Review
Microbiology
Ruth Breuer, Jose-Vicente Gomes-Filho, Lennart Randau
Summary: Post-transcriptional modifications play crucial roles in ribosomal RNA maturation across all three domains of life. Ribose 2'-O-methylations, the most common chemical rRNA modification, are involved in RNA folding and stabilization. In archaea, variable sets of C/D box sRNAs guide the activity of rRNA 2'-O-methyltransferase fibrillarin, with the evolution of guide sequences and pairing influencing rRNA modification patterns and RNA chaperone activities.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Cell Biology
Hai-juan Bao, Xi Chen, Xin Liu, Wu Wu, Qian-hui Li, Jing-yuan Xian, Yang Zhao, Shuo Chen
Summary: This study assessed the dysregulation of SNORD89 in endometrial cancer and found its association with cancer development. SNORD89 inhibits the translation process of the Bim gene by interacting with Fbl, thereby promoting endometrial cancer occurrence and development. Moreover, inhibiting SNORD89 can suppress endometrial cancer cell proliferation and migration ability. Therefore, SNORD89 may serve as a potential therapeutic target for endometrial cancer.
CELL DEATH DISCOVERY
(2022)
Article
Biochemical Research Methods
Daniela Barros-Silva, Johan Tsui, Carmen Jeronimo, Guido Jenster, Elena S. Martens-Uzunova
Summary: Ribose 2'O-methylation is the most abundant RNA modification in rRNA, and alterations at individual Nm sites may reflect cellular processes. A new quantitative PCR-based method is developed to sensitively assess ribomethylation levels at specific rRNA sites in low input amounts of total RNA.
Article
Biochemistry & Molecular Biology
Daniela Barros-Silva, Jonathan Klavert, Guido Jenster, Carmen Jeronimo, Denis L. J. Lafontaine, Elena S. Martens-Uzunova
Summary: Ribosomes are crucial nanomachines responsible for protein production, and in cancer, pathways controlling ribosome biogenesis and function are often deregulated. Ribosomal RNAs undergo abundant modifications, and snoRNA expression and ribosome methylation profiles are altered in cancer.
Review
Plant Sciences
Deniz Streit, Enrico Schleiff
Summary: The translation delves into ribosome assembly in eukaryotes, focusing on the processes in Arabidopsis thaliana and the significance of ribosome biogenesis factors and small nucleolar RNAs. It also discusses the various types of rRNA modifications and the role of snoRNPs in directing these modifications. The study compares plant-specific modifications in Arabidopsis thaliana with those in humans and yeast, shedding light on the diversity in ribosome biogenesis.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Eri Asano-Inami, Akira Yokoi, Mai Sugiyama, Toshinori Hyodo, Tomonari Hamaguchi, Hiroaki Kajiyama
Summary: Stress granules (SGs) are composed of non-translating mRNAs and proteins, and play critical roles in cell survival under stressed conditions. UBAP2L is identified as a crucial component of SGs, and its depletion suppresses SG organization.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
R. Elizabeth Dreggors-Walker, Lauren N. Cohen, Sohail Khoshnevis, Virginie Marchand, Yuri Motorin, Homa Ghalei
Summary: Regulation of protein synthesis is essential for gene expression control in cells. Defects in ribosome production, function, or regulation can lead to cellular damage and human diseases such as PEHO syndrome. This study reveals that mutations in the ZNHIT3 gene, which encodes a nuclear protein, cause a decrease in protein levels and defects in rRNA processing and translation in yeast, providing insights into the molecular basis of PEHO syndrome.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Isabel S. Naarmann-de Vries, Christiane Zorbas, Amina Lemsara, Michael Piechotta, Felix G. M. Ernst, Ludivine Wacheul, Denis L. J. Lafontaine, Christoph Dieterich
Summary: This study presents a targeted direct rRNA sequencing method that uses substrate selection and the JACUSA2 software to identify differential modification sites. The approach reliably identifies differential base methylation and acetylation events. Additionally, the study demonstrates the detection of human rRNA modifications using direct RNA sequencing on Flongle flow cells, which reduces the RNA input requirements and enhances the suitability for clinical analysis of samples with limited availability.
Article
Biochemistry & Molecular Biology
Junnan Liang, Ganxun Li, Jingyu Liao, Zhao Huang, Jingyuan Wen, Yu Wang, Zeyu Chen, Guangzhen Cai, Weiqi Xu, Zeyang Ding, Huifang Liang, Pran K. Datta, Liang Chu, Xiaoping Chen, Bixiang Zhang
Summary: This study reveals the role of SNORD17 in hepatocellular carcinoma (HCC) and its interaction with p53, suggesting it as a potential therapeutic target for HCC.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Biochemistry & Molecular Biology
Laeya Baldini, Anne Robert, Bruno Charpentier, Stephane Labialle
Summary: The eutherian-specific SNORD116 family of repeated box C/D snoRNA genes is believed to play a major role in Prader-Willi syndrome (PWS), and their molecular function has been further confirmed by analysis of eutherian orthologs in RNA target identification and function verification. There are extensive birth-and-death and conversion events in the history of SNORD116 gene, affecting the phylogenetic conservation along the gene sequence. Despite this, the standard snoRNA elements essential for RNA stability and protein association are highly conserved, supporting the hypothesis that SNORD116 generate genuine snoRNAs. In addition, SNORD116 has been shown to control the expression and splicing levels of certain mRNAs, revealing unexpected molecular links with Fragile X syndrome and autism spectrum disorders.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Mariam Jaafar, Julia Contreras, Carine Dominique, Sara Martin-Villanueva, Regine Capeyrou, Patrice Vitali, Olga Rodriguez-Galan, Carmen Velasco, Odile Humbert, Nicholas J. Watkins, Eduardo Villalobo, Katherine E. Bohnsack, Markus T. Bohnsack, Yves Henry, Raghida Abou Merhi, Jesus de la Cruz, Anthony K. Henras
Summary: This study investigates the functions of box C/D snoRNP snR190 and helicase Dbp7 in eukaryotic ribosome biogenesis. The snR190 snoRNA acts as an RNA chaperone to assist in structuring 25S rRNA, while Dbp7 is crucial for facilitating remodeling events in the peptidyl transferase center region of 25S rRNAs. The molecular events underlying the assembly and maturation of early pre-60S particles during eukaryotic ribosome synthesis are complex and not well understood.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Dimitar Plamenov Petrov, Steffen Kaiser, Stefanie Kaiser, Kirsten Jung
Summary: This study compared the efficiency of size-dependent separation by electrophoresis and rRNA depletion for enrichment of Escherichia coli mRNA, finding that neither method allowed complete removal of rRNA. However, the researchers were able to quantitatively analyze several modified nucleosides in different RNA types, showing evidence for stress dependent RNA modification reprofiling in rRNA and significant changes in modified nucleosides in the mRNA enriched fractions.
Article
Biochemistry & Molecular Biology
J. Azevedo-Favory, C. Gaspin, L. Ayadi, C. Montacie, V Marchand, E. Jobet, M. Rompais, C. Carapito, Y. Motorin, J. Saez-Vasquez
Summary: This study used RiboMethSeq to explore rRNA 2'MODIFIER LETTER PRIME-O-methylation sites in A. thaliana plants, discovering new C/D snoRNA-guided methylation sites and some orphan sites. Moreover, disruption of Nucleolin 1 gene was found to decrease 2'MODIFIER LETTER PRIME-O-methylation at specific rRNA sites, suggesting a functional/structural interconnection with nucleolus organization and plant development.
Article
Biotechnology & Applied Microbiology
Jose M. Uribe-Salazar, Gulhan Kaya, Aadithya Sekar, KaeChandra Weyenberg, Cole Ingamells, Megan Y. Dennis
Summary: Our study systematically assessed the accuracy of CRISPR/Cas9 tool predictions for on- and off-target gene editing in zebrafish embryos, revealing large discrepancies between experimentally observed editing efficiencies and predictions made by commonly used gRNA design tools. We also investigated potential confounders of G(0)-based CRISPR screens by analyzing control embryos, identifying potentially lasting effects from the microinjection process. This research provides a valuable resource for the zebrafish community to enhance the design and implementation of CRISPR/Cas9 experiments.
Article
Biology
Jiayin Wang, Songlin Wu, Keqiong Ye
Summary: This study reveals the global landscape of RNA-guided 2'-O-methylation in an archaeon and unexpected targeting rules employed by C/D RNA.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Gerald Ryan R. Aquino, Nicolai Krogh, Philipp Hackert, Roman Martin, Jimena Davila Gallesio, Robert W. van Nues, Claudia Schneider, Nicholas J. Watkins, Henrik Nielsen, Katherine E. Bohnsack, Markus T. Bohnsack
Summary: RNA helicase Dbp3 plays a crucial role in efficient processing of specific snoRNAs and 2'-O-methylation of rRNA, with the absence of Dbp3 causing accumulation of snoRNPs on pre-ribosomes; snoRNA interactions with ribosomes are crucial for rRNA modification.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Immunology
Fatima A. H. Al-Jaberi, Martin Kongsbak-Wismann, Alejandro Aguayo-Orozco, Nicolai Krogh, Terkild B. Buus, Daniel V. Lopez, Anna K. O. Rode, Eva Gravesen, Klaus Olgaard, Soren Brunak, Anders Woetmann, Niels odum, Charlotte M. Bonefeld, Carsten Geisler
Summary: This study reveals the impact of a point mutation in the DNA-binding domain of VDR on 1,25(OH)(2)D-3 signaling, with effects on VDR subcellular localization and transcriptional activity. The study also demonstrates that the expression level of wild-type VDR determines the responsiveness of T cells to 1,25(OH)(2)D-3. Additionally, the study shows that vitamin A inhibits the translocation of VDR to the nucleus and upregulation of CYP24A1 induced by 1,25(OH)(2)D-3.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biology
Steinar Daae Johansen, Sylvia Chi, Arseny Dubin, Tor Erik Jorgensen
Summary: The complete mitochondrial genome and transcriptome of the carpet sea anemone Stichodactyla haddoni reveal the presence of complex catalytic group I introns. The genome is vertebrate-like in size, organization, and gene content, with the presence of nonconventional and optional mitochondrial genes challenging current taxonomy as phylogenetic analyses place S. haddoni within the family Actiniidae.
Article
Biochemistry & Molecular Biology
Martin D. Jansson, Sophia J. Hafner, Kubra Altinel, Disa Tehler, Nicolai Krogh, Emil Jakobsen, Jens Andersen, Kasper L. Andersen, Erwin M. Schoof, Patrice Menard, Henrik Nielsen, Anders H. Lund
Summary: Variation in ribosome composition due to differential 2'-O-methylation of ribosomal RNA can lead to ribosome heterogeneity, impacting translation of select mRNAs and resulting in changes in cellular phenotypes. This suggests a broader mechanism where specific regulation of rRNA modification patterns fine tunes translation.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Ana Martinez-Val, Dorte B. Bekker-Jensen, Sophia Steigerwald, Claire Koenig, Ole ostergaard, Adi Mehta, Trung Tran, Krzysztof Sikorski, Estefania Torres-Vega, Ewa Kwasniewicz, Solveig Hlin Brynjolfsdottir, Lisa B. Frankel, Rasmus Kjobsted, Nicolai Krogh, Alicia Lundby, Simon Bekker-Jensen, Fridtjof Lund-Johansen, Jesper V. Olsen
Summary: Dynamic changes in subcellular localization of signaling proteins are a general concept evolved by eukaryotic cells to coordinate responses to stimuli. A high-throughput workflow based on sequential cell fractionation can provide comprehensive maps of global proteome and phospho-proteome dynamics in different subcellular fractions. Proteomics data generated in this study can be explored through https://SpatialProteoDynamics.github.io.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Gerald Ryan R. Aquino, Philipp Hackert, Nicolai Krogh, Kuan-Ting Pan, Mariam Jaafar, Anthony K. Henras, Henrik Nielsen, Henning Urlaub, Katherine E. Bohnsack, Markus T. Bohnsack
Summary: Early pre-60S ribosomal particles are complex structures undergoing dynamic changes, with RNA helicase Dbp7 playing a key role in regulating the assembly process. Dbp7 influences compaction of domain V/VI and impacts binding and activity of factors like ribosomal protein uL3 in early ribosomal assembly.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jan Diesend, Ulf Birkedal, Jonas Kjellin, Jingwen Zhang, Kim Philipp Jablonski, Fredrik Soderbom, Henrik Nielsen, Christian Hammann
Summary: Using bioinformatics and RNA-seq data, we identified 30 novel box C/D snoRNAs in Dictyostelium discoideum and determined their interactions with RNA in the soil.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Katherine E. Bohnsack, Anthony K. Henras, Henrik Nielsen, Markus T. Bohnsack
Summary: This article discusses the diverse mechanisms employed in different organisms to establish connections between the 5' and 3' ends of the large subunit (LSU) ribosomal RNA (rRNA) for rRNA domain compaction and subunit assembly.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Cell Biology
Sophia J. Hafner, Martin D. Jansson, Kubra Altinel, Kasper L. Andersen, Zehra Abay-Norgaard, Patrice Menard, Martin Fontenas, Daniel M. Sorensen, David M. Gay, Frederic S. Arendrup, Disa Tehler, Nicolai Krogh, Henrik Nielsen, Matthew L. Kraushar, Agnete Kirkeby, Anders H. Lund
Summary: Translational regulation plays a crucial role in pluripotency maintenance and cell differentiation. This study reveals ribosome heterogeneity through rRNA 2'-O-methylation during early development and differentiation, indicating a direct role for ribosomes in regulating translation during cell fate acquisition.
DEVELOPMENTAL CELL
(2023)
Article
Multidisciplinary Sciences
Ulises H. H. Guzman, Henriette Aksnes, Rasmus Ree, Nicolai Krogh, Magnus E. E. Jakobsson, Lars J. J. Jensen, Thomas Arnesen, Jesper V. V. Olsen
Summary: Protein N-terminal (Nt) acetylation is a common modification in eukaryotes and plays a crucial role in promoting stability of the proteome. However, the functional impact of Nt-acetylation has been hindered by its pleiotropic effects. In this study, we used proteomics approaches to analyze the effects of NatA deficiency in Saccharomyces cerevisiae and found that it leads to global proteome remodeling and decreased thermostability of ribosomes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ase Emblem, Erik Knutsen, Tor Erik Jorgensen, Hilde Fure, Steinar Daae Johansen, Ole-Lars Brekke, Tom Eirik Mollnes, Bard Ove Karlsen
Summary: Understanding the expression of long non-coding RNAs containing Alu elements in inflammation is crucial for predicting the development of severe diseases. By using a computational approach, we identified 48 immune genes with Alu insertion as potential candidates for further study, and one of these candidates located within the C5aR1 gene holds promise as a target for RNA therapeutics.
Article
Biochemistry & Molecular Biology
Giulia Beneventi, Roberto Munita, Phuong Cao Thi Ngoc, Magdalena Madej, Maciej Ciesla, Sowndarya Muthukumar, Nicolai Krogh, Henrik Nielsen, Vinay Swaminathan, Cristian Bellodi
Summary: SCARNA15 directs alternative splicing and stress adaptation in cancer cells, impacting the expression and function of key tumor suppressors ATRX and p53.
