YB-3 substitutes YB-1 in global mRNA binding

References

• Eliseeva IA, Kim ER, Guryanov SG, et al. Y-box-binding protein 1 (YB-1) and its functions. Biochemistry (Mosc). 2011;76:1402–1433.
   PubMed Web of Science ®Google Scholar
• Lyabin DN, Eliseeva IA, Ovchinnikov LP. YB-1 protein: functions and regulation. Wiley Interdiscip Rev RNA. 2014;5:95–110.
   PubMed Web of Science ®Google Scholar
• Shurtleff MJ, Temoche-Diaz MM, Karfilis KV, et al. Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction. eLife. 2016;5.
   PubMed Web of Science ®Google Scholar
• Dolfini D, Mantovani R. YB-1 (YBX1) does not bind to Y/CCAAT boxes in vivo. Oncogene. 2013;32:4189–4190.
   PubMed Web of Science ®Google Scholar
• Evdokimova V, Ruzanov P, Imataka H, et al. The major mRNA-associated protein YB-1 is a potent 5ʹ cap-dependent mRNA stabilizer. Embo J. 2001;20:5491–5502.
   PubMed Web of Science ®Google Scholar
• Nekrasov MP, Ivshina MP, Chernov KG, et al. The mRNA-binding protein YB-1 (p50) prevents association of the eukaryotic initiation factor eIF4G with mRNA and inhibits protein synthesis at the initiation stage. J Biol Chem. 2003;278:13936–13943.
   PubMed Web of Science ®Google Scholar
• Evdokimova V, Tognon C, Ng T, et al. Translational activation of snail1 and other developmentally regulated transcription factors by YB-1 promotes an epithelial-mesenchymal transition. Cancer Cell. 2009;15:402–415.
   PubMed Web of Science ®Google Scholar
• Lu ZH, Books JT, Ley TJ. YB-1 is important for late-stage embryonic development, optimal cellular stress responses, and the prevention of premature senescence. Mol Cell Biol. 2005;25:4625–4637.
   PubMed Web of Science ®Google Scholar
• Minich WB, Ovchinnikov LP. Role of cytoplasmic mRNP proteins in translation. Biochimie. 1992;74:477–483.
   PubMed Web of Science ®Google Scholar
• Basaki Y, Taguchi K, Izumi H, et al. Y-box binding protein-1 (YB-1) promotes cell cycle progression through CDC6-dependent pathway in human cancer cells. Eur J Cancer. 2010;46:954–965.
   PubMed Web of Science ®Google Scholar
• En-Nia A, Yilmaz E, Klinge U, et al. Transcription factor YB-1 mediates DNA polymerase alpha gene expression. J Biol Chem. 2005;280:7702–7711.
   PubMed Web of Science ®Google Scholar
• Evdokimova VM, Kovrigina EA, Nashchekin DV, et al. The major core protein of messenger ribonucleoprotein particles (p50) promotes initiation of protein biosynthesis in vitro. J Biol Chem. 1998;273:3574–3581.
   PubMed Web of Science ®Google Scholar
• Dooley S, Said HM, Gressner AM, et al. Y-box protein-1 is the crucial mediator of antifibrotic interferon-gamma effects. J Biol Chem. 2006;281:1784–1795.
   PubMed Web of Science ®Google Scholar
• Lindquist JA, Mertens PR. Cold shock proteins: from cellular mechanisms to pathophysiology and disease. Cell Commun Signal. 2018;16:63.
   PubMed Web of Science ®Google Scholar
• Fraser DJ, Phillips AO, Zhang X, et al. Y-box protein-1 controls transforming growth factor-beta1 translation in proximal tubular cells. Kidney Int. 2008;73:724–732.
   PubMed Web of Science ®Google Scholar
• Kato M, Wang L, Putta S, et al. Post-transcriptional up-regulation of Tsc-22 by Ybx1, a target of miR-216a, mediates TGF-{beta}-induced collagen expression in kidney cells. J Biol Chem. 2010;285:34004–34015.
   PubMed Web of Science ®Google Scholar
• Lu ZH, Books JT, Ley TJ. Cold shock domain family members YB-1 and MSY4 share essential functions during murine embryogenesis. Mol Cell Biol. 2006;26:8410–8417.
   PubMed Web of Science ®Google Scholar
• Kleene KC. Y-box proteins combine versatile cold shock domains and arginine-rich motifs (ARMs) for pleiotropic functions in RNA biology. Biochem J. 2018;475:2769–2784.
   PubMed Web of Science ®Google Scholar
• Bouvet P, Matsumoto K, Wolffe AP. Sequence-specific RNA recognition by the Xenopus Y-box proteins. An essential role for the cold shock domain. J Biol Chem. 1995;270:28297–28303.
   PubMed Web of Science ®Google Scholar
• Yang XJ, Zhu H, Mu SR, et al. Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA. J Biol Chem. 2019;294:10998–11010.
   Web of Science ®Google Scholar
• Asakuno K, Kohno K, Uchiumi T, et al. Involvement of a DNA binding protein, MDR-NF1/YB-1, in human MDR1 gene expression by actinomycin D. Biochem Biophys Res Commun. 1994;199:1428–1435.
   PubMed Web of Science ®Google Scholar
• Fujita T, Ito K, Izumi H, et al. Increased nuclear localization of transcription factor Y-box binding protein 1 accompanied by up-regulation of P-glycoprotein in breast cancer pretreated with paclitaxel. Clin Cancer Res. 2005;11:8837–8844.
   PubMed Web of Science ®Google Scholar
• Koike K, Uchiumi T, Ohga T, et al. Nuclear translocation of the Y-box binding protein by ultraviolet irradiation. FEBS Lett. 1997;417:390–394.
   PubMed Web of Science ®Google Scholar
• Stein U, Jurchott K, Walther W, et al. Hyperthermia-induced nuclear translocation of transcription factor YB-1 leads to enhanced expression of multidrug resistance-related ABC transporters. J Biol Chem. 2001;276:28562–28569.
   PubMed Web of Science ®Google Scholar
• Tanaka T, Ohashi S, Saito H, et al. Indirubin 3ʹ-oxime inhibits anticancer agent-induced YB-1 nuclear translocation in HepG2 human hepatocellular carcinoma cells. Biochem Biophys Res Commun. 2018;496:7–11.
   PubMed Web of Science ®Google Scholar
• Evdokimova VM, Wei CL, Sitikov AS, et al. The major protein of messenger ribonucleoprotein particles in somatic cells is a member of the Y-box binding transcription factor family. J Biol Chem. 1995;270:3186–3192.
   PubMed Web of Science ®Google Scholar
• Murray MT, Schiller DL, Franke WW. Sequence analysis of cytoplasmic mRNA-binding proteins of Xenopus oocytes identifies a family of RNA-binding proteins. Proc Natl Acad Sci U S A. 1992;89:11–15.
   PubMed Web of Science ®Google Scholar
• Dong J, Akcakanat A, Stivers DN, et al. RNA-binding specificity of Y-box protein 1. RNA Biol. 2009;6:59–64.
   PubMed Web of Science ®Google Scholar
• Evdokimova V, Ruzanov P, Anglesio MS, et al. Akt-mediated YB-1 phosphorylation activates translation of silent mRNA species. Mol Cell Biol. 2006;26:277–292.
   PubMed Web of Science ®Google Scholar
• Wu SL, Fu X, Huang J, et al. Genome-wide analysis of YB-1-RNA interactions reveals a novel role of YB-1 in miRNA processing in glioblastoma multiforme. Nucleic Acids Res. 2015;43:8516–8528.
   PubMed Web of Science ®Google Scholar
• Svitkin YV, Evdokimova VM, Brasey A, et al. General RNA-binding proteins have a function in poly(A)-binding protein-dependent translation. Embo J. 2009;28:58–68.
   PubMed Web of Science ®Google Scholar
• Skabkin MA, Kiselyova OI, Chernov KG, et al. Structural organization of mRNA complexes with major core mRNP protein YB-1. Nucleic Acids Res. 2004;32:5621–5635.
   PubMed Web of Science ®Google Scholar
• Pisarev AV, Skabkin MA, Thomas AA, et al. Positive and negative effects of the major mammalian messenger ribonucleoprotein p50 on binding of 40 S ribosomal subunits to the initiation codon of beta-globin mRNA. J Biol Chem. 2002;277:15445–15451.
   PubMed Web of Science ®Google Scholar
• Skabkin MA, Evdokimova V, Thomas AA, et al. The major messenger ribonucleoprotein particle protein p50 (YB-1) promotes nucleic acid strand annealing. J Biol Chem. 2001;276:44841–44847.
   PubMed Web of Science ®Google Scholar
• Snyder E, Soundararajan R, Sharma M, et al. Compound heterozygosity for Y box proteins causes sterility due to loss of translational repression. PLoS Genet. 2015;11:e1005690.
   PubMed Web of Science ®Google Scholar
• Kohno Y, Matsuki Y, Tanimoto A, et al. Expression of Y-box-binding protein dbpC/contrin, a potentially new cancer/testis antigen. Br J Cancer. 2006;94:710–716.
   PubMed Web of Science ®Google Scholar
• Tekur S, Pawlak A, Guellaen G, et al. Contrin, the human homologue of a germ-cell Y-box-binding protein: cloning, expression, and chromosomal localization. J Andrology. 1999;20:135–144.
   PubMedGoogle Scholar
• Sears D, Luong P, Yuan M, et al. Functional phosphoproteomic analysis reveals cold-shock domain protein A to be a Bcr-Abl effector-regulating proliferation and transformation in chronic myeloid leukemia. Cell Death Dis. 2010;1:e93.
   PubMed Web of Science ®Google Scholar
• Matsumoto S, Uchiumi T, Tanamachi H, et al. Ribonucleoprotein Y-box-binding protein-1 regulates mitochondrial oxidative phosphorylation (OXPHOS) protein expression after serum stimulation through binding to OXPHOS mRNA. Biochem J. 2012;443:573–584.
   PubMed Web of Science ®Google Scholar
• Siegel PM, Massague J. Cytostatic and apoptotic actions of TGF-beta in homeostasis and cancer. Nat Rev Cancer. 2003;3:807–821.
   PubMed Web of Science ®Google Scholar
• Lyabin DN, Eliseeva IA, Skabkina OV, et al. Interplay between Y-box-binding protein 1 (YB-1) and poly(A) binding protein (PABP) in specific regulation of YB-1 mRNA translation. RNA Biol. 2011;8:883–892.
   PubMed Web of Science ®Google Scholar
• Skabkina OV, Lyabin DN, Skabkin MA, et al. YB-1 autoregulates translation of its own mRNA at or prior to the step of 40S ribosomal subunit joining. Mol Cell Biol. 2005;25:3317–3323.
   PubMed Web of Science ®Google Scholar
• Muller-McNicoll M, Rossbach O, Hui J, et al. Auto-regulatory feedback by RNA-binding proteins. J Mol Cell Biol. 2019;11:930–939.
   Web of Science ®Google Scholar
• Kemmerer K, Fischer S, Weigand JE. Auto- and cross-regulation of the hnRNPs D and DL. RNA. 2018;24:324–331.
   PubMed Web of Science ®Google Scholar
• Ran FA, Hsu PD, Wright J, et al. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013;8:2281–2308.
   PubMed Web of Science ®Google Scholar
• Glukhova KF, Marchenkov VV, Melnik TN, et al. Isoforms of green fluorescent protein differ from each other in solvent molecules ‘trapped’ inside this protein. J Biomol Struct Dyn. 2017;35:1215–1225.
   PubMed Web of Science ®Google Scholar
• Eliseeva I, Vasilieva M, Ovchinnikov LP. Translation of human beta-Actin mRNA is regulated by mTOR pathway. Genes (Basel). 2019;10:96.
   PubMed Web of Science ®Google Scholar
• Wakiyama M, Futami T, Miura K. Poly(A) dependent translation in rabbit reticulocyte lysate. Biochimie. 1997;79:781–785.
   PubMed Web of Science ®Google Scholar
• Presolski SI, Hong VP, Finn MG. Copper-catalyzed azide-alkyne click chemistry for bioconjugation. Curr Protoc Chem Biol. 2011;3:153–162.
   PubMedGoogle Scholar
• Terenin IM, Andreev DE, Dmitriev SE, et al. A novel mechanism of eukaryotic translation initiation that is neither m7G-cap-, nor IRES-dependent. Nucleic Acids Res. 2013;41:1807–1816.
   PubMed Web of Science ®Google Scholar
• Guryanov SG, Filimonov VV, Timchenko AA, et al. The major mRNP protein YB-1: structural and association properties in solution. Biochim Biophys Acta. 2013;1834:559–567.
   PubMed Web of Science ®Google Scholar
• Gerashchenko MV, Gladyshev VN. Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic Acids Res. 2014;42:e134.
   PubMed Web of Science ®Google Scholar
• Ingolia NT, Brar GA, Rouskin S, et al. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012;7:1534–1550.
   PubMed Web of Science ®Google Scholar
• Tenenbaum SA, Carson CC, Lager PJ, et al. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A. 2000;97:14085–14090.
   PubMed Web of Science ®Google Scholar
• Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17:3.
   Google Scholar
• Meyer LR, Zweig AS, Hinrichs AS, et al. The UCSC genome browser database: extensions and updates 2013. Nucleic Acids Res. 2013;41:D64–9.
   PubMed Web of Science ®Google Scholar
• Harrow J, Frankish A, Gonzalez JM, et al. GENCODE: the reference human genome annotation for the ENCODE project. Genome Res. 2012;22:1760–1774.
   PubMed Web of Science ®Google Scholar
• Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
   PubMed Web of Science ®Google Scholar
• Dunn JG, Weissman JS. Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data. BMC Genomics. 2016;17:958.
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–140.
   PubMed Web of Science ®Google Scholar
• Sergushichev AA. An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation. BioRxiv. 2016. doi:10.1101/060012
   Google Scholar
• Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102:15545–15550.
   PubMed Web of Science ®Google Scholar