Ribosomal RNA-based epitranscriptomic regulation of chondrocyte translation and proteome in osteoarthritis
Tài liệu tham khảo
Trachana, 2019, Understanding the role of chondrocytes in osteoarthritis: utilizing proteomics, Expert Rev Proteom, 16, 201, 10.1080/14789450.2019.1571918
Gay, 2022, Translational control through ribosome heterogeneity and functional specialization, Trends Biochem Sci, 47, 66, 10.1016/j.tibs.2021.07.001
Khatter, 2015, Structure of the human 80S ribosome, Nature, 520, 640, 10.1038/nature14427
Steitz, 2003, RNA, the first macromolecular catalyst: the ribosome is a ribozyme, Trends Biochem Sci, 28, 411, 10.1016/S0968-0004(03)00169-5
Sloan, 2017, Tuning the ribosome: the influence of rRNA modification on eukaryotic ribosome biogenesis and function, RNA Biol, 14, 1138, 10.1080/15476286.2016.1259781
Taoka, 2018, Landscape of the complete RNA chemical modifications in the human 80S ribosome, Nucleic Acids Res, 46, 9289, 10.1093/nar/gky811
Motorin, 2021, Constitutive and variable 2'-O-methylation (Nm) in human ribosomal RNA, RNA Biol, 1
Kiss-Laszlo, 1996, Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs, Cell, 85, 1077, 10.1016/S0092-8674(00)81308-2
Jaafar, 2021, 2'O-Ribose methylation of ribosomal RNAs: natural diversity in living organisms, biological processes, and diseases, Cells, 10, 10.3390/cells10081948
Jansson, 2021, Regulation of translation by site-specific ribosomal RNA methylation, Nat Struct Mol Biol, 28, 889, 10.1038/s41594-021-00669-4
van den Akker, 2021, Current practice in bicistronic IRES reporter use: a systematic review, Int J Mol Sci, 22
Ayadi, 2018, Quantification of 2'-O-Me residues in RNA using next-generation sequencing (Illumina RiboMethSeq protocol), Methods Mol Biol, 1649, 29, 10.1007/978-1-4939-7213-5_2
Marchand, 2016, Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA, Nucleic Acids Res, 44, e135, 10.1093/nar/gkw547
Berman, 2000, The protein data bank, Nucleic Acids Res, 28, 235, 10.1093/nar/28.1.235
Natchiar, 2017, Visualization of chemical modifications in the human 80S ribosome structure, Nature, 551, 472, 10.1038/nature24482
Sanjana, 2014, Improved vectors and genome-wide libraries for CRISPR screening, Nat Methods, 11, 783, 10.1038/nmeth.3047
Pauli, 2020, Site-specific methylation of 18S ribosomal RNA by SNORD42A is required for acute myeloid leukemia cell proliferation, Blood, 135, 2059, 10.1182/blood.2019004121
Di Ceglie, 2017, Genetic modification of ER-Hoxb8 osteoclast precursors using CRISPR/Cas9 as a novel way to allow studies on osteoclast biology, J Leukoc Biol, 101, 957, 10.1189/jlb.1AB0416-180RR
Shalem, 2014, Genome-scale CRISPR-Cas9 knockout screening in human cells, Science, 343, 84, 10.1126/science.1247005
Ripmeester, 2020, Impaired chondrocyte U3 snoRNA expression in osteoarthritis impacts the chondrocyte protein translation apparatus, Sci Rep, 10, 10.1038/s41598-020-70453-9
Anderson, 2019, The synovial fluid proteome differentiates between septic and nonseptic articular pathologies, J Proteom, 202, 10.1016/j.jprot.2019.04.020
Peffers, 2014, Proteomic analysis reveals age-related changes in tendon matrix composition, with age- and injury-specific matrix fragmentation, J Biol Chem, 289, 25867, 10.1074/jbc.M114.566554
Peffers, 2013, Transcriptomic signatures in cartilage ageing, Arthritis Res Ther, 15, R98, 10.1186/ar4278
Panda, 2017, Polysome fractionation to analyze mRNA distribution profiles, Bio Protoc, 7, 10.21769/BioProtoc.2126
Housmans, 2022, Synovial fluid from end-stage osteoarthritis induces proliferation and fibrosis of articular chondrocytes via MAPK and RhoGTPase signaling, Osteoarthr Cartil, 30, 862, 10.1016/j.joca.2021.12.015
Nazar, 1983, Effect of 2'-O-methylation on the structure of mammalian 5.8S rRNAs and the 5.8S-28S rRNA junction, Nucleic Acids Res, 11, 5989, 10.1093/nar/11.17.5989
Marcel, 2020, Ribosomal RNA 2'O-methylation as a novel layer of inter-tumour heterogeneity in breast cancer, NAR Cancer, 2, zcaa036, 10.1093/narcan/zcaa036
Munholland, 1987, Methylation of ribosomal RNA as a possible factor in cell differentiation, Cancer Res, 47, 169
Nazar, 1975, Tissue specific differences in the 2'-O-methylation of eukaryotic 5.8S ribosomal RNA, FEBS Lett, 59, 83, 10.1016/0014-5793(75)80346-2
Huttenhofer, 2001, RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse, EMBO J, 20, 2943, 10.1093/emboj/20.11.2943
Dmitriev, 2020, A quick guide to small-molecule inhibitors of eukaryotic protein synthesis, Biochemistry, 85, 1389
Lestrade, 2006, snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs, Nucleic Acids Res, 34, D158, 10.1093/nar/gkj002
Helser, 1981, Characterization of a 40S ribosomal subunit complex in polyribosomes of Saccharomyces cerevisiae treated with cycloheximide, Mol Cell Biol, 1, 51
Wong, 2014, Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, Elife, 3
Mazumder, 1975, Sites of action of fusidic acid in eukaryotes. Inhibition by fusidic acid of a ribosome-independent GTPase from Artemia salina embryos, Eur J Biochem, 58, 549, 10.1111/j.1432-1033.1975.tb02404.x
Tafforeau, 2013, The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of Pre-rRNA processing factors, Mol Cell, 51, 539, 10.1016/j.molcel.2013.08.011
Weingarten-Gabbay, 2016, Comparative genetics. Systematic discovery of cap-independent translation sequences in human and viral genomes, Science, 351
Godet, 2019, IRES trans-acting factors, key actors of the stress response, Int J Mol Sci, 20, 10.3390/ijms20040924
van den Akker, 2022, Ribosome dysfunction in osteoarthritis, Curr Opin Rheumatol, 34, 61, 10.1097/BOR.0000000000000858
Jaafar, 2016, Translation initiation by the hepatitis C virus IRES requires eIF1A and ribosomal complex remodeling, Elife, 5
Penzo, 2018, Turning uridines around: role of rRNA pseudouridylation in ribosome biogenesis and ribosomal function, Biomolecules, 8, 10.3390/biom8020038
Yusupov, 2001, Crystal structure of the ribosome at 5.5 A resolution, Science, 292, 883, 10.1126/science.1060089
Abou Elela, 1994, Inhibition of protein synthesis by an efficiently expressed mutation in the yeast 5.8S ribosomal RNA, Nucleic Acids Res, 22, 686, 10.1093/nar/22.4.686
Abou Elela, 1997, Role of the 5.8S rRNA in ribosome translocation, Nucleic Acids Res, 25, 1788, 10.1093/nar/25.9.1788
Walker, 1990, Inhibition of protein synthesis by anti-5.8 S rRNA oligodeoxyribonucleotides, J Biol Chem, 265, 2428, 10.1016/S0021-9258(19)39815-1
Talkish, 2014, Ribosome assembly factors Pwp1 and Nop12 are important for folding of 5.8S rRNA during ribosome biogenesis in Saccharomyces cerevisiae, Mol Cell Biol, 34, 1863, 10.1128/MCB.01322-13
Ji, 2019, Single-cell RNA-seq analysis reveals the progression of human osteoarthritis, Ann Rheum Dis, 78, 100, 10.1136/annrheumdis-2017-212863
Rim, 2020, The role of fibrosis in osteoarthritis progression, Life, 11, 10.3390/life11010003
Caron, 2021, Discovery of bone morphogenetic protein 7-derived peptide sequences that attenuate the human osteoarthritic chondrocyte phenotype, Mol Ther Methods Clin Dev, 21, 247, 10.1016/j.omtm.2021.03.009
Housmans, 2023, Direct comparison of non-osteoarthritic and osteoarthritic synovial fluid-induced intracellular chondrocyte signaling and phenotype changes, Osteoarthr Cartil, 31, 60, 10.1016/j.joca.2022.09.004
Bailey, 2022, Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling, Elife, 11
Deryusheva, 2021, SnoRNA guide activities: real and ambiguous, RNA, 27, 1363, 10.1261/rna.078916.121
Nwagwu, 1980, Ribonucleic acid synthesis in embryonic chick muscle, rates of synthesis and half-lives of transfer and ribosomal RNA species, J Embryol Exp Morphol, 56, 253
Yang, 2003, Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes, Genome Res, 13, 1863, 10.1101/gr.1272403