1. Han C, Sun L-Y, Luo X-Q et al. Chromatin-associated orphan snoRNA regulates DNA damage-mediated differentiation via a non-canonical complex. Cell Rep 2022;38:110421. https://doi.org/10.1016/j.celrep.2022.110421 2. Watkins NJ, Bohnsack MT. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA: Box C/D and H/ACA snoRNPs. Wiley Interdiscip Rev RNA 2012;3:397-414. https://doi.org/10.1002/wrna.117 3. Khosraviani N, Ostrowski LA, Mekhail K. Roles for non-coding RNAs in spatial genome organization. Front Cell Dev Biol 2019;7:336. https://doi.org/10.3389/fcell.2019.00336 

ˇ ˇ 4. Bratkovic T, Božic J, Rogelj B. Functional diversity of small nucleolar RNAs. Nucleic Acids Res 2020;48:1627-51. https://doi.org/10.1093/nar/gkz1140 5. Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023;20:715-36. https://doi.org/10.1080/15476286.2023.2254540 6. Garus A, Autexier C. Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance. RNA 2021;27:1441-58. https://doi.org/10.1261/rna.078953.121 7. Shubina MY, Musinova YR, Sheval EV. Proliferation, cancer, and aging—novel functions of the nucleolar methyltransferase fibrillarin? Cell Biol Int 2018;42:1463-6. https://doi.org/10.1002/cbin.11044 8. Kiss DJ, Oláh J, Tóth G et al. The structure-derived mechanism of Box H/ACA pseudouridine synthase offers a plausible paradigm for programmable RNA editing. ACS Catal 2022;12:2756-69. https://doi.org/10.1021/acscatal.1c04870 9. Gumienny R, Jedlinski DJ, Schmidt A et al. High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Res 2017;45:2756-69. 

10. Vitali P, Kiss T. Cooperative 2 -O-methylation of the wobble cytidine of human elongator tRNA Met (CAT) by a nucleolar

Downloaded from https://academic.oup.com/nargab/article/7/1/lqaf013/8052394 by guest on 20 September 2025 https://doi.org/10.1038/nrm4040

15. McMahon M, Contreras A, Ruggero D. Small RNAs with big implications: new insights into H/ACA snoRNA function and their role in human disease. Wiley Interdiscip Rev RNA 2015;6:173-89. https://doi.org/10.1002/wrna.1266

16. Kiss T, Fayet-Lebaron E, Jády BE. Box H/ACA small ribonucleoproteins. Mol Cell 2010;37:597-606. https://doi.org/10.1016/j.molcel.2010.01.032

17. Savage SA, Alter BP. Dyskeratosis Congenita. Hematol Oncol Clin North Am 2009;23:215-31. https://doi.org/10.1016/j.hoc.2009.01.003

18. Ruggero D, Grisendi S, Piazza F et al. Dyskeratosis congenita and

cancer in mice deficient in ribosomal RNA modification. Science 2003;299:259-62. https://doi.org/10.1126/science.1079447

19. Armistead J, Khatkar S, Meyer B et al. Mutation of a gene essential for ribosome biogenesis, EMG1, causes Bowen-Conradi syndrome. Am Hum Genet 2009;84:728-39. https://doi.org/10.1016/j.ajhg.2009.04.017

20. Balogh E, Chandler JC, Varga M et al. Pseudouridylation defect

due to DKC1 and NOP10 mutations causes nephrotic syndrome

with cataracts, hearing impairment, and enterocolitis. Proc Natl Acad Sci USA 2020;117:15137-47. https://doi.org/10.1073/pnas.2002328117

21. McMahon M, Contreras A, Holm M et al. A single H/ACA small

nucleolar RNA mediates tumor suppression downstream of oncogenic RAS. eLife 2019;8:e48847. https://doi.org/10.7554/eLife.48847

22. Liang J, Wen J, Huang Z et al. Small nucleolar RNAs: insight

into their function in cancer. Front Oncol 2019;9:587. https://doi.org/10.3389/fonc.2019.00587

23. Huang H, Weng H, Deng X et al. RNA modifications in cancer:

Functions, mechanisms, and therapeutic implications. Annu Rev Cancer Biology 2019;4:25.

24. Babaian A, Rothe K, Girodat D et al. Loss of m1acp3 ribosomal RNA modification is a major feature of cancer. Cell Rep 2020;31:107611. https://doi.org/10.1016/j.celrep.2020.107611

25. Marcel V, Ghayad SE, Belin S et al. p53 acts as a safeguard of translational control by regulating fibrillarin and rRNA methylation in cancer. Cancer Cell 2013;24:318-30. https://doi.org/10.1016/j.ccr.2013.08.013

26. Zhang J, Yang G, Li Q et al. Increased fibrillarin expression is

associated with tumor progression and an unfavorable prognosis in hepatocellular carcinoma. Oncol Lett 2021;21:92. https://doi.org/10.3892/ol.2020.12353

27. Long FNV, Lardy-Cleaud A, Carène D et al. Low level of Fibrillarin, a ribosome biogenesis factor, is a new independent

marker of poor outcome in breast cancer. BMC Cancer 2022;22:526. https://doi.org/10.1186/s12885- 022- 09552- x

28. Zhu W, Niu J, He M et al. SNORD89 promotes stemness

phenotype of ovarian cancer cells by regulating Notch1-c-Myc pathway. J Transl Med 2019;17:259. https://doi.org/10.1186/s12967- 019- 2005- 1

29. Chen L, Han L, Wei J et al. SNORD76, a box C/D snoRNA, acts as a tumor suppressor in glioblastoma. Sci Rep 2015;5:8588. https://doi.org/10.1038/srep08588 

30. Huang C, Shi J, Guo Y et al. A snoRNA modulates mRNA 3 end processing and regulates the expression of a subset of mRNAs. Nucleic Acids Res 2017;45:8647-60. https://doi.org/10.1093/nar/gkx651 

31. Falaleeva M, Stamm S. Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs. Bioessays 2013;35:46-54. https://doi.org/10.1002/bies.201200117 

32. Bergeron D, Fafard-Couture É, Scott MS. Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action. Biochem Soc Trans 2020;48:645-56. https://doi.org/10.1042/BST20191046

49. Dash SN, Patnaik L. Flight for fish in drug discovery: a review of zebrafish-based screening of molecules. Biol Lett 2023;19:20220541. https://doi.org/10.1098/rsbl.2022.0541

50. White RM, Patton EE. Adult zebrafish as advanced models of

human disease. Dis Model Mech 2023;16:dmm050351. https://doi.org/10.1242/dmm.050351

51. Patton EE, Zon LI, Langenau DM. Zebrafish disease models in drug discovery: from preclinical modelling to clinical trials. Nat Rev Drug Discov 2021. 20 611-28. https://doi.org/10.1038/s41573- 021- 00210- 8

52. Higa-Nakamine S, Suzuki T, Uechi T et al. Loss of ribosomal

RNA modification causes developmental defects in zebrafish. Nucleic Acids Res 2012;40:391-8.

https://doi.org/10.1093/nar/gkr700

53. The Galaxy Community. The Galaxy platform for accessible,

33. Kufel J, Grzechnik P. Small nucleolar RNAs tell a different tale. Trends Genet 2019;35:104-17. https://doi.org/10.1016/j.tig.2018.11.005 

34. Kiss T, Fayet E, Jády BE et al. Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harb Symp Quant Biol 2006;71:407-17. https://doi.org/10.1101/sqb.2006.71.025 

35. Bergeron D, Faucher-Giguère L, Emmerichs A-K et al. Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences. Genome Biol 2023;24:160. https://doi.org/10.1186/s13059- 023- 03002- y

36. Nepal C, Hadzhiev Y, Balwierz P et al. Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nat Commun 2020;11:168. https://doi.org/10.1038/s41467- 019- 13687- 0 

37. Canzler S, Stadler PF, Schor J. The fungal snoRNAome. RNA 2018;24:342-60. https://doi.org/10.1261/rna.062778.117 

38. Jorjani H, Kehr S, Jedlinski DJ et al. An updated human snoRNAome. Nucleic Acids Res 2016;44:5068-82. https://doi.org/10.1093/nar/gkw386 

39. Fafard-Couture É, Bergeron D, Couture S et al. Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships. Genome Biol 2021;22:172. https://doi.org/10.1186/s13059- 021- 02391- 2 

40. Varga M. The Doctor of Delayed Publications: The Remarkable Life of George Streisinger (1927-1984). Zebrafish 2018;15:314-9. https://doi.org/10.1089/zeb.2017.1531 

41. Lieschke GJ, Currie PD. Animal models of human disease: zebrafish swim into view. Nat Rev Genet 2007;8:353-67. https://doi.org/10.1038/nrg2091 

42. Kemmler CL, Moran HR, Murray BF et al. Next-generation plasmids for transgenesis in zebrafish and beyond. Development 2023;150:dev201531. https://doi.org/10.1242/dev.201531 

43. Kwan KM, Fujimoto E, Grabher C et al. The Tol2kit: a multisite gateway-based construction kit for Tol2 transposon transgenesis constructs. Dev Dyn 2007;236:3088-99. https://doi.org/10.1002/dvdy.21343 

44. Kawakami K. Tol2: a versatile gene transfer vector in vertebrates. Genome Biol 2007;Suppl 1:S7. https://doi.org/10.1186/gb2007- 8- s1- s7 

45. Uribe-Salazar JM, Kaya G, Sekar A et al. Evaluation of CRISPR gene-editing tools in zebrafish. BMC Genomics 2022;23:12. https://doi.org/10.1186/s12864- 021- 08238- 1 

46. Liu K, Petree C, Requena T et al. Expanding the CRISPR Toolbox in Zebrafish for Studying Development and Disease. Front Cell Dev Biol 2019;7:13. https://doi.org/10.3389/fcell.2019.00013

47. Varshney GK, Pei W, LaFave MC et al. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res 2015;25:1030-42. https://doi.org/10.1101/gr.186379.114 

48. Huang H, Lindgren A, Wu X et al. High-throughput screening for bioactive molecules using primary cell culture of transgenic zebrafish embryos. Cell Rep 2012;2:695-704. https://doi.org/10.1016/j.celrep.2012.08.015

Downloaded from https://academic.oup.com/nargab/article/7/1/lqaf013/8052394 by guest on 20 September 2025 reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Res 2024;52:W83-94. https://doi.org/10.1093/nar/gkae410

54. Zhang B, Han D, Korostelev Y et al. Changes in snoRNA and snRNA Abundance in the human, chimpanzee, macaque, and mouse brain. Genome Biol Evol 2016;8:840-50.

55. Locati MD, Pagano JFB, Abdullah F et al. Identifying small

RNAs derived from maternaland somatic-type rRNAs in

zebrafish development. Genome 2018;61:371-8.

https://doi.org/10.1139/gen2017- 0202

56. Qu G, Kruszka K, Plewka P et al. Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. BMC Genomics

2015;16:1009. https://doi.org/10.1186/s12864- 015- 2221- x

57. Bhatia PS, Iovleff S, Govaert G. Blockcluster: an R package for model-based co-clustering. J Stat Soft 2017;76:1-24. https://doi.org/10.18637/jss.v076.i09

58. Liu P, Si Y. Cluster analysis of RNA-sequencing data. In: Statistical analysis of next generation sequencing data. New York: Springer, 2014, 191-217.

https://doi.org/10.1007/978- 3- 319- 07212- 8_10

59. Videm P, Rose D, Costa F et al. BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. Bioinformatics 2014;30:i274-82.

https://doi.org/10.1093/bioinformatics/btu270

60. Lawrence M, Huber W, Pagès H et al. Software for computing and annotating genomic ranges. PLoS Comput Biol 2013;9:e1003118. https://doi.org/10.1371/journal.pcbi.1003118

61. Lawrence M, Gentleman R, Carey V. rtracklayer: an R package for interfacing with genome browsers. Bioinformatics 2009;25:1841-2. https://doi.org/10.1093/bioinformatics/btp328 62. Wickham H, Averick M, Bryan J et al. Welcome to the Tidyverse. J Open Source Softw 2019;4:1686.

https://doi.org/10.21105/joss.01686 63. Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 2017;33:2938-40. https://doi.org/10.1093/bioinformatics/btx364

64. Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag, 2016. https://ggplot2.tidyverse.org 65. Kolde R. pheatmap: Pretty Heatmaps. R package version 1.0.12. 2018. https://github.com/raivokolde/pheatmap

66. RStudio_Team. RStudio: Integrated Development for R RStudio.

Boston, MA, USA: PBC, 2020. 67. Hamar R, Varga M. Curated RNA Sequencing Data for

Zebrafish (Danio rerio) snoRNA Expression Analysis [Data set]. Zenodo 2024. https://doi.org/10.5281/zenodo.12822217

68. Chang W, Cheng J, Allaire J et al. Shiny: web application framework for R. R package version 1.10.0.9000. 2025. https://github.com/rstudio/shiny

69. Sievert C. Interactive web-based data visualization with R, plotly, and shiny. Chapman and Hall/CRC. 2020. https://doi.org/10.1201/9780429447273-38

70. Cui X, Lu Z, Wang S et al. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. Bioinformatics 2016;32:i332-40. https://doi.org/10.1093/bioinformatics/btw271 

71. Oliveira JV, de A, Costa F et al. SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. BMC Bioinf 2016;17:464. https://doi.org/10.1186/s12859- 016- 1345- 6 

72. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005;33:W686-9. https://doi.org/10.1093/nar/gki366 

73. Pundhir S, Poirazi P, Gorodkin J. Emerging applications of read profiles towards the functional annotation of the genome. Front

89. He J, Navarrete S, Jasinski M et al. Targeted disruption of Dkc1, the gene mutated in X-linked dyskeratosis congenita, causes

embryonic lethality in mice. Oncogene 2002;21:7740-4.

https://doi.org/10.1038/sj.onc.1205969 90. Ge J, Rudnick DA, He J et al. Dyskerin Ablation in Mouse Liver

Inhibits rRNA Processing and Cell Division. Mol Cell Biol

2010;30:413-22. https://doi.org/10.1128/MCB.01128-09 91. Pereboom TC, Weele LJv, Bondt A et al. A zebrafish model of

dyskeratosis congenita reveals hematopoietic stem cell formation

failure resulting from ribosomal protein-mediated p53

stabilization. Blood 2011;118:5458-65.

https://doi.org/10.1182/blood2011- 04- 351460 92. Zhang Y, Morimoto K, Danilova N et al. Zebrafish models for dyskeratosis congenita reveal critical roles of p53 activation contributing to hematopoietic defects through RNA processing. Genet 2015;6:188. https://doi.org/10.3389/fgene.2015.00188

74. Locati MD, Pagano JFB, Girard G et al. Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development. RNA 2017;23:1188-99. https://doi.org/10.1261/rna.061515.117 

75. Wilson CA, Postlethwait JH. A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome. G3 (Bethesda) 2024;14:jkae050. https://doi.org/10.1093/g3journal/jkae050

76. Ojha S, Malla S, Lyons SM. snoRNPs: functions in ribosome biogenesis. Biomolecules 2020;10:783. https://doi.org/10.3390/biom10050783 

77. Penzo M, Clima R, Trerè D et al. Separated Siamese twins: intronic small nucleolar RNAs and matched host genes may be altered in conjunction or separately in multiple cancer types. Cells 2020;9:387. https://doi.org/10.3390/cells9020387 

78. Xiao H, Feng X, Liu M et al. SnoRNA and lncSNHG: advances of nucleolar small RNA host gene transcripts in anti-tumor immunity. Front Immunol 2023;14:1143980. https://doi.org/10.3389/fimmu.2023.1143980 

79. Deogharia M, Majumder M. Guide snoRNAs: drivers or passengers in human disease? Biology 2018;8:1. https://doi.org/10.3390/biology8010001 

80. Huang Z, Du Y, Wen J et al. snoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology. Cell Death Discov 2022;8:259. https://doi.org/10.1038/s41420- 022- 01056- 8 

81. Weinstein LB, Steitz JA. Guided tours: from precursor snoRNA to functional snoRNP. Curr Opin Cell Biol 1999;11:378-84. https://doi.org/10.1016/S0955- 0674(99)80053- 2 

82. Kiss T. SnoRNP biogenesis meets pre-mRNA splicing. Mol Cell 2006;23:775-6. https://doi.org/10.1016/j.molcel.2006.08.023

83. Liang X, Liu Q, Fournier MJ. Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing. RNA 2009;15:1716-28. https://doi.org/10.1261/rna.1724409 

84. Jack K, Bellodi C, Landry DM et al. rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. Mol Cell 2011;44:660-6. https://doi.org/10.1016/j.molcel.2011.09.017 

85. Sloan KE, Warda AS, Sharma S et al. Tuning the ribosome: the influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol 2017;14:1138-52. https://doi.org/10.1080/15476286.2016.1259781 

86. Zhao Y, Rai J, Yu H et al. CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations. Structure 2022;30:983-92. https://doi.org/10.1016/j.str.2022.04.002

87. Dörner K, Ruggeri C, Zemp I et al. Ribosome biogenesis factors—from names to functions. EMBO J 2023;42:e112699. https://doi.org/10.15252/embj.2022112699 

88. Zhao Y, Rai J, Li H. Regulation of translation by ribosomal RNA pseudouridylation. Sci Adv 2023;9:eadg8190. https://doi.org/10.1126/sciadv.adg8190 

Downloaded from https://academic.oup.com/nargab/article/7/1/lqaf013/8052394 by guest on 20 September 2025 PLoS One 2012;7:e30188.

https://doi.org/10.1371/journal.pone.0030188

93. Anchelin M, Alcaraz-Pérez F, Martínez CM et al. Premature aging in telomerase-deficient zebrafish. Dis Model Mech 2013;6:1101-12.

94. Bellodi C, McMahon M, Contreras A et al. H/ACA small RNA dysfunctions in disease reveal key roles for noncoding RNA modifications in hematopoietic stem cell differentiation. Cell Rep 2013;3:1493-502. https://doi.org/10.1016/j.celrep.2013.04.030

95. Delhermite J, Tafforeau L, Sharma S et al. Systematic mapping of rRNA 2'-O methylation during frog development and involvement of the methyltransferase Fibrillarin in eye and craniofacial development in Xenopus laevis. PLoS Genet

2022;18:e1010012. https://doi.org/10.1371/journal.pgen.1010012

96. Breznak SM, Peng Y, Deng L et al. H/ACA snRNP-dependent ribosome biogenesis regulates translation of polyglutamine proteins. Sci Adv 2023;9:eade5492. https://doi.org/10.1126/sciadv.ade5492

97. Ni C, Buszczak M. Ribosome biogenesis and function in development and disease. Development 2023;150:dev201187. https://doi.org/10.1242/dev.201187

98. Bellodi C, Krasnykh O, Haynes N et al. Loss of function of the tumor suppressor DKC1 perturbs p27 translation control and contributes to pituitary tumorigenesis. Cancer Res 2010;70:6026-35.

https://doi.org/10.1158/0008- 5472.CAN09- 4730

99. Bohnsack KE, Bohnsack MT. Uncovering the assembly pathway of human ribosomes and its emerging links to disease. EMBO J 2019;38:e100278. https://doi.org/10.15252/embj.2018100278

100. Kampen KR, Sulima SO, Vereecke S et al. Hallmarks of

ribosomopathies. Nucleic Acids Res 2020;48:1013-28.

https://doi.org/10.1093/nar/gkz637

101. Kang J, Brajanovski N, Chan KT et al. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Sig Transduct Target Ther 2021;6:323. https://doi.org/10.1038/s41392- 021- 00728- 8

102. Barozzi C, Zacchini F, Corradini AG et al. Alterations of ribosomal RNA pseudouridylation in human breast cancer. NAR

Cancer 2023;5:zcad026. https://doi.org/10.1093/narcan/zcad026

103. Dong X-Y, Rodriguez C, Guo P et al. SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. Hum Mol Genet 2008;17:1031-42. https://doi.org/10.1093/hmg/ddm375

104. Zhou F, Liu Y, Rohde C et al. AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia. Nat Cell Biol 2017;19:844-55. https://doi.org/10.1038/ncb3563

105. Zhang X, Wang C, Xia S et al. The emerging role of snoRNAs in human disease. Genes Dis 2023;10:2064-81. https://doi.org/10.1016/j.gendis.2022.11.018

106. Cheng Y, Wang S, Zhang H et al. A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence. Cell 2024. 187:4770-89. https://doi.org/10.1016/j.cell.2024.06.019

107. Carlile TM, Rojas-Duran MF, Zinshteyn B et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 2014;515:143-6. https://doi.org/10.1038/nature13802 

108. Schwartz S, Bernstein DA, Mumbach MR et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 2014;159:148-62. https://doi.org/10.1016/j.cell.2014.08.028

109. Li X, Zhu P, Ma S et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat Chem Biol 2015;11:592-7. https://doi.org/10.1038/nchembio.1836

110. Martinez NM, Su A, Burns MC et al. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. Mol Cell 2022;82:645-59. https://doi.org/10.1016/j.molcel.2021.12.023 

118. Chikne V, Doniger T, Rajan KS et al. A pseudouridylation switch

in rRNA is implicated in ribosome function during the life cycle

of Trypanosoma brucei. Sci Rep 2016;6:25296.

https://doi.org/10.1038/srep25296 119. Hebras J, Krogh N, Marty V et al. Developmental changes of

rRNA ribose methylations in the mouse. RNA Biol 2020;17:150-64. https://doi.org/10.1080/15476286.2019.1670598

120. Marchand V, Pichot F, Neybecker P et al. HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA. Nucleic Acids Res 2020;48:e110. https://doi.org/10.1093/nar/gkaa769 121. Rajan KS, Madmoni H, Bashan A et al. A single pseudouridine

on rRNA regulates ribosome structure and function in the

mammalian parasite Trypanosoma brucei. Nat Commun

111. Nir R, Hoernes TP, Muramatsu H et al. A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA. Nucleic Acids Res 2022;50:4900-16. https://doi.org/10.1093/nar/gkac347 

112. Rodell R, Robalin N, Martinez NM. Why U matters: detection and functions of pseudouridine modifications in mRNAs. Trends Biochem Sci 2024;49:12-27. https://doi.org/10.1016/j.tibs.2023.10.008 

113. Zhang M, Jiang Z, Ma Y et al. Quantitative profiling of pseudouridylation landscape in the human transcriptome. Nat Chem Biol 2023;19:1185-95. https://doi.org/10.1038/s41589- 023- 01304- 7 

114. Sun H, Li K, Liu C et al. Regulation and functions of non-m6A mRNA modifications. Nat Rev Mol Cell Biol 2023;24:714-31. https://doi.org/10.1038/s41580- 023- 00622- x 

115. Hamar R, Varga M. The role of post-transcriptional modifications during development. Biol Futur 2023;74:45-59. https://doi.org/10.1007/s42977- 022- 00142- 3 

116. Dai Q, Zhang L-S, Sun H-L et al. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nat Biotechnol 2023;41:344-54. https://doi.org/10.1038/s41587- 022- 01505- w 

117. Pederiva C, Trevisan DM, Peirasmaki D et al. Control of protein synthesis through mRNA pseudouridylation by dyskerin. Sci Adv 2023;9:344-54. https://doi.org/10.1126/sciadv.adg1805

Downloaded from https://academic.oup.com/nargab/article/7/1/lqaf013/8052394 by guest on 20 September 2025

2023;14:7462. https://doi.org/10.1038/s41467- 023- 43263- 6

122. Xue S, Barna M. Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat Rev Mol Cell Biol 2012;13:355-69. https://doi.org/10.1038/nrm3359

123. Shi Z, Barna M. Translating the genome in time and space:

specialized ribosomes, RNA regulons, and RNA-binding proteins. Annu Rev Cell Dev Biol 2014;31:31-54.

124. Badrock AP, Uggenti C, Wacheul L et al. Analysis of U8 snoRNA variants in zebrafish reveals how bi-allelic variants cause

leukoencephalopathy with calcifications and cysts. Am Hum Genet 2020;106:694-706. https://doi.org/10.1016/j.ajhg.2020.04.003

125. Pagano JFB, Locati MD, Ensink WA et al. Maternaland somatic-type snoRNA expression and processing in zebrafish development. bioRxiv, https://doi.org/10.1101/858936, 6 February 2020, preprint: not peer reviewed.

126. Csabai L, Fazekas D, Kadlecsik T et al. SignaLink3: a multi-layered resource to uncover tissue-specific signaling

networks. Nucleic Acids Res 2022;50:D701-9. https://doi.org/10.1093/nar/gkab909

127. Bradford YM, Slyke CEV, Ruzicka L et al. Zebrafish information network, the knowledgebase for Danio rerio research. Genetics

2022;220:iyac016. https://doi.org/10.1093/genetics/iyac016

Received: July 27, 2024. Revised: February 8, 2025. Editorial Decision: February 12, 2025. Accepted: February 14, 2025

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