DNA. “If the cells lack YME1L, there is a deficiency of DNA building blocks inside the cell”, Thomas MacVicar describes. “This deficiency triggers the release of mitochondrial DNA, which in turn causes an inflammatory response in the cell: the cell stimulates similar inflammatory reactions as it does during a bacterial or viral infection. If we add DNA building blocks to the cells from the outside, that also stops the inflammation.”

New therapeutic approaches based on the metabolism of DNA building blocks

The discovered link between the cellular inflammatory response and the metabolism of DNA building blocks could have far-reaching consequences, explains Thomas MacVicar: “Some viral inhibitors stop the production of certain DNA building blocks, thereby triggering an inflammatory response. The release of mitochondrial DNA could be a crucial factor in this, contributing to the effect of these inhibitors.” Several ageing-associated inflammatory diseases, including cardiac and neurodegenerative diseases, as well as obesity and cancer, are linked to mitochondrial DNA. The authors hope that modulating the metabolism of DNA building blocks will offer new therapeutic opportunities in such diseases.

Featured image: Electron micrograph of mitochondria in a nerve cell. © Hans-Georg Sprenger


Reference: Hans-Georg Sprenger, Thomas MacVicar, Amir Bahat, Kai Uwe Fiedler, Steffen Hermans, Denise Ehrentraut, Katharina Ried, Dusanka Milenkovic, Nina Bonekamp, Nils-Göran Larsson, Hendrik Nolte, Patrick Giavalisco and Thomas Langer, “Equal first authorsCellular nucleotide imbalance triggers mitochondrial DNA-dependent innate immunity”, Nature Metabolism, 2021. Source


Provided by Max Planck Gesellschaft