RNA Biology Group - UPatras

09/08/2024

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21/07/2024

One more important report in NSMB on the processing of NEAT1 long noncoding RNA which orchestrates paraspeckle assembly and impacts tumorigenesis, fertility and immunity. Its maturation requires RNase P cleavage yielding an unstable transfer RNA-like multiple endocrine neoplasia-β tRNA-like transcript (menRNA) due to CCACCA addition. Our alumni Ilias Skeparnias together with our collaborator Jinwei Zhang at NIDDK-NIH report the crystal structure of human menRNA, which partially mimics tRNAs to drive RNase P and ELAC2 processing and uncover an RNA-centric, riboswitch-like mechanism whereby the nascent CCA reshapes the RNA folding landscape and propels a spontaneous conformational isomerization that directs repeat CCA addition, marking the menRNA and defective tRNAs for degradation. Congratulations Ilias and Jinwei!

https://www.nature.com/articles/s41594-024-01361-z?fbclid=IwZXh0bgNhZW0CMTAAAR3O5PFKLC5i8YoSOms0QzQ33rU8h1C7CYnq1AopiMcI1yrMrFwv5EkLybw_aem_Y4XQFa-YYdKurJcQQHAJDA

This study reveals the mechanisms of NEAT1 lncRNA maturation and menRNA biogenesis and uncovers an RNA-centric, riboswitch-like mechanism where menRNA drives its own conformational isomerization that directs repeat CCA addition and rapid degradation.

11/07/2024

Our new story is already online in RNA! Read all about the remarkable diversity of T-box riboswitch structures from pathogens that we are currently exploiting further for the development of new antibacterials that can target essential RNA conformations https://rnajournal.cshlp.org/content/early/recent ! Many thanks to our collaborating team led by Dr Jinwei Zhang at the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and also to Ελληνικό Ίδρυμα Έρευνας & Καινοτομίας - ΕΛΙΔΕΚ for supporting our research on novel aspects of RNA biology!

03/07/2024

The structural basis of MALAT1 lncRNA processing was published in Nature Structural and Molecular Biology by our group alumni Ilias Skeparnias and the lab of our collaborator Jinwei Zhang at NIDDK-NIH. MALAT1 has a key role in many cancers and matures as a pre-tRNA by adopting tRNA-like structures. Congratulations Ilias! Read the exciting story.

The authors uncover a Père David’s deer-like design for long noncoding RNAs such as metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), which partially mimics the transfer RNA (tRNA) structure to recruit select tRNA processing enzymes for maturation and to create novel regulatory RNA...

21/06/2024

What better way to close a very stressful week than celebrating the achievements of our lab members. The "legendary" Nikoleta Giarimoglou who has swept all the available awards during her PhD tenure (University of Patras 2 times in a row, HSBMB, Mikrobiokosmos, etc.) is the winner of the 2023 best PhD thesis award from Antibiotics MDPI (together with Tim M.J. Ewoldt from Department of Hospital Pharmacy, Erasmus University Medical Center) which comes with a prize of 800 CHF and an opportunity to publish a paper in the journal! At the same time, her latest paper on the structural idiosyncrasies of RNA-mediated regulation of gene expression by T-box riboswitches from prominent human pathogens was accepted today in RNA, together with an invitation from the editor to be portrayed in the "Meet the first author" section at the same issue that her paper will appear!!! 👏👏👏
Congratulations Nikoleta!!! Fantastic job!!! But it's not over yet! 😉

17/06/2024

Happy to watch our former students, returning home after a productive tenure abroad. Dimitrios Anastasakis obtained his PhD at RNA Biology Group - UPatras working on the novel ribonuclease PNLDC1 which, among others, is responsible for the maturation of piRNAs. His PhD work was published in an important paper in Nucleic Acids Research https://academic.oup.com/nar/article/44/18/8908/2468357?login=false.

On June the 17th 2024, Dr Dimitrios Anastasakis, gave a seminar at IMBB on the impact of RNA-binding proteins on gene expression regulation in health and disease.
Dr Anastasakis is a Research Fellow at NIAMS Labs ,🇺🇸 in the RNA Molecular Biology Lab led by Dr. Markus Hafner.

Dr. Anastasakis has recently been appointed Assistant Professor at the University of Crete, School of Medicine, and anticipates starting his new position as a group leader by the end of the year.

Πανεπιστήμιο Κρήτης- University of Crete

14/06/2024

Vault RNAs is an overlooked class of Pol III transcripts that play role in the assembly of vault particles. The exact role of vault RNAs as free molecules is poorly understood and the detection of vault RNA fragments remains a mystery regarding their role in cellular physiology. Our PhD candidate Alexandros Maniatis Αλέξανδρος Μανιάτης is exploring the essential nature of individual vault genes in cancer and the synchronization of their expression with other important Pol III transcripts which alltogether represent more than 70% of the total noncoding RNome in cells.

Leonard Rome’s lab discovered an odd, abundant component of cells in the 1980s—and he’s still trying to figure out what it does.

Learn more: https://scim.ag/7jt

09/06/2024

mRNA-The future of vaccines.

Penn Medicine mRNA research built the historic COVID-19 vaccines. Explore the history of mRNA technology and its impact on treating infectious diseases.

01/06/2024

A great effort from NIH is on the way to decipher the multi facets of RNA and necessary to harness its full potential!

Science community is rallying behind a multibillion-dollar project to better understand DNA’s overlooked cousin

16/05/2024

What sequence characteristics define a promoter? Despite the critical role that promoters play in transcription initiation of every gene, their nature in the human genome remains inadequately understood. Dudnyk et al. developed an explainable machine learning model called Puffin to determine how transcription initiation depends on the sequence, revealing a small set of motifs and rules that explain most human promoters. These findings present a unified model for transcription initiation in most human promoters and shed new light on fundamental questions related to promoter sequence and function.

Transcription initiation is a process that is essential to ensuring the proper function of any gene, yet we still lack a unified understanding of sequence patterns and rules that explain most transcription start sites in the human genome. By predicting ...

19/04/2024

Another great day for our group with the PhD defense of Dr Giorgos Kyriakopoulos MD. George joined our group as an undergraduate from the School of Pharmacy working on the role of specific miRNAs in the deregulation of transcription and translation in cancer. Along the way, he joined the School of Medicine for his MD degree and at the same time he worked hard for his PhD research. George excelled in every aspect of his academic life, and as a FULBRIGHT FOUNDATION GREECE fellow he joined National Cancer Institute where he worked under the supervision of Drs Glenn Merlino and Romina Goldszmid. Together with Prof. Hubert D. Becker from the University of Strasbourg we all celebrated his hard work on noncoding RNAs and related RBPs that derail transcription and translation in lung cancer and melanoma and play role in resistance to current chemotherapies. With a combination of genome editing and omics analyses, George revealed novel regulatory circuits regarding the signaling of the most common KRAS and BRAF mutations that are directly linked to drug resistance. George was not only instrumental regarding all the cancer related projects in our group but also an excellent friend and mentor for younger members. He is now on a bright path to become a brilliant oncologist abroad with the hope that one day he will return! Congratulations George and thank you for everything! The best are yet to come!

07/04/2024

Nature Reviews Molecular Cell Biology

01/04/2024

And now it's time for the RNome! More than 20 years after the first draft of the human genome it is time to discover the elusive RNA molecules and their modifications which are responsible for hundreds of diseases. The dawn of an exciting new "RNA world" era.

U.S. report lays out an ambitious plan to harness the “RNome” for medicine and more—but funding is uncertain

19/03/2024

Funded PhD positions in RNA Biology in Vienna, Austria.

The Medical University of Vienna organises a Ph.D. call twice a year and offers 15 fully funded Ph.D. studentships with a flexible starting date in the summer or autumn of 2024.

17/03/2024

A very thoughtful approach on a sensitive topic that will be in the epicenter of future efforts.

26/02/2024

Nature - Debate over figure connecting genes, race and ethnicity reignites concerns among geneticists about how to represent human diversity.

22/02/2024

It's not only the code..

Nature Reviews Gastroenterology & Hepatology

18/02/2024

Genes activated in new environments include those used during development.

15/12/2023

The role of circular RNAs (circRNAs) remains elusive to a great extent. Emerging data have shown that previously defined noncoding genomes might encode peptides that bind human leukocyte antigen (HLA) as cryptic antigens to stimulate adaptive immunity. However, the significance and mechanisms of action of cryptic antigens in anti-tumour immunity remain unclear. In this report the authors used mass spectrometry of the HLA class I (HLA-I) peptidome coupled with ribosome sequencing of human breast cancer samples and identified HLA-I-binding cryptic antigenic peptides that were noncanonically translated by a tumour-specifc circular RNA (circRNA). Their findings reveal that noncanonical translation of circRNAs can drive eficient anti-tumour immunity, which suggests that vaccination exploiting tumour-specific circRNAs may serve as an immunotherapeutic strategy against malignant tumours.

https://www.nature.com/articles/s41586-023-06834-7?utm_medium=Social&utm_campaign=nature&utm_source=Facebook&fbclid=IwAR3OZqCszpRgW5Sv9sXHLde98uZ0H7vdvrKOS4sfiQKfT-6tLXX4CRDMKLQ =1702486653-1

The tumour-specific circular RNA FAM53B is highly immunogenic and can induce anti-tumour responses in mouse models of breast cancer and melanoma, expanding the repertoire of anticancer targets for development.

11/11/2023

Α breakthrough paper was published in Cell reporting the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. The report demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs. A great example of synthetic biology progress.

Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo…

20/10/2023

11 years ago, the revolutionary genetic tool CRISPR/Cas9 was published in Science, work that Emmanuelle Charpentier and Jennifer Doudna won a Nobel Prize for in 2020.

On , read the landmark paper that describes the discovery: https://scim.ag/4wp

08/10/2023

RNA modifications are known more almost 60 years and are crucial for function. Read this interesting review on potential clinical applications.

Nature Reviews Genetics

02/10/2023

RNA biologists all over the world celebrate today one of the most important Nobel prizes. Both researchers although they faced disbelief and fought against the odds, they were armored with mind strength and they exhibited unmatched work ethics. We also feel proud for all those in the RNA field (and the few in Greece) who work day and night to make people understand the paramount value of the RNA world for a better world.

BREAKING NEWS
The Nobel Assembly at Karolinska Institutet has today decided to award the 2023 Nobel Prize in Physiology or Medicine to Katalin Karikó and Drew Weissman for their discoveries concerning nucleoside base modifications that enabled the development of effective mRNA vaccines against COVID-19.

The discoveries by the two Nobel Prize laureates were critical for developing effective mRNA vaccines against COVID-19 during the pandemic that began in early 2020. Through their groundbreaking findings, which have fundamentally changed our understanding of how mRNA interacts with our immune system, the laureates contributed to the unprecedented rate of vaccine development during one of the greatest threats to human health in modern times.

Learn more
Press release: https://bit.ly/3RypmGw
Advanced information: https://bit.ly/3rrshGw

30/09/2023

Nature Reviews Molecular Cell Biology: This Review discusses the established multi-omics technologies, the cutting-edge and state-of-the-art methods in the field, how multi-omics technologies have adapted and improved, and its limitations.

Single-cell multi-omics methods are essential for characterizing cell states and types. The past decade has ushered in improvements in spatial resolution and computational data integration and in new omics modalities. Consequently, single-cell multi-omics have advanced fundamental and translational....

21/09/2023

The 2023 Lasker Award goes to AlphaFold!

John Jumper and Demis Hassabis received this year’s 2023 Albert Lasker Basic Medical Research Award for their work on the artificial intelligence system AlphaFold, which changed the landscape of protein biology.

19/09/2023

12/09/2023

A study in Nature Biomedical Engineering shows that RNAs derived from transposable elements and other repeat elements are enriched in the cell-free transcriptome of patients with cancer, and that they serve as signatures for the accurate classification of the disease. Read the paper: https://go.nature.com/3LbaXvX

25/08/2023

https://www.facebook.com/100064843296393/posts/682471763924261/

A decade ago, NIH reached an agreement with the family of the late Henrietta Lacks, allowing biomedical researchers controlled access to the whole genome data of cells derived from her tumor. These cells, known as HeLa cells, have helped make possible some of the most important medical advances of the past 60 years. NIH is grateful for the Lacks family support and continues to honor their preferences while responsibly advancing scientific discovery. Read more in the NIH Director’s statement: https://go.nih.gov/cMvBuzZ

26/07/2023

Nature Reviews Molecular Cell Biology

25/07/2023

One of our most brilliant students and sparkling personalities defended her PhD today. Nikoleta Giarimoglou joined our RNA Biology Group - UPatras as a Masters student after graduating from the Department of Biochemistry and Biotechnology Πανεπιστήμιο Θεσσαλίας and uplifted a fantastic project on the tRNA-mediated regulation of transcription and translation by riboswitches which was supported by Ελληνικό Ίδρυμα Έρευνας & Καινοτομίας - ΕΛΙΔΕΚ. The quality of her work not only was awarded in national and international conferences, but was published in major journals like Nature Structural and Molecular Biology and Nucleic Acids Research. Moreover, her latest paper received the Πανεπιστήμιο Πατρών University of Patras "P. Kanellopoulos" award for the best publication in 2022. Nikoleta's work ethics was an inspiration for everyone in the lab, always full of joy and love for science! Nikoleta thank you for being such a great scientist and a fantastic human being! A bright future lies ahead for you!