Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function

Gene expression regulation mediated through reversible m6A RNA methylation

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The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution

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Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

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Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

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MODOMICS: a database of RNA modification pathways—2013 update

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X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions

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Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs

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The RNA modification database, RNAMDB: 2011 update

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Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae

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Specialized ribosomes: a new frontier in gene regulation and organismal biology

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Is There Any Sequence Feature in the RNA Pseudouridine Modification Prediction Problem?

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Ribosome recycling in mRNA translation, quality control, and homeostasis

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Increased fibrillarin expression is associated with tumor progression and an unfavorable prognosis in hepatocellular carcinoma

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RNA helicase-mediated regulation of snoRNP dynamics on pre-ribosomes and rRNA 2′-O-methylation

Aquino, G. R., Krogh, N., Hackert, P., Martin, R., Gallesio, J. D., van Nues, R. W., Schneider, C., Watkins, N. J., Nielsen, H., Bohnsack, K. E., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab159 · Cited by 30

m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network

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Translation Regulation in Skin Cancer from a tRNA Point of View

Grafanaki, K., Anastasakis, D. G., Kyriakopoulos, G. C., Skeparnias, I., Georgiou, S., & Stathopoulos, C. (2018) · Epigenomics · doi:10.2217/epi-2018-0176 · Cited by 31

Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster

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Charting the epitranscriptomic landscape across RNA biotypes using native RNA nanopore sequencing

Diensthuber, G., & Novoa, E. M. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.12.014 · Cited by 28

Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions

Dannfald, A., Favory, J.-J., & Deragon, J. (2021) · RNA Biology · doi:10.1080/15476286.2021.1931756 · Cited by 30

A Ribosomal Perspective on Neuronal Local Protein Synthesis

Dastidar, S. G., & Nair, D. (2022) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2022.823135 · Cited by 28

Identification and Verification of m7G Modification Patterns and Characterization of Tumor Microenvironment Infiltration via Multi-Omics Analysis in Clear Cell Renal Cell Carcinoma

Dong, K., Gu, D., Shi, J., Bao, Y., Fu, Z., Fang, Y., Qu, L., Zhu, W., Jiang, A., & Wang, L. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.874792 · Cited by 29

A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis

Martin, E. T., Blatt, P., Nguyen, E., Lahr, R. M., Selvam, S., Yoon, H. A. M., Pocchiari, T., Emtenani, S., Siekhaus, D. E., Berman, A. J., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.03.005 · Cited by 26

Mitochondrial RNA methyltransferase TRMT61B is a new, potential biomarker and therapeutic target for highly aneuploid cancers

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Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution

Pellegrino, S., Dent, K. C., Spikes, T. E., & Warren, A. J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad194 · Cited by 33

Proliferation, cancer, and aging—novel functions of the nucleolar methyltransferase fibrillarin?

Shubina, M. Y., Musinova, Y. R., & Sheval, E. V. (2018) · Cell Biology International · doi:10.1002/cbin.11044 · Cited by 35

nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class ClassificationPreprint

Ueda, H. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.13.295089 · Cited by 29

N7-methylguanosine modification: from regulatory roles to therapeutic implications in cancer.

Cai, M., Yang, C., & Wang, Z. (2023) · PubMed Central · Cited by 28

A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

Rajan, K. S., Madmoni, H., Bashan, A., Taoka, M., Aryal, S., Nobe, Y., Doniger, T., Galili, B., Blumberg, A., Cohen‐Chalamish, S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43263-6 · Cited by 28

The large repertoire of 2’-O-methylation guided by C/D snoRNAs on Trypanosoma brucei rRNA

Rajan, K. S., Zhu, Y., Adler, K., Doniger, T., Cohen‐Chalamish, S., Srivastava, A., Shalev-Benami, M., Matzov, D., Unger, R., Tschudi, C., et al. (2020) · RNA Biology · doi:10.1080/15476286.2020.1750842 · Cited by 28

Non-Coding RNA-Driven Regulation of rRNA Biogenesis

Kaliatsi, E. G., Γιαρίμογλου, Ν., Stathopoulos, C., & Stamatopoulou, V. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21249738 · Cited by 28

SNORA23 inhibits HCC tumorigenesis by impairing the 2'-O-ribose methylation level of 28S rRNA

Liu, Z., Pang, Y., Jia, Y. H., Qin, Q., Wang, R., Li, W., Jie, J., Liu, H., & Liu, S. (2021) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2020.0343 · Cited by 28

Regulatory roles of RNA modifications in breast cancer

Kumari, K., Groza, P., & Aguiló, F. (2021) · NAR Cancer · doi:10.1093/narcan/zcab036 · Cited by 30

Epitranscriptomics: An Additional Regulatory Layer in Plants’ Development and Stress Response

Shoaib, Y., Usman, B., Kang, H., & Jung, K. (2022) · Plants · doi:10.3390/plants11081033 · Cited by 28

Identifying ribosome heterogeneity using ribosome profiling

Alkan, F., Wilkins, O. G., Hernández-Pérez, S., Ramalho, S., Silva, J., Ule, J., & Faller, W. J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac484 · Cited by 28

The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future

Prall, W., Ganguly, D. R., & Gregory, B. D. (2023) · The Plant Cell · doi:10.1093/plcell/koad044 · Cited by 28

Alterations of ribosomal RNA pseudouridylation in human breast cancer

Barozzi, C., Zacchini, F., Corradini, A. G., Morara, M., Serra, M., Sanctis, V. D., Bertorelli, R., Dassi, E., & Montanaro, L. (2023) · NAR Cancer · doi:10.1093/narcan/zcad026 · Cited by 31

Metabolic Regulation of the Epitranscriptome

Thomas, J. M., Batista, P. J., & Meier, J. L. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.8b00951 · Cited by 30

Decoding the ribosome's hidden language: rRNA modifications as key players in cancer dynamics and targeted therapies

Cui, L., Zheng, J., Lin, Y., Lin, P., Lu, Y., Zheng, Y., Guo, B., & Zhao, X. (2024) · Clinical and Translational Medicine · doi:10.1002/ctm2.1705 · Cited by 31

Base-pairing interactions between substrate RNA and H/ACA guide RNA modulate the kinetics of pseudouridylation, but not the affinity of substrate binding by H/ACA small nucleolar ribonucleoproteins

Kelly, E., Czekay, D. P., & Kothe, U. (2019) · RNA · doi:10.1261/rna.071043.119 · Cited by 27

Destabilization of mutated human PUS3 protein causes intellectual disability

Lin, T., Śmigiel, R. S., Kuźniewska, B., Chmielewska, J. J., Kosińska, J., Biela, M., Biela, A., Kościelniak, A., Dobosz, D., Łaczmańska, I., et al. (2022) · Human Mutation · doi:10.1002/humu.24471 · Cited by 27

Regulation of translation by methylation multiplicity of 18S rRNA

Liu, K., Santos, D. A., Hussmann, J. A., Wang, Y., Sutter, B. M., Weissman, J. S., & Tu, B. P. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108825 · Cited by 27

The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function

Finet, O., Yague‐Sanz, C., Marchand, F., & Hermand, D. (2022) · RNA Biology · doi:10.1080/15476286.2022.2078094 · Cited by 25

Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases

Strassler, S. E., Bowles, I. E., Dey, D., Jackman, J. E., & Conn, G. L. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102393 · Cited by 26

Varying strength of selection contributes to the intragenomic diversity of rRNA genes

Sultanov, D., & Hochwagen, A. (2022) · Nature Communications · doi:10.1038/s41467-022-34989-w · Cited by 27

Critical roles and clinical perspectives of RNA methylation in cancer

Li, G., Yao, Q., Liu, P., Zhang, H., Liu, Y., Li, S., Shi, Y., Li, Z., & Zhu, W. (2024) · MedComm · doi:10.1002/mco2.559 · Cited by 29

Unique Aspects of rRNA Biogenesis in Trypanosomatids

Rajan, K. S., Chikne, V., Decker, K., Ben‐Asher, H. W., & Michaeli, S. (2019) · Trends in Parasitology · doi:10.1016/j.pt.2019.07.012 · Cited by 27

Methyltransferase ATMETTL5 writes m6A on 18S ribosomal RNA to regulate translation in Arabidopsis

Song, P., Tian, E., Cai, Z., Chen, X., Chen, S., Yu, K., Bian, H., He, K., & Jia, G. (2024) · New Phytologist · doi:10.1111/nph.20034 · Cited by 25

BMAL1 Associates with NOP58 in the Nucleolus and Contributes to Pre-rRNA Processing

Cervantes, M., Forné, I., Ranjit, S., Gratton, E., Imhof, A., & Sassone‐Corsi, P. (2020) · iScience · doi:10.1016/j.isci.2020.101151 · Cited by 25

NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis

Abel, Y., Paiva, A. C. F., Bizarro, J., Chagot, M.-E., Santo, P. E., Robert, M.-C., Quinternet, M., Vandermoere, F., Sousa, P. M. F., Fort, P., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1226 · Cited by 26

Upon heat stress processing of ribosomal RNA precursors into mature rRNAs is compromised after cleavage at primary P site in Arabidopsis thalian a

Darrière, T., Jobet, E., Zavala, D., Escande, M., Durut, N., de Bures, A., Blanco‐Herrera, F., Vidal, E. A., Rompais, M., Carapito, C., et al. (2022) · RNA Biology · doi:10.1080/15476286.2022.2071517 · Cited by 25

Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A Perspective

Dias-Fields, L., & Adamala, K. P. (2022) · Plants · doi:10.3390/plants11162097 · Cited by 29

18S rRNA methyltransferases DIMT1 and BUD23 drive intergenerational hormesis

Liberman, N., Rothi, M. H., Gerashchenko, M. V., Zorbas, C., Boulias, K., MacWhinnie, F. G., Ying, K., Taylor, A. F., Haddad, J. A., Shibuya, H., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.08.014 · Cited by 25

METTL3 as a master regulator of translation in cancer: mechanisms and implications

Esteva-Socias, M., & Aguiló, F. (2024) · NAR Cancer · doi:10.1093/narcan/zcae009 · Cited by 25

Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation

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Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs

Baldini, L., Charpentier, B., & Labialle, S. (2021) · Non-Coding RNA · doi:10.3390/ncrna7020030 · Cited by 28

The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

Streit, D., & Schleiff, E. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.684626 · Cited by 22

The epitranscriptome in ageing and stress resistance: A systematic review

Wagner, A., & Schosserer, M. (2022) · Ageing Research Reviews · doi:10.1016/j.arr.2022.101700 · Cited by 26

An integrated model of acinar to ductal metaplasia-related N7-methyladenosine regulators predicts prognosis and immunotherapy in pancreatic carcinoma based on digital spatial profiling

Yang, H., Messina‐Pacheco, J., Corredor, A. L. G., Gregorieff, A., Liu, J., Nehme, A., Najafabadi, H. S., Riazalhosseini, Y., Gao, B., & Gao, Z. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.961457 · Cited by 23

Mapping targets for small nucleolar RNAs in yeast

Dudnakova, T., Dunn-Davies, H., Peters, R., & Tollervey, D. W. (2018) · Wellcome Open Research · doi:10.12688/wellcomeopenres.14735.2 · Cited by 24

NEP-TC a rRNA Methyltransferase Involved on Somatic Embryogenesis of Tamarillo (Solanum betaceum Cav.)

Correia, S. I., Alhinho, A. T., Casimiro, B., Miguel, C. M. G., Oliveira, M. M., Verı́ssimo, P., & Canhoto, J. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00438 · Cited by 23

The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region

Choudhury, P., Kretschmer, J., Hackert, P., Bohnsack, K. E., & Bohnsack, M. T. (2020) · RNA Biology · doi:10.1080/15476286.2020.1829366 · Cited by 23

Non-coding RNAs: ever-expanding diversity of types and functions

Lakhotia, S. C., Mallick, B., & Roy, J. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-817193-6.00002-9 · Cited by 25

Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity

Birikmen, M., Bohnsack, K. E., Tran, V., Somayaji, S., Bohnsack, M. T., & Ebersberger, I. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.739000 · Cited by 23

Compound heterozygous variants in SHQ1 are associated with a spectrum of neurological features, including early-onset dystonia

Sleiman, S., Marshall, A. E., Dong, X., Mhanni, A. A., Alidou-D’Anjou, I., Frosk, P., Marin, S. E., Stark, Z., Bigio, M. R. D., McBride, A., et al. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab247 · Cited by 24

Nuclear dynamics: Formation of bodies and trafficking in plant nuclei

Díaz, E. M., & Sáez‐Vasquez, J. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.984163 · Cited by 22

Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2

Vries, I. S. N., Zorbas, C., Lemsara, A., Piechotta, M., Ernst, F. G. M., Wacheul, L., Lafontaine, D. L. J., & Dieterich, C. (2023) · RNA Biology · doi:10.1080/15476286.2023.2248752 · Cited by 23

Utp14 interaction with the small subunit processome

Black, J. J., Wang, Z., Goering, L. M., & Johnson, A. M. (2018) · RNA · doi:10.1261/rna.066373.118 · Cited by 23

Chemical Modifications of Ribosomal RNA

Sharma, S., & Entian, K. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2501-9_9 · Cited by 24

Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

Rojas, J., Hose, J., Dutcher, H. A., Place, M., Wolters, J. F., Hittinger, C. T., & Gasch, A. P. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100656 · Cited by 22

Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae

Black, J. J., Sardana, R., Elmir, E., & Johnson, A. M. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1009215 · Cited by 22

Mapping N6‐Methyladenosine (m6A) in RNA: Established Methods, Remaining Challenges, and Emerging Approaches

Hartstock, K., & Rentmeister, A. (2018) · Chemistry - A European Journal · doi:10.1002/chem.201804043 · Cited by 22

Interactions and activities of factors involved in the late stages of human 18S rRNA maturation

Sloan, K. E., Knox, A. A., Wells, G. R., Schneider, C., & Watkins, N. J. (2019) · RNA Biology · doi:10.1080/15476286.2018.1564467 · Cited by 22

Genetic Variation and Potential for Resistance Development to the tTA Overexpression Lethal System in Insects

Knudsen, K. E., Reid, W. R., Barbour, T. M., Bowes, L. M., Duncan, J., Philpott, E., Potter, S., & Scott, M. J. (2020) · G3 Genes Genomes Genetics · doi:10.1534/g3.120.400990 · Cited by 22

Structural and catalytic roles of the human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation

Shen, H., Stoute, J., & Liu, K. F. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.014236 · Cited by 22

The ribosome epitranscriptome: inert—or a platform for functional plasticity?

Georgeson, J. M., & Schwartz, S. (2021) · RNA · doi:10.1261/rna.078859.121 · Cited by 21

Systematic mapping of rRNA 2’-O methylation during frog development and involvement of the methyltransferase Fibrillarin in eye and craniofacial development in Xenopus laevis

Delhermite, J., Tafforeau, L., Sharma, S., Marchand, V., Wacheul, L., Lattuca, R., Desiderio, S., Motorin, Y., Bellefroid, E., & Lafontaine, D. L. J. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010012 · Cited by 21

Regulation of Nucleolar Activity by MYC

Brown, I. N., Lafita‐Navarro, M. C., & Conacci‐Sorrell, M. (2022) · Cells · doi:10.3390/cells11030574 · Cited by 23

Specialised ribosomes as versatile regulators of gene expression

Joo, M., Yeom, J., Choi, Y., Jun, H., Song, W., Kim, H.-L., Lee, K., & Shin, E. (2022) · RNA Biology · doi:10.1080/15476286.2022.2135299 · Cited by 25

Ribosomal RNA-based epitranscriptomic regulation of chondrocyte translation and proteome in osteoarthritis

Chabronova, A., van den Akker, G., Housmans, B., Caron, M. M. J., Cremers, A., Surtel, D. A., Wichapong, K., Peffers, M. J., van Rhijn, L. W., Marchand, V., et al. (2023) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2022.12.010 · Cited by 22

RNA methylation and cellular response to oxidative stress-promoting anticancer agents

Ponzetti, M., Rucci, N., & Falone, S. (2023) · Cell Cycle · doi:10.1080/15384101.2023.2165632 · Cited by 22

The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited

Streit, D., Shanmugam, T., Garbelyanski, A., Simm, S., & Schleiff, E. (2020) · Plants · doi:10.3390/plants9081016 · Cited by 19

Life and Death of Ribosomes in Archaea

Ferreira-Cerca, S. (2017) · Nucleic acids and molecular biology · doi:10.1007/978-3-319-65795-0_6 · Cited by 22

Translational error in mice increases with ageing in an organ-dependent manner

Böttger, E. C., Kumar, H. S., Steiner, A. C., Sotirakis, E., Thiam, K., Isnard, P., Seebeck, P., Wolfer, D. P., Shcherbakov, D., & Akbergenov, R. (2025) · Nature Communications · doi:10.1038/s41467-025-57203-z · Cited by 23

A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life

Jüttner, M., & Ferreira-Cerca, S. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2501-9_1 · Cited by 19

Identification and verification of m7G-Related genes as biomarkers for prognosis of sarcoma

Qin, H., Sheng, W., Weng, J., Li, G., Chen, Y., Zhu, Y., Wang, Q., Chen, Y., Yang, Q., Yu, F., et al. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1101683 · Cited by 21

Novel sights on therapeutic, prognostic, and diagnostics aspects of non-coding RNAs in glioblastoma multiforme

Ramaiah, M. J., Adusumilli, K., Chamarthy, S., & Angirekula, H. S. R. (2023) · Metabolic Brain Disease · doi:10.1007/s11011-023-01234-2 · Cited by 23

Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives

Imbriano, C., Moresi, V., Belluti, S., Renzini, A., Cavioli, G., Maretti, E., & Molinari, S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242015161 · Cited by 20

Functional Interplay between Small Non-Coding RNAs and RNA Modification in the Brain

Leighton, L. J., & Bredy, T. W. (2018) · Non-Coding RNA · doi:10.3390/ncrna4020015 · Cited by 20

Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome

Pellegrino, S., Meyer, M., Könst, Z. A., Holm, M., Voora, V. K., Kashinskaya, D., Zanette, C., Mobley, D. L., Yusupova, G. Z., Vanderwal, C. D., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz053 · Cited by 20

Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics

Sabi, R., & Tuller, T. (2019) · npj Systems Biology and Applications · doi:10.1038/s41540-019-0089-0 · Cited by 19

N4‐methylcytidine ribosomal RNA methylation in chloroplasts is crucial for chloroplast function, development, and abscisic acid response in Arabidopsis

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O-Glycosylated RNA Identification and Prediction by Solid-Phase Chemoenzymatic TnORNA Method and PONglyRNA Tool

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