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YBX1 (Y box binding protein 1)

Written2010-11Valentina Evdokimova, Alexey Sorokin
Institute of Protein Research, Pushchino, Moscow Region 142290, Russian Federation

(Note : for Links provided by Atlas : click)


Alias (NCBI)BP-8
HGNC (Hugo) YBX1
HGNC Alias symbYB-1
HGNC Previous nameNSEP1
HGNC Previous namenuclease sensitive element binding protein 1
LocusID (NCBI) 4904
Atlas_Id 46554
Location 1p34.2  [Link to chromosome band 1p34]
Location_base_pair Starts at 42682418 and ends at 42703805 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping YBX1.png]
Local_order The human YBX1 gene maps on 1p34 between the PPIH and the LOC100287607 loci.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ALDH1A1 (9q21.13)::YBX1 (1p34.2)YBX1 (1p34.2)::MUC1 (1q22)YBX1 (1p34.2)::NCBP2 (3q29)
YBX1 (1p34.2)::YBX1 (1p34.2)


  Genomic organization of YBX1. Box = exon (blue = 5'UTR, yellow = CDS, light red = 3'UTR). Line = intron.
Description The human YBX1 gene consists of 8 exons and 7 introns spanning a 19.2-kb genomic region. Intron number 1 is phase 1 (between 1st and 2nd base of codon). Introns number 2 and 6 are phase 2 (between 2nd and 3rd base of codon). Introns number 3, 4, 5 are phase 0 (between codons). According to the SNP source (dbSNP NCBI), non-synonymous polymorphism has been reported for the codons 30 (rs11558135), 237 (rs3887881), 251 (rs55676223), and 261 (rs3887879). The YBX1 promoter region contains no typical TATA or CCAAT box, but has multiple E-boxes located between -1855 and -422 nucleotides (relative to the start of exon 1) and several GT and GC boxes. The gene also contains a large and highly conserved CpG island at the immediate 5' promoter region which extends to the first exon encoding 5' UTR of YBX1 mRNA. The region between nucleotides -119 to +127 was shown to be essential for transcriptional activity in the reporter assays (Makino et al., 1996). YBX1 is constitutively expressed in multiple human tissues and its expression can be further induced by the E-box-binding transcription factors such as c-myc (Uramoto et al., 2002), Twist (Shiota et al., 2008) and Math2 (Ohashi et al., 2009).
Transcription The main processed mRNA is 1514 bp. It encompasses exons 1-8. The 70-amino acid cold-shock domain (CSD) is encoded separately by exons 2-5. Four additional splice variants in human were predicted (Ensembl), two of which (YBX1-004 and YBX1-201) preserve exons 2 and 3 coding for core elements of the CSD, the RNP1 and RNP2 motifs, respectively. An alternative transcript for ctYB-1, the YBX1 homologous gene in C. tentans, has been reported (Nashchekin et al., 2007).
DescriptionSymbolNCBI gene IDPositionIntrons/exonsORFIdentity with YBX1Gaps
nuclease sensitive element binding protein 1 pseudogenebA327L3.41583739p13.1IntronlessStops after E881477/1515 (97%)2/1515 (0%)
Y box binding protein 1 pseudogene 1YBX1P1506314q23.3Intronless 1496 bp-1488/1531 (97%)20/1511 (1%)
Y box binding protein 1 pseudogene 2YBX1P26465317q22.32 exons, 1 intron, 1553 bpStops after E881431/1529 (93%)43/1529 (2%)
Y box binding protein 1 pseudogeneLOC1001310121001310127q36.1Intronless, 820 bp-287/353 (81%)26/353 (7%)


  Structural and functional organization of YB-1. YB-1 is composed by three domains: N-terminal Ala/Pro rich (AP) domain, cold shock domain (CSD) and the C-terminal domain (CTD) containing clusters of positively and negatively charged amino acids. Indicated are some known molecular partners of YB-1 and sites of their interactions (from Sorokin et al., 2005). The arrow indicates proteasomal cleavage sites.
Description The YBX1 gene encodes the Y-box protein 1 (YB-1) which consists of 324 amino acid residues and has the isoelectric point 10.3. Theoretical MW is 35924, however YB-1 is known to migrate as a ~45-50 kDa protein in SDS-polyacrylamide gels due to its anomalous electrophoretic mobility. YB-1 belongs to the family of multifunctional DNA/RNA binding proteins that are highly conserved throughout evolution and found in eukaryotes, prokaryotes and archaea. The most conserved region in YB-1 is the 80 amino acid CSD which exhibits >40% identity and >60% similarity to the major E. coli cold shock protein CspA (Matsumoto and Wolffe, 1998; Sommerville, 1999). The CSD possesses RNP1 and RNP2-like consensus motifs and is represented by a five-stranded beta-barrel structure which creates a surface rich in aromatic and basic amino acids that may act as a large nucleic acid-binding site (Wolffe et al., 1992; Wolffe, 1994). The CSD has a preference for binding single-stranded pyrimidine-rich sequences. The N-terminal AP domain of YB-1 is similar to that found in several other transcription factors and may thus be important for its transcriptional activity. This region is also essential for interaction with p53 and modulation of p53-mediated transcription (Okamoto et al., 2000), and for association with actin microfilaments and mRNA compartmentalization (Ruzanov et al., 1999). The C-terminal region of YB-1 is responsible for sequence-nonspecific binding to DNA and RNA and mediation of protein-protein interactions (Wolffe, 1994; Sommerville and Ladomery, 1996). An inverted CCAAT-box found in HLA class II gene promoters, a so-called Y-box, was originally determined as the YB-1 binding motif (Didier et al., 1988). Later studies have concluded that YB-1 rather recognizes the DNA structure than a defined nucleotide sequence, making prediction of its target genes not feasible with conventional in silico analyses (Swamynathan et al., 1998). YB-1 is also capable of unwinding DNA and RNA duplexes, especially those containing mismatches, thereby promoting strand exchange and formation of perfectly matched duplex structures (Skabkin et al., 2001; Gaudreault et al., 2004).
Expression According to Human Protein Atlas, YB-1 is variably expressed in most normal human tissues. Its expression is elevated in multiple cancer types (Kohno et al., 2003).
Localisation Mostly cytosolic. Shuttles between cytoplasm and nucleus. Localized in cytoplasmic stress granules and processing bodies containing untranslated mRNAs (Kedersha and Anderson, 2007). Nuclear translocation is induced in response to various stresses, including adenoviral infection (Holm et al., 2002), hyperthermia (Stein et al., 2001), DNA damage (Kohno et al., 2003) and activation of PI3K-Akt signaling (Sutherland et al., 2005).
Function The diverse biological functions of YB-1 appear to arise from its broad nucleic acid binding properties. YB-1 has been implicated in pre-mRNA splicing, transcriptional regulation, mRNA translation and stability as well as in chromatin remodelling, DNA repair and environmental stress responses (Kohno et al., 2003; Matsumoto and Bay, 2005).
Splicing. YB-1 regulates splice site selection via direct binding to splicing recognition motifs in pre-mRNA, including A/C-rich exon enhancers (Stickeler et al., 2001) or via interaction with splicing factors from the SR family (Li et al., 2003; Raffetseder et al., 2003).
Transcription. YB-1 is capable of binding to promoters of many genes, many of which lack the Y-box, and either activates or represses transcription. Among the genes activated by YB-1 are thymidine kinase, proliferating cell nuclear antigen (PCNA), cyclin A and cyclin B1, DNA topoisomerase II alpha, gelatinase A, matrix metalloproteinase 2, multidrug resistance 1 (MDR1), EGFR and protein tyrosine phosphatase 1B. Genes that are transcriptionally repressed by YB-1 include MHC class II, collagen alpha1, granulocyte-macrophage colony-stimulating factor (GM-CSF), etc (reviewed in Ladomery and Sommerville, 1995; Kohno et al., 2003; Kuwano et al., 2003). Overall, YB-1 is considered as an important regulator of growth- and stress-associated genes.
mRNA translation and stability. YB-1 (p50) is known as a major structural component of messenger ribonucleoprotein particles (mRNPs) which exerts positive or negative effects on translation, depending on the amount bound to mRNA (Evdokimova and Ovchinnikov, 1999). YB-1 regulates translational activity of many growth- and differentiation-associated mRNAs, including Snail1, and selectively protects capped mRNAs against degradation (Evdokimova et al., 2001; Evdokimova et al., 2006; Evdokimova et al., 2009). YB-1 appears to play a role in stabilization of short-lived mRNAs, including IL-2 (Chen et al., 2000), GM-CSF (Capowski et al., 2001) and VEGF (Coles et al., 2004).
DNA repair and stress response. YB-1 is involved in base excision and mismatch repair pathways via interaction with multiple DNA repair proteins including glycosylase NEIL2, DNA polymerase beta and delta, DNA ligase III, APE1, MSH2, Ku80, WRN, endonuclease III, etc (Marenstein et al., 2001; Gaudreault et al., 2004; Das et al., 2007). YB-1 also directly binds and promotes separation of DNA strands that contain mismatches or are modified by cisplatin (Ise et al., 1999; Skabkin et al., 2001; Gaudreault et al., 2004). Various stresses, including DNA damage, adenovirus infection and hyperthermia, induce nuclear translocation of YB-1 (Ohga et al., 1996; Kohno et al., 2003) and its proteasomal cleavage (Sorokin et al., 2005). Accumulation of the full-length and/or truncated YB-1 proteins in the nucleus is associated with increased survival and multidrug resistance (Kohno et al., 2003; Sorokin et al., 2005). YB-1 knock-out in mice is lethal (Lu et al., 2005; Lu et al., 2006). Fibroblasts derived from YB-1(-/-) embryos exhibit a reduced ability to respond to oxidative, genotoxic and oncogene-induced stresses, further implicating YB-1 in stress responses and embryonic development.
Tumorigenesis. YB-1 is frequently overexpressed in multiple human cancers (reviewed in Kohno et al., 2003; Kuwano et al., 2003). In many cases, YB-1 levels are elevated in the nucleus, positively correlating with multiple drug resistance and poor patient outcome (Bargou et al., 1997; Janz et al., 2002). Ectopic expression of YB-1 in breast cancer cells and mouse models stimulated tumor growth (Bergmann et al., 2005; Sutherland et al., 2005). Yet, the role of YB-1 in tumorigenesis is controversial. YB-1 overexpression blocked oncogenic transformation caused by PI3K or Akt (Bader et al., 2003). These apparently contradictory results were proposed to be due to differential localization of YB-1; its interference with oncogenic transformation is associated with cytosolic localization and a consequent function in translational control (Bader and Vogt, 2004; Bader and Vogt, 2005).
Homology YB-1 is highly homologous to human DbpA (12p13; expressed predominantly in heart and muscle) and DbpC/contrin (17p11; expressed exclusively in germ cells). They share greater than 90% identity within the CSD and a high degree of similarity in the N- and C-terminal domains, including C-terminal clusters of basic and acidic amino acids. Mouse orthologues are YB-1 (encoded by Ybx1; 99% overall aminoacid identity with human YB-1), MSY2 (Ybx2; ~93% identity with contrin) and MSY4 (~86% identity with DbpA).


Note Mutations in YBX1 are not reported.

Implicated in

Entity Breast cancer
Note Elevated expression and nuclear localization of YB-1 is associated with increased proliferation, multidrug resistance and tumor aggressiveness across all tumor subtypes. Nuclear localization positively correlates with increased expression of MDR1/P-gp and HER2/ErbB2 (Bargou et al., 1997; Saji et al., 2003; Fujii et al., 2008; Habibi et al., 2008). Enforced YB-1 expression in mammary glands of transgenic mice induced chromosomal instability and tumorigenesis (Bergmann et al., 2005). YB-1 effects on tumorigenesis are likely dependent on cellular signaling. It blocks oncogenic transformation induced by Akt or PI3K but not by Src, Jun or Qin oncoproteins (Bader et al., 2003), and decreases proliferation of tumor cells with activated MAPK-Ras signaling, while inducing their metastatic ability (Evdokimova et al., 2009).
Prognosis Nuclear YB-1 is considered as a marker of poor clinical outcome. Patients with high YB-1 levels are likely to benefit from dose-intensified chemotherapy regimens (Gluz et al., 2009).
Entity Prostate cancer
Note YB-1 is upregulated during prostate cancer tumor progression and is reported to increase P-glycoprotein activity (Giménez-Bonafé et al., 2004).
Entity Lung cancer
Note Nuclear YB-1 is associated with poor survival and expression of HER2/ErbB2 and HER3/ErbB3 in non-small cell lung cancer (Kashihara et al., 2009).
Prognosis Patients with nuclear YB-1 expression and p53 mutations appear to have the worst prognosis (median survival 3 months), while best outcome was found in patients with no nuclear YB-1 and wild-type p53 (Gessner et al., 2004).
Entity Colon cancer
Note YB-1 expression levels are elevated in colorectal carcinoma and positively correlate with DNA topoisomerase II alpha and PCNA expression but not with P-gp (Shibao et al., 1999). In colon cancer cells, YB-1 accumulates in the nuclei in response to vinblastin and is associated with development of vinblastin resistance and elevated expression of P-gp (Vaiman et al., 2007).
Entity Ovarian cancer
Note YB-1 levels are elevated in the nuclei of cisplatin-resistant cancer cell lines and cancer patients, indicating that nuclear YB-1 may be associated with acquired cisplatin resistance in ovarian cancers (Yahata et al., 2002).
Prognosis Co-expression of YB-1 and P-gp is indicative of unfavourable prognosis in ovarian cancer (Huang et al., 2004).
Entity Haematopoietic malignancies
Disease Large B-cell lymphoma, multiple myeloma.
Nuclear expression of YB-1 is associated with P-gp expression and poor response to chemotherapy in large B-cell lymphoma (Xu et al., 2009). YB-1 is strongly expressed in normal plasma cell precursor blasts as well as in a multiple myeloma tumor specimens and cell lines but not in normal bone marrow or plasma cells. Its expression is associated with an immature morphology, a highly proliferative phenotype and doxorubicin resistance, indicating its involvement in drug resistance and disease progression in multiple myeloma (Chatterjee et al., 2008).
Entity Bone and soft tissue tumors
Disease Rhabdomyosarcoma, synovial sarcoma and osteosarcoma.
Nuclear expression of YB-1 protein positively correlates with P-gp expression and a higher proliferative index in embryonal (ERMS) but not in alveolar rhabdomyosarcoma (ARMS) (Oda et al., 2008), synovial sarcoma (Oda et al., 2003) and osteosarcoma (Oda et al., 1998).
Entity Melanoma
Note YB-1 expression is increased in melanoma cells compared to benign melanocytes, and nuclear YB-1 is found in invasive and metastatic melanoma cells. YB-1 expression is associated with increased proliferation, tumor invasion and chemoresistance (Schittek et al., 2007).
Entity Nervous system tumors
Disease Glioblastoma, neuroblastoma.
YB-1 levels are elevated in pediatric glioblastoma (Faury et al., 2007) and neuroblastoma (Wachowiak et al., 2010).
Prognosis In neuroblastoma, no correlation of YB-1 expression with survival, risk factors or stage of the disease was found.


Y box-binding protein 1 induces resistance to oncogenic transformation by the phosphatidylinositol 3-kinase pathway.
Bader AG, Felts KA, Jiang N, Chang HW, Vogt PK.
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12384-9. Epub 2003 Oct 6.
PMID 14530393
Inhibition of protein synthesis by Y box-binding protein 1 blocks oncogenic cell transformation.
Bader AG, Vogt PK.
Mol Cell Biol. 2005 Mar;25(6):2095-106.
PMID 15743808
Nuclear localization and increased levels of transcription factor YB-1 in primary human breast cancers are associated with intrinsic MDR1 gene expression.
Bargou RC, Jurchott K, Wagener C, Bergmann S, Metzner S, Bommert K, Mapara MY, Winzer KJ, Dietel M, Dorken B, Royer HD.
Nat Med. 1997 Apr;3(4):447-50.
PMID 9095180
YB-1 provokes breast cancer through the induction of chromosomal instability that emerges from mitotic failure and centrosome amplification.
Bergmann S, Royer-Pokora B, Fietze E, Jurchott K, Hildebrandt B, Trost D, Leenders F, Claude JC, Theuring F, Bargou R, Dietel M, Royer HD.
Cancer Res. 2005 May 15;65(10):4078-87.
PMID 15899797
Y box-binding factor promotes eosinophil survival by stabilizing granulocyte-macrophage colony-stimulating factor mRNA.
Capowski EE, Esnault S, Bhattacharya S, Malter JS.
J Immunol. 2001 Nov 15;167(10):5970-6.
PMID 11698476
The Y-box binding protein YB-1 is associated with progressive disease and mediates survival and drug resistance in multiple myeloma.
Chatterjee M, Rancso C, Stuhmer T, Eckstein N, Andrulis M, Gerecke C, Lorentz H, Royer HD, Bargou RC.
Blood. 2008 Apr 1;111(7):3714-22. Epub 2007 Nov 15.
PMID 18006704
Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA stabilization during T-cell activation.
Chen CY, Gherzi R, Andersen JS, Gaietta G, Jurchott K, Royer HD, Mann M, Karin M.
Genes Dev. 2000 May 15;14(10):1236-48.
PMID 10817758
A multi-protein complex containing cold shock domain (Y-box) and polypyrimidine tract binding proteins forms on the vascular endothelial growth factor mRNA. Potential role in mRNA stabilization.
Coles LS, Bartley MA, Bert A, Hunter J, Polyak S, Diamond P, Vadas MA, Goodall GJ.
Eur J Biochem. 2004 Feb;271(3):648-60.
PMID 14728692
Stimulation of NEIL2-mediated oxidized base excision repair via YB-1 interaction during oxidative stress.
Das S, Chattopadhyay R, Bhakat KK, Boldogh I, Kohno K, Prasad R, Wilson SH, Hazra TK.
J Biol Chem. 2007 Sep 28;282(39):28474-84. Epub 2007 Aug 7.
PMID 17686777
Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box.
Didier DK, Schiffenbauer J, Woulfe SL, Zacheis M, Schwartz BD.
Proc Natl Acad Sci U S A. 1988 Oct;85(19):7322-6.
PMID 3174636
Translational activation of snail1 and other developmentally regulated transcription factors by YB-1 promotes an epithelial-mesenchymal transition.
Evdokimova V, Tognon C, Ng T, Ruzanov P, Melnyk N, Fink D, Sorokin A, Ovchinnikov LP, Davicioni E, Triche TJ, Sorensen PH.
Cancer Cell. 2009 May 5;15(5):402-15.
PMID 19411069
Molecular profiling identifies prognostic subgroups of pediatric glioblastoma and shows increased YB-1 expression in tumors.
Faury D, Nantel A, Dunn SE, Guiot MC, Haque T, Hauser P, Garami M, Bognar L, Hanzely Z, Liberski PP, Lopez-Aguilar E, Valera ET, Tone LG, Carret AS, Del Maestro RF, Gleave M, Montes JL, Pietsch T, Albrecht S, Jabado N.
J Clin Oncol. 2007 Apr 1;25(10):1196-208.
PMID 17401009
Expression of HER2 and estrogen receptor alpha depends upon nuclear localization of Y-box binding protein-1 in human breast cancers.
Fujii T, Kawahara A, Basaki Y, Hattori S, Nakashima K, Nakano K, Shirouzu K, Kohno K, Yanagawa T, Yamana H, Nishio K, Ono M, Kuwano M, Kage M.
Cancer Res. 2008 Mar 1;68(5):1504-12.
PMID 18316615
YB-1 promotes strand separation in vitro of duplex DNA containing either mispaired bases or cisplatin modifications, exhibits endonucleolytic activities and binds several DNA repair proteins.
Gaudreault I, Guay D, Lebel M.
Nucleic Acids Res. 2004 Jan 12;32(1):316-27. Print 2004.
PMID 14718551
Nuclear YB-1 expression as a negative prognostic marker in nonsmall cell lung cancer.
Gessner C, Woischwill C, Schumacher A, Liebers U, Kuhn H, Stiehl P, Jurchott K, Royer HD, Witt C, Wolff G.
Eur Respir J. 2004 Jan;23(1):14-9.
PMID 14738225
YB-1 is upregulated during prostate cancer tumor progression and increases P-glycoprotein activity.
Gimenez-Bonafe P, Fedoruk MN, Whitmore TG, Akbari M, Ralph JL, Ettinger S, Gleave ME, Nelson CC.
Prostate. 2004 May 15;59(3):337-49.
PMID 15042610
Y-box-binding protein YB-1 identifies high-risk patients with primary breast cancer benefiting from rapidly cycled tandem high-dose adjuvant chemotherapy.
Gluz O, Mengele K, Schmitt M, Kates R, Diallo-Danebrock R, Neff F, Royer HD, Eckstein N, Mohrmann S, Ting E, Kiechle M, Poremba C, Nitz U, Harbeck N.
J Clin Oncol. 2009 Dec 20;27(36):6144-51. Epub 2009 Nov 9.
PMID 19901122
Redefining prognostic factors for breast cancer: YB-1 is a stronger predictor of relapse and disease-specific survival than estrogen receptor or HER-2 across all tumor subtypes.
Habibi G, Leung S, Law JH, Gelmon K, Masoudi H, Turbin D, Pollak M, Nielsen TO, Huntsman D, Dunn SE.
Breast Cancer Res. 2008;10(5):R86. Epub 2008 Oct 16.
PMID 18925950
YB-1 relocates to the nucleus in adenovirus-infected cells and facilitates viral replication by inducing E2 gene expression through the E2 late promoter.
Holm PS, Bergmann S, Jurchott K, Lage H, Brand K, Ladhoff A, Mantwill K, Curiel DT, Dobbelstein M, Dietel M, Gansbacher B, Royer HD.
J Biol Chem. 2002 Mar 22;277(12):10427-34. Epub 2002 Jan 11.
PMID 11788582
Co-expression of Y box-binding protein-1 and P-glycoprotein as a prognostic marker for survival in epithelial ovarian cancer.
Huang X, Ushijima K, Komai K, Takemoto Y, Motoshima S, Kamura T, Kohno K.
Gynecol Oncol. 2004 May;93(2):287-91.
PMID 15099935
Transcription factor Y-box binding protein 1 binds preferentially to cisplatin-modified DNA and interacts with proliferating cell nuclear antigen.
Ise T, Nagatani G, Imamura T, Kato K, Takano H, Nomoto M, Izumi H, Ohmori H, Okamoto T, Ohga T, Uchiumi T, Kuwano M, Kohno K.
Cancer Res. 1999 Jan 15;59(2):342-6.
PMID 9927044
Y-box factor YB-1 predicts drug resistance and patient outcome in breast cancer independent of clinically relevant tumor biologic factors HER2, uPA and PAI-1.
Janz M, Harbeck N, Dettmar P, Berger U, Schmidt A, Jurchott K, Schmitt M, Royer HD.
Int J Cancer. 2002 Jan 20;97(3):278-82.
PMID 11774277
Nuclear Y-box binding protein-1, a predictive marker of prognosis, is correlated with expression of HER2/ErbB2 and HER3/ErbB3 in non-small cell lung cancer.
Kashihara M, Azuma K, Kawahara A, Basaki Y, Hattori S, Yanagawa T, Terazaki Y, Takamori S, Shirouzu K, Aizawa H, Nakano K, Kage M, Kuwano M, Ono M.
J Thorac Oncol. 2009 Sep;4(9):1066-74.
PMID 19648825
Mammalian stress granules and processing bodies.
Kedersha N, Anderson P.
Methods Enzymol. 2007;431:61-81. (REVIEW)
PMID 17923231
The pleiotropic functions of the Y-box-binding protein, YB-1.
Kohno K, Izumi H, Uchiumi T, Ashizuka M, Kuwano M.
Bioessays. 2003 Jul;25(7):691-8. (REVIEW)
PMID 12815724
The basic and clinical implications of ABC transporters, Y-box-binding protein-1 (YB-1) and angiogenesis-related factors in human malignancies.
Kuwano M, Uchiumi T, Hayakawa H, Ono M, Wada M, Izumi H, Kohno K.
Cancer Sci. 2003 Jan;94(1):9-14. (REVIEW)
PMID 12708467
A role for Y-box proteins in cell proliferation.
Ladomery M, Sommerville J.
Bioessays. 1995 Jan;17(1):9-11. (REVIEW)
PMID 7702598
Regulation of alternative splicing by SRrp86 and its interacting proteins.
Li J, Hawkins IC, Harvey CD, Jennings JL, Link AJ, Patton JG.
Mol Cell Biol. 2003 Nov;23(21):7437-47.
PMID 14559993
Cold shock domain family members YB-1 and MSY4 share essential functions during murine embryogenesis.
Lu ZH, Books JT, Ley TJ.
Mol Cell Biol. 2006 Nov;26(22):8410-7. Epub 2006 Sep 5.
PMID 16954378
Structural and functional analysis of the human Y-box binding protein (YB-1) gene promoter.
Makino Y, Ohga T, Toh S, Koike K, Okumura K, Wada M, Kuwano M, Kohno K.
Nucleic Acids Res. 1996 May 15;24(10):1873-8.
PMID 8657568
Stimulation of human endonuclease III by Y box-binding protein 1 (DNA-binding protein B). Interaction between a base excision repair enzyme and a transcription factor.
Marenstein DR, Ocampo MT, Chan MK, Altamirano A, Basu AK, Boorstein RJ, Cunningham RP, Teebor GW.
J Biol Chem. 2001 Jun 15;276(24):21242-9. Epub 2001 Apr 3.
PMID 11287425
Significance of the Y-box proteins in human cancers.
Matsumoto K, Bay BH.
J Mol Genet Med. 2005 Aug 3;1(1):11-7.
PMID 19565008
Two splicing isoforms of the Y-box protein ctYB-1 appear on the same mRNA molecule.
Nashchekin D, Masich S, Soop T, Kukalev A, Kovrigina E, Nashchekina O, Daneholt B.
FEBS J. 2007 Jan;274(1):202-11.
PMID 17222182
Different expression profiles of Y-box-binding protein-1 and multidrug resistance-associated proteins between alveolar and embryonal rhabdomyosarcoma.
Oda Y, Kohashi K, Yamamoto H, Tamiya S, Kohno K, Kuwano M, Iwamoto Y, Tajiri T, Taguchi T, Tsuneyoshi M.
Cancer Sci. 2008 Apr;99(4):726-32.
PMID 18377424
Nuclear expression of Y-box-binding protein-1 correlates with P-glycoprotein and topoisomerase II alpha expression, and with poor prognosis in synovial sarcoma.
Oda Y, Ohishi Y, Saito T, Hinoshita E, Uchiumi T, Kinukawa N, Iwamoto Y, Kohno K, Kuwano M, Tsuneyoshi M.
J Pathol. 2003 Feb;199(2):251-8.
PMID 12533839
Nuclear expression of YB-1 protein correlates with P-glycoprotein expression in human osteosarcoma.
Oda Y, Sakamoto A, Shinohara N, Ohga T, Uchiumi T, Kohno K, Tsuneyoshi M, Kuwano M, Iwamoto Y.
Clin Cancer Res. 1998 Sep;4(9):2273-7.
PMID 9748149
YB-1 transcription in the postnatal brain is regulated by a bHLH transcription factor Math2 through an E-box sequence in the 5'-UTR of the gene.
Ohashi S, Fukumura R, Higuchi T, Kobayashi S.
Mol Cell Biochem. 2009 Jul;327(1-2):267-75. Epub 2009 Feb 19.
PMID 19225866
Role of the human Y box-binding protein YB-1 in cellular sensitivity to the DNA-damaging agents cisplatin, mitomycin C, and ultraviolet light.
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Cancer Res. 1996 Sep 15;56(18):4224-8.
PMID 8797596
Direct interaction of p53 with the Y-box binding protein, YB-1: a mechanism for regulation of human gene expression.
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Oncogene. 2000 Dec 14;19(54):6194-202.
PMID 11175333
Splicing factor SRp30c interaction with Y-box protein-1 confers nuclear YB-1 shuttling and alternative splice site selection.
Raffetseder U, Frye B, Rauen T, Jurchott K, Royer HD, Jansen PL, Mertens PR.
J Biol Chem. 2003 May 16;278(20):18241-8. Epub 2003 Feb 25.
PMID 12604611
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PMID 10504297
Nuclear expression of YB-1 protein correlates with P-glycoprotein expression in human breast carcinoma.
Saji H, Toi M, Saji S, Koike M, Kohno K, Kuwano M.
Cancer Lett. 2003 Feb 20;190(2):191-7.
PMID 12565174
The increased expression of Y box-binding protein 1 in melanoma stimulates proliferation and tumor invasion, antagonizes apoptosis and enhances chemoresistance.
Schittek B, Psenner K, Sauer B, Meier F, Iftner T, Garbe C.
Int J Cancer. 2007 May 15;120(10):2110-8.
PMID 17266041
Enhanced coexpression of YB-1 and DNA topoisomerase II alpha genes in human colorectal carcinomas.
Shibao K, Takano H, Nakayama Y, Okazaki K, Nagata N, Izumi H, Uchiumi T, Kuwano M, Kohno K, Itoh H.
Int J Cancer. 1999 Dec 10;83(6):732-7.
PMID 10597187
Twist promotes tumor cell growth through YB-1 expression.
Shiota M, Izumi H, Onitsuka T, Miyamoto N, Kashiwagi E, Kidani A, Yokomizo A, Naito S, Kohno K.
Cancer Res. 2008 Jan 1;68(1):98-105.
PMID 18172301
The major messenger ribonucleoprotein particle protein p50 (YB-1) promotes nucleic acid strand annealing.
Skabkin MA, Evdokimova V, Thomas AA, Ovchinnikov LP.
J Biol Chem. 2001 Nov 30;276(48):44841-7. Epub 2001 Oct 3.
PMID 11585833
Activities of cold-shock domain proteins in translation control.
Sommerville J.
Bioessays. 1999 Apr;21(4):319-25. (REVIEW)
PMID 10377894
Proteasome-mediated cleavage of the Y-box-binding protein 1 is linked to DNA-damage stress response.
Sorokin AV, Selyutina AA, Skabkin MA, Guryanov SG, Nazimov IV, Richard C, Th'ng J, Yau J, Sorensen PH, Ovchinnikov LP, Evdokimova V.
EMBO J. 2005 Oct 19;24(20):3602-12. Epub 2005 Sep 29.
PMID 16193061
Hyperthermia-induced nuclear translocation of transcription factor YB-1 leads to enhanced expression of multidrug resistance-related ABC transporters.
Stein U, Jurchott K, Walther W, Bergmann S, Schlag PM, Royer HD.
J Biol Chem. 2001 Jul 27;276(30):28562-9. Epub 2001 May 21.
PMID 11369762
The RNA binding protein YB-1 binds A/C-rich exon enhancers and stimulates splicing of the CD44 alternative exon v4.
Stickeler E, Fraser SD, Honig A, Chen AL, Berget SM, Cooper TA.
EMBO J. 2001 Jul 16;20(14):3821-30.
PMID 11447123
Akt phosphorylates the Y-box binding protein 1 at Ser102 located in the cold shock domain and affects the anchorage-independent growth of breast cancer cells.
Sutherland BW, Kucab J, Wu J, Lee C, Cheang MC, Yorida E, Turbin D, Dedhar S, Nelson C, Pollak M, Leighton Grimes H, Miller K, Badve S, Huntsman D, Blake-Gilks C, Chen M, Pallen CJ, Dunn SE.
Oncogene. 2005 Jun 16;24(26):4281-92.
PMID 15806160
Role of single-stranded DNA regions and Y-box proteins in transcriptional regulation of viral and cellular genes.
Swamynathan SK, Nambiar A, Guntaka RV.
FASEB J. 1998 May;12(7):515-22. (REVIEW)
PMID 9576478
p73 Interacts with c-Myc to regulate Y-box-binding protein-1 expression.
Uramoto H, Izumi H, Ise T, Tada M, Uchiumi T, Kuwano M, Yasumoto K, Funa K, Kohno K.
J Biol Chem. 2002 Aug 30;277(35):31694-702. Epub 2002 Jun 21.
PMID 12080043
Development of drug resistance in the population of colon cancer cells under the effect of multifunctional protein YB-1.
Vaiman AV, Stromskaya TP, Rybalkina EY, Sorokin AV, Ovchinnikov LP, Stavrovskaya AA.
Bull Exp Biol Med. 2007 Apr;143(4):463-6.
PMID 18214301
Y-box-binding protein-1 is a potential novel tumour marker for neuroblastoma.
Wachowiak R, Thieltges S, Rawnaq T, Kaifi JT, Fiegel H, Metzger R, Quaas A, Mertens PR, Till H, Izbicki JR.
Anticancer Res. 2010 Apr;30(4):1239-42.
PMID 20530434
The Y-box factors: a family of nucleic acid binding proteins conserved from Escherichia coli to man.
Wolffe AP, Tafuri S, Ranjan M, Familari M.
New Biol. 1992 Apr;4(4):290-8. (REVIEW)
PMID 1622927
Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins.
Wolffe AP.
Bioessays. 1994 Apr;16(4):245-51. (REVIEW)
PMID 8031301
Nuclear expression of YB-1 in diffuse large B-cell lymphoma: correlation with disease activity and patient outcome.
Xu W, Zhou L, Qin R, Tang H, Shen H.
Eur J Haematol. 2009 Oct;83(4):313-9. Epub 2009 Jun 2.
PMID 19500133
Increased nuclear localization of transcription factor YB-1 in acquired cisplatin-resistant ovarian cancer.
Yahata H, Kobayashi H, Kamura T, Amada S, Hirakawa T, Kohno K, Kuwano M, Nakano H.
J Cancer Res Clin Oncol. 2002 Nov;128(11):621-6. Epub 2002 Oct 22.
PMID 12458343


This paper should be referenced as such :
Evdokimova, V ; Sorokin, A
YBX1 (Y box binding protein 1)
Atlas Genet Cytogenet Oncol Haematol. 2011;15(7):598-604.
Free journal version : [ pdf ]   [ DOI ]

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(9;13)(p12;q21) PAX5::DACH1

External links


HGNC (Hugo)YBX1   8014
Entrez_Gene (NCBI)YBX1    Y-box binding protein 1
AliasesBP-8; CBF-A; CSDA2; CSDB; 
GeneCards (Weizmann)YBX1
Ensembl hg19 (Hinxton)ENSG00000065978 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000065978 [Gene_View]  ENSG00000065978 [Sequence]  chr1:42682418-42703805 [Contig_View]  YBX1 [Vega]
ICGC DataPortalENSG00000065978
TCGA cBioPortalYBX1
AceView (NCBI)YBX1
Genatlas (Paris)YBX1
SOURCE (Princeton)YBX1
Genetics Home Reference (NIH)YBX1
Genomic and cartography
GoldenPath hg38 (UCSC)YBX1  -     chr1:42682418-42703805 +  1p34.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)YBX1  -     1p34.2   [Description]    (hg19-Feb_2009)
GoldenPathYBX1 - 1p34.2 [CytoView hg19]  YBX1 - 1p34.2 [CytoView hg38]
Genome Data Viewer NCBIYBX1 [Mapview hg19]  
Gene and transcription
Genbank (Entrez)AK309996 AK311708 BC000064 BC002411 BC010430
RefSeq transcript (Entrez)NM_004559
Consensus coding sequences : CCDS (NCBI)YBX1
Gene ExpressionYBX1 [ NCBI-GEO ]   YBX1 [ EBI - ARRAY_EXPRESS ]   YBX1 [ SEEK ]   YBX1 [ MEM ]
Gene Expression Viewer (FireBrowse)YBX1 [ Firebrowse - Broad ]
GenevisibleExpression of YBX1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4904
GTEX Portal (Tissue expression)YBX1
Human Protein AtlasENSG00000065978-YBX1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP67809   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP67809  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP67809
Domaine pattern : Prosite (Expaxy)CSD_1 (PS00352)    CSD_2 (PS51857)   
Domains : Interpro (EBI)CSD    CSD_1    CSP_DNA-bd    NA-bd_OB-fold   
Domain families : Pfam (Sanger)CSD (PF00313)   
Domain families : Pfam (NCBI)pfam00313   
Domain families : Smart (EMBL)CSP (SM00357)  
Conserved Domain (NCBI)YBX1
PDB (RSDB)1H95    5YTS    5YTT    5YTV    5YTX    6A6L    6KTC    6KUG    6LMR    6LMS   
PDB Europe1H95    5YTS    5YTT    5YTV    5YTX    6A6L    6KTC    6KUG    6LMR    6LMS   
PDB (PDBSum)1H95    5YTS    5YTT    5YTV    5YTX    6A6L    6KTC    6KUG    6LMR    6LMS   
PDB (IMB)1H95    5YTS    5YTT    5YTV    5YTX    6A6L    6KTC    6KUG    6LMR    6LMS   
Structural Biology KnowledgeBase1H95    5YTS    5YTT    5YTV    5YTX    6A6L    6KTC    6KUG    6LMR    6LMS   
SCOP (Structural Classification of Proteins)1H95    5YTS    5YTT    5YTV    5YTX    6A6L    6KTC    6KUG    6LMR    6LMS   
CATH (Classification of proteins structures)1H95    5YTS    5YTT    5YTV    5YTX    6A6L    6KTC    6KUG    6LMR    6LMS   
AlphaFold pdb e-kbP67809   
Human Protein Atlas [tissue]ENSG00000065978-YBX1 [tissue]
Protein Interaction databases
IntAct (EBI)P67809
Ontologies - Pathways
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  mRNA splicing, via spliceosome  in utero embryonic development  nucleic acid binding  DNA binding  chromatin binding  double-stranded DNA binding  single-stranded DNA binding  RNA binding  RNA binding  mRNA binding  protein binding  extracellular region  nucleus  nucleoplasm  U12-type spliceosomal complex  cytoplasm  cytosol  regulation of transcription, DNA-templated  Notch signaling pathway  epidermis development  regulation of gene expression  cytoplasmic stress granule  negative regulation of translation  nuclear membrane  miRNA binding  intracellular membrane-bounded organelle  positive regulation of transcription by RNA polymerase II  mRNA stabilization  embryonic morphogenesis  RNA transport  GTPase binding  tRNA transport  negative regulation of striated muscle cell differentiation  positive regulation of cell division  C5-methylcytidine-containing RNA binding  extracellular exosome  extracellular exosome  CRD-mediated mRNA stabilization  CRD-mediated mRNA stability complex  histone pre-mRNA 3'end processing complex  cellular response to interleukin-7  protein localization to cytoplasmic stress granule  messenger ribonucleoprotein complex  miRNA transport  sequence-specific double-stranded DNA binding  ribonucleoprotein complex  negative regulation of cellular senescence  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  mRNA splicing, via spliceosome  in utero embryonic development  nucleic acid binding  DNA binding  chromatin binding  double-stranded DNA binding  single-stranded DNA binding  RNA binding  RNA binding  mRNA binding  protein binding  extracellular region  nucleus  nucleoplasm  U12-type spliceosomal complex  cytoplasm  cytosol  regulation of transcription, DNA-templated  Notch signaling pathway  epidermis development  regulation of gene expression  cytoplasmic stress granule  negative regulation of translation  nuclear membrane  miRNA binding  intracellular membrane-bounded organelle  positive regulation of transcription by RNA polymerase II  mRNA stabilization  embryonic morphogenesis  RNA transport  GTPase binding  tRNA transport  negative regulation of striated muscle cell differentiation  positive regulation of cell division  C5-methylcytidine-containing RNA binding  extracellular exosome  extracellular exosome  CRD-mediated mRNA stabilization  CRD-mediated mRNA stability complex  histone pre-mRNA 3'end processing complex  cellular response to interleukin-7  protein localization to cytoplasmic stress granule  messenger ribonucleoprotein complex  miRNA transport  sequence-specific double-stranded DNA binding  ribonucleoprotein complex  negative regulation of cellular senescence  
Pathways : BIOCARTATranscriptional activation of dbpb from mRNA [Genes]   
REACTOMEP67809 [protein]
REACTOME PathwaysR-HSA-9017802 [pathway]   
NDEx NetworkYBX1
Atlas of Cancer Signalling NetworkYBX1
Wikipedia pathwaysYBX1
Orthology - Evolution
GeneTree (enSembl)ENSG00000065978
Phylogenetic Trees/Animal Genes : TreeFamYBX1
Homologs : HomoloGeneYBX1
Homology/Alignments : Family Browser (UCSC)YBX1
Gene fusions - Rearrangements
Fusion Cancer (Beijing)YBX1 [1p34.2]  -  MUC1 [1q22]  [FUSC003046]
Fusion : QuiverYBX1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerYBX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)YBX1
Exome Variant ServerYBX1
GNOMAD BrowserENSG00000065978
Varsome BrowserYBX1
ACMGYBX1 variants
Genomic Variants (DGV)YBX1 [DGVbeta]
DECIPHERYBX1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisYBX1 
ICGC Data PortalYBX1 
TCGA Data PortalYBX1 
Broad Tumor PortalYBX1
OASIS PortalYBX1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICYBX1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DYBX1
Mutations and Diseases : HGMDYBX1
intOGen PortalYBX1
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
DgiDB (Drug Gene Interaction Database)YBX1
DoCM (Curated mutations)YBX1
CIViC (Clinical Interpretations of Variants in Cancer)YBX1
NCG (London)YBX1
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry YBX1
NextProtP67809 [Medical]
Target ValidationYBX1
Huge Navigator YBX1 [HugePedia]
Clinical trials, drugs, therapy
Protein Interactions : CTDYBX1
Pharm GKB GenePA31791
Clinical trialYBX1
DataMed IndexYBX1
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Oct 8 21:31:07 CEST 2021

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