A PRC2-independent function for EZH2 in regulating rRNA 2'-O methylation and IRES-dependent translation.
Chromosomal Proteins, Non-Histone
/ genetics
DNA Methylation
/ genetics
Enhancer of Zeste Homolog 2 Protein
/ genetics
Gene Expression Regulation, Neoplastic
Genes, rRNA
/ genetics
Humans
Internal Ribosome Entry Sites
/ genetics
Multiprotein Complexes
/ genetics
Neoplasms
/ genetics
Nuclear Proteins
/ genetics
Protein Binding
/ genetics
Protein Biosynthesis
/ genetics
Ribonucleoproteins, Small Nucleolar
/ genetics
Journal
Nature cell biology
ISSN: 1476-4679
Titre abrégé: Nat Cell Biol
Pays: England
ID NLM: 100890575
Informations de publication
Date de publication:
04 2021
04 2021
Historique:
received:
22
02
2020
accepted:
24
02
2021
pubmed:
3
4
2021
medline:
29
6
2021
entrez:
2
4
2021
Statut:
ppublish
Résumé
Dysregulated translation is a common feature of cancer. Uncovering its governing factors and underlying mechanism are important for cancer therapy. Here, we report that enhancer of zeste homologue 2 (EZH2), previously known as a transcription repressor and lysine methyltransferase, can directly interact with fibrillarin (FBL) to exert its role in translational regulation. We demonstrate that EZH2 enhances rRNA 2'-O methylation via its direct interaction with FBL. Mechanistically, EZH2 strengthens the FBL-NOP56 interaction and facilitates the assembly of box C/D small nucleolar ribonucleoprotein. Strikingly, EZH2 deficiency impairs the translation process globally and reduces internal ribosome entry site (IRES)-dependent translation initiation in cancer cells. Our findings reveal a previously unrecognized role of EZH2 in cancer-related translational regulation.
Identifiants
pubmed: 33795875
doi: 10.1038/s41556-021-00653-6
pii: 10.1038/s41556-021-00653-6
pmc: PMC8162121
mid: NIHMS1698128
doi:
Substances chimiques
Chromosomal Proteins, Non-Histone
0
Internal Ribosome Entry Sites
0
Multiprotein Complexes
0
NOP56 protein, human
0
Nuclear Proteins
0
Ribonucleoproteins, Small Nucleolar
0
fibrillarin
0
EZH2 protein, human
EC 2.1.1.43
Enhancer of Zeste Homolog 2 Protein
EC 2.1.1.43
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
341-354Subventions
Organisme : NCI NIH HHS
ID : P50 CA180995
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA196390
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM138192
Pays : United States
Organisme : NCI NIH HHS
ID : R00 CA207865
Pays : United States
Organisme : NICHD NIH HHS
ID : R01 HD095463
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA208257
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM124765
Pays : United States
Références
Pelletier, J., Thomas, G. & Volarevic, S. Ribosome biogenesis in cancer: new players and therapeutic avenues. Nat. Rev. Cancer 18, 51–63 (2018).
pubmed: 29192214
doi: 10.1038/nrc.2017.104
Polikanov, Y. S., Melnikov, S. V., Soll, D. & Steitz, T. A. Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat. Struct. Mol. Biol. 22, 342–344 (2015).
pubmed: 25775268
pmcid: 4401423
doi: 10.1038/nsmb.2992
Sharma, S. & Lafontaine, D. L. J. ‘View from a bridge’: a new perspective on eukaryotic rRNA base modification. Trends Biochem. Sci. 40, 560–575 (2015).
pubmed: 26410597
doi: 10.1016/j.tibs.2015.07.008
Monaco, P. L., Marcel, V., Diaz, J.-J. & Catez, F. 2′-O-Methylation of ribosomal RNA: towards an epitranscriptomic control of translation?. Biomolecules 8, 106 (2018).
pmcid: 6316387
doi: 10.3390/biom8040106
Massenet, S., Bertrand, E. & Verheggen, C. Assembly and trafficking of box C/D and H/ACA snoRNPs. RNA Biol. 14, 680–692 (2017).
pubmed: 27715451
doi: 10.1080/15476286.2016.1243646
Falaleeva, M., Welden, J. R., Duncan, M. J. & Stamm, S. C/D‐box snoRNAs form methylating and non‐methylating ribonucleoprotein complexes: old dogs show new tricks. Bioessays 39, 1600264 (2017).
doi: 10.1002/bies.201600264
Shubina, M. Y., Musinova, Y. R. & Sheval, E. V. Nucleolar methyltransferase fibrillarin: evolution of structure and functions. Biochem. Biokhimiia 81, 941–950 (2016).
doi: 10.1134/S0006297916090030
Rodriguez-Corona, U., Sobol, M., Rodriguez-Zapata, L. C., Hozak, P. & Castano, E. Fibrillarin from Archaea to human. Biol. Cell 107, 159–174 (2015).
pubmed: 25772805
doi: 10.1111/boc.201400077
Erales, J. et al. Evidence for rRNA 2′-O-methylation plasticity: control of intrinsic translational capabilities of human ribosomes. Proc. Natl Acad. Sci. USA 114, 12934–12939 (2017).
pubmed: 29158377
doi: 10.1073/pnas.1707674114
pmcid: 5724255
Kass, S., Tyc, K., Steitz, J. A. & Sollner-Webb, B. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell 60, 897–908 (1990).
pubmed: 2156625
doi: 10.1016/0092-8674(90)90338-F
Tessarz, P. et al. Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature 505, 564–568 (2014).
pubmed: 24352239
doi: 10.1038/nature12819
Li, D. et al. Activity dependent LoNA regulates translation by coordinating rRNA transcription and methylation. Nat. Commun. 9, 1726 (2018).
pubmed: 29712923
pmcid: 5928123
doi: 10.1038/s41467-018-04072-4
Iyer-Bierhoff, A. et al. SIRT7-dependent deacetylation of fibrillarin controls histone H2A methylation and rRNA synthesis during the cell cycle. Cell Rep. 25, 2946–2954.e5 (2018).
pubmed: 30540930
doi: 10.1016/j.celrep.2018.11.051
Ren, X. et al. Maintenance of nucleolar homeostasis by CBX4 alleviates senescence and osteoarthritis. Cell Rep. 26, 3643–3656.e7 (2019).
pubmed: 30917318
doi: 10.1016/j.celrep.2019.02.088
Nachmani, D. et al. Germline NPM1 mutations lead to altered rRNA 2′-O-methylation and cause dyskeratosis congenita. Nat. Genet. 51, 1518–1529 (2019).
pubmed: 31570891
pmcid: 6858547
doi: 10.1038/s41588-019-0502-z
Marcel, V. et al. p53 acts as a safeguard of translational control by regulating fibrillarin and rRNA methylation in cancer. Cancer Cell 24, 318–330 (2013).
pubmed: 24029231
pmcid: 7106277
doi: 10.1016/j.ccr.2013.08.013
Koh, C. M. et al. Alterations in nucleolar structure and gene expression programs in prostatic neoplasia are driven by the MYC oncogene. Am. J. Pathol. 178, 1824–1834 (2011).
pubmed: 21435462
pmcid: 3078425
doi: 10.1016/j.ajpath.2010.12.040
Su, H. et al. Elevated snoRNA biogenesis is essential in breast cancer. Oncogene 33, 1348–1358 (2014).
pubmed: 23542174
doi: 10.1038/onc.2013.89
Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).
pubmed: 12351676
doi: 10.1126/science.1076997
Margueron, R. & Reinberg, D. The Polycomb complex PRC2 and its mark in life. Nature 469, 343–349 (2011).
pubmed: 21248841
pmcid: 3760771
doi: 10.1038/nature09784
Plath, K. et al. Role of histone H3 lysine 27 methylation in X inactivation. Science 300, 131–135 (2003).
pubmed: 12649488
doi: 10.1126/science.1084274
Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).
pubmed: 16153702
pmcid: 3006442
doi: 10.1016/j.cell.2005.08.020
Ezhkova, E. et al. Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells. Cell 136, 1122–1135 (2009).
pubmed: 19303854
pmcid: 2716120
doi: 10.1016/j.cell.2008.12.043
Varambally, S. et al. The Polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419, 624–629 (2002).
pubmed: 12374981
doi: 10.1038/nature01075
Kleer, C. G. et al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc. Natl Acad. Sci. USA 100, 11606–11611 (2003).
pubmed: 14500907
doi: 10.1073/pnas.1933744100
pmcid: 208805
Lee, S. T. et al. Context-specific regulation of NF-κB target gene expression by EZH2 in breast cancers. Mol. Cell 43, 798–810 (2011).
pubmed: 21884980
doi: 10.1016/j.molcel.2011.08.011
Xu, K. et al. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science 338, 1465–1469 (2012).
pubmed: 23239736
pmcid: 3625962
doi: 10.1126/science.1227604
Zhao, Y. et al. EZH2 cooperates with gain-of-function p53 mutants to promote cancer growth and metastasis. EMBO J. 38, e99599 (2019).
pubmed: 30723117
pmcid: 6396169
doi: 10.15252/embj.201899599
Cao, Q. et al. The central role of EED in the orchestration of Polycomb group complexes. Nat. Commun. 5, 3127 (2014).
pubmed: 24457600
doi: 10.1038/ncomms4127
Han, Z. et al. Structural basis of EZH2 recognition by EED. Structure 15, 1306–1315 (2007).
pubmed: 17937919
doi: 10.1016/j.str.2007.08.007
Qin, W. et al. Quantitative time-resolved chemoproteomics reveals that stable O-GlcNAc regulates box C/D snoRNP biogenesis. Proc. Natl Acad. Sci. USA 114, E6749–E6758 (2017).
pubmed: 28760965
pmcid: 5565422
Dong, Z. W. et al. RTL-P: a sensitive approach for detecting sites of 2′-O-methylation in RNA molecules. Nucleic Acids Res. 40, e157 (2012).
pubmed: 22833606
pmcid: 3488209
doi: 10.1093/nar/gks698
Marchand, V., Blanloeil-Oillo, F., Helm, M. & Motorin, Y. Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA. Nucleic Acids Res. 44, e135 (2016).
pubmed: 27302133
pmcid: 5027498
doi: 10.1093/nar/gkw547
Ruggero, D. Translational control in cancer etiology. Cold Spring Harbor Perspect. Biol. 5, a012336 (2013).
doi: 10.1101/cshperspect.a012336
Walters, B. & Thompson, S. R. Cap-independent translational control of carcinogenesis. Front. Oncol. 6, 128 (2016).
pubmed: 27252909
pmcid: 4879784
doi: 10.3389/fonc.2016.00128
Van Eden, M. E., Byrd, M. P., Sherrill, K. W. & Lloyd, R. E. Demonstrating internal ribosome entry sites in eukaryotic mRNAs using stringent RNA test procedures. RNA 10, 720–730 (2004).
pubmed: 15037781
doi: 10.1261/rna.5225204
Gan, L. et al. Epigenetic regulation of cancer progression by EZH2: from biological insights to therapeutic potential. Biomark. Res. 6, 10 (2018).
pubmed: 29556394
pmcid: 5845366
doi: 10.1186/s40364-018-0122-2
Lechertier, T., Grob, A., Hernandez-Verdun, D. & Roussel, P. Fibrillarin and Nop56 interact before being co-assembled in box C/D snoRNPs. Exp. Cell Res. 315, 928–942 (2009).
pubmed: 19331828
doi: 10.1016/j.yexcr.2009.01.016
Mattson, G. et al. A practical approach to crosslinking. Mol. Biol. Rep. 17, 167–183 (1993).
pubmed: 8326953
doi: 10.1007/BF00986726
David, A. et al. Nuclear translation visualized by ribosome-bound nascent chain puromycylation. J. Cell Biol. 197, 45–57 (2012).
pubmed: 22472439
pmcid: 3317795
doi: 10.1083/jcb.201112145
Oertlin, C. et al. Generally applicable transcriptome-wide analysis of translation using anota2seq. Nucleic Acids Res. 47, e70 (2019).
pubmed: 30926999
pmcid: 6614820
doi: 10.1093/nar/gkz223
Larsson, O., Sonenberg, N. & Nadon, R. Identification of differential translation in genome wide studies. Proc. Natl Acad. Sci. USA 107, 21487–21492 (2010).
pubmed: 21115840
doi: 10.1073/pnas.1006821107
pmcid: 3003104
Zhao, J. et al. IRESbase: a comprehensive database of experimentally validated internal ribosome entry sites. Genomics Proteomics Bioinformatics 18, 129–139 (2020).
pubmed: 32512182
pmcid: 7646085
doi: 10.1016/j.gpb.2020.03.001
Krajewska, M. et al. Elevated expression of inhibitor of apoptosis proteins in prostate cancer. Clin. Cancer Res. 9, 4914–4925 (2003).
pubmed: 14581366
Lewis, S. M. & Holcik, M. IRES in distress: translational regulation of the inhibitor of apoptosis proteins XIAP and HIAP2 during cell stress. Cell Death Differ. 12, 547–553 (2005).
pubmed: 15818406
doi: 10.1038/sj.cdd.4401602
Holcik, M., Lefebvre, C., Yeh, C., Chow, T. & Korneluk, R. G. A new internal-ribosome-entry-site motif potentiates XIAP-mediated cytoprotection. Nat. Cell Biol. 1, 190–192 (1999).
pubmed: 10559907
doi: 10.1038/11109
Ross, A. E. et al. Tissue-based genomics augments post-prostatectomy risk stratification in a natural history cohort of intermediate- and high-risk men. Eur. Urol. 69, 157–165 (2016).
pubmed: 26058959
doi: 10.1016/j.eururo.2015.05.042
Kaur, H. B. et al. Association of tumor-infiltrating T-cell density with molecular subtype, racial ancestry and clinical outcomes in prostate cancer. Mod. Pathol. 31, 1539–1552 (2018).
pubmed: 29849114
pmcid: 6168349
doi: 10.1038/s41379-018-0083-x
Yang, Y. A. & Yu, J. EZH2, an epigenetic driver of prostate cancer. Protein Cell 4, 331–341 (2013).
pubmed: 23636686
pmcid: 4131440
doi: 10.1007/s13238-013-2093-2
Rothe, B. et al. Implication of the box C/D snoRNP assembly factor Rsa1p in U3 snoRNP assembly. Nucleic Acids Res. 45, 7455–7473 (2017).
pubmed: 28505348
pmcid: 5499572
doi: 10.1093/nar/gkx424
Li, Q. et al. Antihistamine drug ebastine inhibits cancer growth by targeting Polycomb group protein EZH2. Mol. Cancer Ther. 19, 2023–2033 (2020).
pubmed: 32855270
pmcid: 7541747
doi: 10.1158/1535-7163.MCT-20-0250
Kim, J. et al. Polycomb- and methylation-independent roles of EZH2 as a transcription activator. Cell Rep. 25, 2808–2820.e4 (2018).
pubmed: 30517868
pmcid: 6342284
doi: 10.1016/j.celrep.2018.11.035
Yu, Y. et al. Progesterone receptor expression during prostate cancer progression suggests a role of this receptor in stromal cell differentiation. Prostate 75, 1043–1050 (2015).
pubmed: 25833156
doi: 10.1002/pros.22988
Xie, N. et al. The expression of glucocorticoid receptor is negatively regulated by active androgen receptor signaling in prostate tumors. Int. J. Cancer 136, E27–E38 (2015).
pubmed: 25138562
doi: 10.1002/ijc.29147
Li, Z. F. & Lam, Y. W. A new rapid method for isolating nucleoli. Methods Mol. Biol. 1228, 35–42 (2015).
pubmed: 25311120
doi: 10.1007/978-1-4939-1680-1_4
Jia, G. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011).
pubmed: 22002720
pmcid: 3218240
doi: 10.1038/nchembio.687
Marchand, V. et al. Next-generation sequencing-based RiboMethSeq protocol for analysis of tRNA 2′-O-methylation. Biomolecules 7, 13 (2017).
pmcid: 5372725
doi: 10.3390/biom7010013
Pichot, F. et al. Holistic optimization of bioinformatic analysis pipeline for detection and quantification of 2′-O-methylations in RNA by RiboMethSeq. Front. Genet. 11, 38 (2020).
pubmed: 32117451
pmcid: 7031861
doi: 10.3389/fgene.2020.00038
Poulin, F., Gingras, A. C., Olsen, H., Chevalier, S. & Sonenberg, N. 4E-BP3, a new member of the eukaryotic initiation factor 4E-binding protein family. J. Biol. Chem. 273, 14002–14007 (1998).
pubmed: 9593750
doi: 10.1074/jbc.273.22.14002
Holcik, M. & Korneluk, R. G. Functional characterization of the X-linked inhibitor of apoptosis (XIAP) internal ribosome entry site element: role of La autoantigen in XIAP translation. Mol. Cell Biol. 20, 4648–4657 (2000).
pubmed: 10848591
pmcid: 85872
doi: 10.1128/MCB.20.13.4648-4657.2000
Huez, I. et al. Two independent internal ribosome entry sites are involved in translation initiation of vascular endothelial growth factor mRNA. Mol. Cell Biol. 18, 6178–6190 (1998).
pubmed: 9774635
pmcid: 109205
doi: 10.1128/MCB.18.11.6178
Martineau, Y. et al. Internal ribosome entry site structural motifs conserved among mammalian fibroblast growth factor 1 alternatively spliced mRNAs. Mol. Cell Biol. 24, 7622–7635 (2004).
pubmed: 15314170
pmcid: 507008
doi: 10.1128/MCB.24.17.7622-7635.2004
Vagner, S. et al. Alternative translation of human fibroblast growth factor 2 mRNA occurs by internal entry of ribosomes. Mol. Cell Biol. 15, 35–44 (1995).
pubmed: 7799942
pmcid: 231905
doi: 10.1128/MCB.15.1.35
Meng, Z., Jackson, N. L., Shcherbakov, O. D., Choi, H. & Blume, S. W. The human IGF1R IRES likely operates through a Shine–Dalgarno-like interaction with the G961 loop (E-site) of the 18S rRNA and is kinetically modulated by a naturally polymorphic polyU loop. J. Cell Biochem. 110, 531–544 (2010).
pubmed: 20432247
pmcid: 2997104
Nanbru, C. et al. Alternative translation of the proto-oncogene c-Myc by an internal ribosome entry site. J. Biol. Chem. 272, 32061–32066 (1997).
pubmed: 9405401
doi: 10.1074/jbc.272.51.32061
McGlincy, N. J. & Ingolia, N. T. Transcriptome-wide measurement of translation by ribosome profiling. Methods 126, 112–129 (2017).
pubmed: 28579404
pmcid: 5582988
doi: 10.1016/j.ymeth.2017.05.028
Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina paired-end read merger. Bioinformatics 30, 614–620 (2014).
pubmed: 24142950
doi: 10.1093/bioinformatics/btt593
Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).
pubmed: 27706213
pmcid: 5051824
doi: 10.1371/journal.pone.0163962
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).
pubmed: 19289445
pmcid: 2672628
doi: 10.1093/bioinformatics/btp120
Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
pubmed: 25260700
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics 16, 284–287 (2012).
pubmed: 22455463
pmcid: 3339379
doi: 10.1089/omi.2011.0118
Chen, K. et al. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 23, 341–351 (2013).
pubmed: 23193179
pmcid: 3561875
doi: 10.1101/gr.142067.112
Li, D., Hsu, S., Purushotham, D., Sears, R. L. & Wang, T. WashU Epigenome browser update 2019. Nucleic Acids Res. 47, W158–W165 (2019).
pubmed: 31165883
pmcid: 6602459
doi: 10.1093/nar/gkz348
Ren, J. et al. DOG 1.0: illustrator of protein domain structures. Cell Res. 19, 271–273 (2009).
pubmed: 19153597
doi: 10.1038/cr.2009.6