The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
The intranuclear localization and function of YT521-B is regulated by tyrosine phosphorylation
Abstract
YT521-B is a ubiquitously expressed nuclear protein that changes alternative splice site usage in a concentration dependent manner. YT521-B is located in a dynamic nuclear compartment, the YT body. We show that YT521-B is tyrosine phosphorylated by c-Abl in the nucleus. The protein shuttles between nucleus and cytosol, where it can be phosphorylated by c-Src or p59(fyn). Tyrosine phosphorylation causes dispersion of YT521-B from YT bodies to the nucleoplasm. Whereas YT bodies are soluble in non-denaturing buffers, the phosphorylated, dispersed form is non-soluble. Non-phosphorylated YT521-B changes alternative splice site selection of the IL-4 receptor, CD44 and SRp20, but phosphorylation of c-Abl minimizes this concentration dependent effect. We propose that tyrosine phosphorylation causes sequestration of YT521-B in an insoluble nuclear form, which abolishes the ability of YT521-B to change alternative splice sites.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Although YTHDC1 has been shown to affect alternative splicing of select mRNAs (Rafalska et al., 2004; Xiao et al., 2016; Zhang et al., 2010)”
From YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs (2017) · cites this paper as Rafalska et al., 2004
Citations
Cites
Listening to silence and understanding nonsense: exonic mutations that affect splicing
Cartegni, L., Chew, S. L., & Krainer, A. R. (2002) · Nature Reviews Genetics · doi:10.1038/nrg775 · Cited by 2,209
Signal-dependent regulation of splicing via phosphorylation of Sam68
Matter, N., Herrlich, P., & König, H. (2002) · Nature · doi:10.1038/nature01153 · Cited by 458
Research works printed but not linked: 69
- Sacco-Bubulya, P. and Spector, D.L. (2002) Disassembly of interchromatin granule clusters alters the coordination of transcription and pre-mRNA splicing. J. Cell Biol., 156, 425–436. · DOI
- Misteli, T., Cáceres, J.F. and Spector, D.L. (1997) The dynamics of a pre-mRNA splicing factor in living cells. Nature, 387, 523–527. · DOI
- Lamond, A.I. and Spector, D.L. (2003) Nuclear speckles: a model for nuclear organelles. Nat. Rev. Mol. Cell Biol., 4, 605–612. · DOI
- Iborra, F.J. and Cook, P.R. (2002) The interdependence of nuclear structure and function. Curr. Opin. Cell Biol., 14, 780–785. · DOI
- Imai, Y., Matsuo, N., Ogawa, S., Tohyama, M. and Takagi, T. (1998) Cloning of a gene, YT521, for a novel RNA splicing-related protein induced by hypoxia/reoxygenation. Brain Res. Mol. Brain Res., 53, 33–40. · DOI
- Hartmann, A.M., Nayler, O., Schwaiger, F.W., Obermeier, A. and Stamm, S. (1999) The interaction and colocalization of Sam68 with the splicing- associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59(fyn). Mol. Biol. Cell, 10, 3909–3926. · DOI
- Stoilov, P., Rafalska, I. and Stamm, S. (2002) YTH: a new domain in nuclear proteins. Trends Biochem. Sci., 27, 495–496. · DOI
- Modrek, B., Resch, A., Grasso, C. and Lee, C. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucl. Acids Res., 29, 2850–2859. · DOI
- Johnson, J.M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.D., Santos, R., Schadt, E.E., Stoughton, R. and Shoemaker, D.D. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302, 2141–2144. · DOI
- Black, D.L. (2003) Mechanisms of Alternative Pre-Messenger RNA Splicing. Annu. Rev. Biochem., 72, 291–336 · DOI · Paper page
- Cramer, P., Srebrow, A., Kadener, S., Werbajh, S., de la Mata, M., Melen, G., Nogues, G. and Kornblihtt, A.R. (2001) Coordination between transcription and pre-mRNA processing. FEBS Lett., 498, 179–182. · DOI
- Maniatis, T. and Tasic, B. (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature, 418, 236–243. · DOI
- Smith, C.W. and Valcarcel, J. (2000) Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci., 25, 381–388. · DOI
- Roberts, G.C. and Smith, C.W. (2002) Alternative splicing: combinatorial output from the genome. Curr. Opin. Chem. Biol., 6, 375–383. · DOI
- Stoilov, P., Daoud, R., Nayler, O. and Stamm, S. (2004) Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA. Hum. Mol. Genet., 13, 509–524. · DOI
- Thanaraj, T.A., Stamm, S., Clark, F., Riethoven, J.J., Le Texier, V. and Muilu, J. (2004) ASD: the Alternative Splicing Database. Nucl. Acids Res., 32, D64–69. · DOI
- Xu, Q., Modrek, B. and Lee, C. (2002) Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucl. Acids Res., 30, 3754–3766. · DOI
- Stoilov, P., Meshorer, E., Gencheva, M., Glick, D., Soreq, H. and Stamm, S. (2002) Defects in pre-mRNA processing as causes of and predisposition to diseases. DNA Cell Biol., 21, 803–818. · DOI
- Meshorer, E., Erb, C., Gazit, R., Pavlovsky, L., Kaufer, D., Friedman, A., Glick, D., Ben-Arie, N. and Soreq, H. (2002) Alternative splicing and neuritic mRNA translocation under long-term neuronal hypersensitivity. Science, 295, 508–512. · DOI
- van der Houven van Oordt, W., Diaz-Meco, M.T., Lozano, J., Krainer, A.R., Moscat, J. and Caceres, J.F. (2000) The MKK(3/6)-p38-signaling cascade alters the subcellular distribution of hnRNP A1 and modulates alternative splicing regulation. J. Cell Biol., 149, 307–316. · DOI
- Daoud, R., Mies, G., Smialowska, A., Oláh, L., Hossmann, K. and Stamm, S. (2002) Ischemia induces a translocation of the splicing factor tra2-beta1 and changes alternative splicing patterns in the brain. J. Neurosci., 22, 5889–5899. · DOI
- Amir-Ahmady, B. and Salati, L.M. (2001) Regulation of the processing of glucose-6-phosphate dehydrogenase mRNA by nutritional status. J. Biol. Chem., 276, 10 514–10 523. · DOI
- Daoud, R., Da Penha Berzaghi, M., Siedler, F., Hubener, M. and Stamm, S. (1999) Activity-dependent regulation of alternative splicing patterns in the rat brain. Eur. J. Neurosci., 11, 788–802. · DOI
- Xie, J. and Black, D.L. (2001) A CaMK IV responsive RNA element mediates depolarization-induced alternative splicing of ion channels. Nature, 410, 936–939. · DOI
- Stork, O., Stork, S., Pape, H.C. and Obata, K. (2001) Identification of genes expressed in the amygdala during the formation of fear memory. Learn. Mem., 8, 209–219. · DOI
- Weg-Remers, S., Ponta, H., Herrlich, P. and Konig, H. (2001) Regulation of alternative pre-mRNA splicing by the ERK MAP-kinase pathway. EMBO J., 20, 4194–4203. · DOI
- Chalfant, C.E., Watson, J.E., Bisnauth, L.D., Kang, J.B., Patel, N., Obeid, L.M., Eichler, D.C. and Cooper, D.R. (1998) Insulin regulates protein kinase CbetaII expression through enhanced exon inclusion in L6 skeletal muscle cells. A novel mechanism of insulin- and insulin-like growth factor-i-induced 5′ splice site selection. J. Biol. Chem., 273, 910–916. · DOI
- Stamm, S. (2002) Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome. Hum. Mol. Genet., 11, 2409–2416. · DOI
- Rothrock, C., Cannon, B., Hahm, B. and Lynch, K.W. (2003) A conserved signal-responsive sequence mediates activation-induced alternative splicing of CD45. Mol. Cell, 12, 1317–1324. · DOI
- Ishizuka, T., Kajita, K., Yamada, K., Miura, A., Kanoh, Y., Ishizawa, M., Wada, H., Itaya, S., Yamamoto, M., Yasuda, K. et al. (1996) Insulin regulated PKC isoform mRNA in rat adipocytes. Diabetes Res. Clin. Pract., 33, 159–167. · DOI
- Scotet, E. and Houssaint, E. (1998) Exon III splicing switch of fibroblast growth factor (FGF) receptor-2 and -3 can be induced by FGF-1 or FGF-2. Oncogene, 17, 67–76. · DOI
- Smith, M.A., Fanger, G.R., O'Connor, L.T., Bridle, P. and Maue, R.A. (1997) Selective regulation of agrin mRNA induction and alternative splicing in PC12 Cells by Ras-dependent actions of nerve growth factor. J. Biol. Chem., 272, 15675–15681. · DOI
- Cans, C., Mangano, R., Barila, D., Neubauer, G. and Superti-Furga, G. (2000) Nuclear tyrosine phosphorylation: the beginning of a map. Biochem. Pharmacol., 60, 1203–1215. · DOI
- Pendergast, A.M. (1996) Nuclear tyrosine kinases: from Abl to Wee1. Curr. Opin. Cell Biol., 8, 174–181. · DOI
- Robinson, D.R., Wu, Y.-M. and Lin, S.-F. (2000) The protein tyrosine kinase family of the human genome. Oncogene, 19, 5548–5557. · DOI
- Nayler, O., Hartmann, A.M. and Stamm, S. (2000) The ER-repeat protein YT521-B localizes to a novel subnuclear compartment. J. Cell Biol., 150, 949–961. · DOI
- Taagepera, S., McDonald, D., Loeb, J.E., Whitaker, L.L., McElroy, A.K., Wang, J.Y. and Hope, T.J. (1998) Nuclear-cytoplasmic shuttling of C-ABL tyrosine kinase. Proc. Natl Acad. Sci. USA, 95, 7457–7462. · DOI
- Debnath, J., Chamorro, M., Czar, M.J., Schaeffer, E.M., Lenardo, M.J., Varmus, H.E. and Schwartzberg, P.L. (1999) rlk/TXK encodes two forms of a novel cysteine string tyrosine kinase activated by Src family kinases. Mol. Cell. Biol., 19, 1498–1507. · DOI
- Van Etten, R.A. (1999) Cycling, stressed-out and nervous: cellular functions of c-Abl. Trends Cell Biol., 9, 179–186. · DOI
- Rongish, B.J. and Kinsey, W.H. (2000) Transient nuclear localization of Fyn kinase during development in zebrafish. Anat. Rec., 260, 115–123. · DOI
- Caceres, J.F., Screaton, G.R. and Krainer, A.R. (1998) A specific subset of SR proteins shuttles continously between the nucleus and the cytoplasm. Genes Dev., 12, 55–66. · DOI
- Neumann, M., Afonina, E., Ceccherini-Silberstein, F., Schlicht, S., Erfle, V., Pavlakis, G.N. and Brack-Werner, R. (2001) Nucleocytoplasmic transport in human astrocytes: decreased nuclear uptake of the HIV Rev shuttle protein. J. Cell Sci., 114, 1717–1729. · DOI
- Lee, S., Neumann, M., Stearman, R., Stauber, R., Pause, A., Pavlakis, G.N. and Klausner, R.D. (1999) Transcription-dependent nuclear-cytoplasmic trafficking is required for the function of the von Hippel-Lindau tumor suppressor protein. Mol. Cell. Biol., 19, 1486–1497. · DOI
- Wrighton, N., Campbell, L.A., Harada, N., Miyajima, A. and Lee, F. (1992) The murine interleukin-4 receptor gene: genomic structure, expression and potential for alternative splicing. Growth Factors, 6, 103–118. · DOI
- Stoss, O., Stoilov, P., Hartmann, A.M., Nayler, O. and Stamm, S. (1999) The in vivo minigene approach to analyze tissue-specific splicing. Brain Research Protocols, 4, 383–394. · DOI
- Buckanovich, R.J. and Darnell, R.B. (1997) The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo. Mol. Cell. Biol., 17, 3194–3201. · DOI · Paper page
- Abdennebi, L., Lesport, A.S., Remy, J.J., Grebert, D., Pisselet, C., Monniaux, D. and Salesse, R. (2002) Differences in splicing of mRNA encoding LH receptor in theca cells according to breeding season in ewes. Reproduction, 123, 819–826. · DOI
- Holdiman, A.J., Fergus, D.J. and England, S.K. (2002) 17beta-Estradiol upregulates distinct maxi-K channel transcripts in mouse uterus. Mol. Cell. Endocrinol., 192, 1–6. · DOI
- Stoss, O., Olbrich, M., Hartmann, A.M., Konig, H., Memmott, J., Andreadis, A. and Stamm, S. (2001) The STAR/GSG family protein rSLM-2 regulates the selection of alternative splice sites. J. Biol. Chem., 276, 8665–8673. · DOI
- Matera, A.G. (1999) Nuclear bodies: multifaceted subdomains of the interchromatin space. Trends Cell Biol., 9, 302–309. · DOI
- Lamond, A.I. and Earnshaw, W.C. (1998) Structure and function in the nucleus. Science, 280, 547–553. · DOI
- Spector, D.L. (2003) The dynamics of chromosome organization and gene regulation. Annu. Rev. Biochem., 72, 573–608. · DOI
- Nayler, O., Schnorrer, F., Stamm, S. and Ullrich, A. (1998) The cellular localization of the murine serine/arginine-rich protein kinase CLK2 is regulated by serine 141 autophosphorylation. J. Biol. Chem., 273, 34341–34348. · DOI
- Stojdl, D.F. and Bell, J.C. (1999) SR protein kinases: the splice of life. Biochem. Cell Biol., 77, 293–298. · DOI
- Hartmann, A.M., Rujescu, D., Giannakouros, T., Nikolakaki, E., Goedert, M., Mandelkow, E.M., Gao, Q.S., Andreadis, A. and Stamm, S. (2001) Regulation of alternative splicing of human tau exon 10 by phosphorylation of splicing factors. Mol. Cell. Neurosci., 18, 80–90. · DOI
- Shin, C., Feng, Y. and Manley, J.L. (2004) Dephosphorylated SRp38 acts as a splicing repressor in response to heat shock. Nature, 427, 553–558. · DOI
- Baskaran, R., Dahmus, M.E. and Wang, J.Y. (1993) Tyrosine phosphorylation of mammalian RNA polymerase II carboxyl-terminal domain. Proc. Natl Acad. Sci. USA, 90, 11 167–11 171. · DOI
- Welch, P.J. and Wang, J.Y. (1993) A C-terminal protein-binding domain in the retinoblastoma protein regulates nuclear c-Abl tyrosine kinase in the cell cycle. Cell, 75, 779–790. · DOI
- Darnell, J.E., Jr (1997) Phosphotyrosine signaling and the single cell:metazoan boundary. Proc. Natl Acad. Sci. USA, 94, 11 767–11 769. · DOI
- Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O. and Zhang, M.Q. (2000) An alternative-exon database and its statistical analysis. DNA Cell Biol., 19, 739–756. · DOI
- Maniatis, T. and Reed, R. (2002) An extensive network of coupling among gene expression machines. Nature, 416, 499–506. · DOI
- Wu, J.Y. and Maniatis, T. (1993) Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell, 75, 1061–1070. · DOI
- Cazalla, D., Zhu, J., Manche, L., Huber, E., Krainer, A.R. and Caceres, J.F. (2002) Nuclear export and retention signals in the RS domain of SR proteins. Mol. Cell. Biol., 22, 6871–6882. · DOI
- Xu, Q. and Lee, C. (2003) Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucl. Acids Res., 31, 5635–5643. · DOI
- Hao, Q.-L., Ferris, D.K., White, G., Heisterkamp, N. and Groffen, J. (1991) Nuclear and cytoplasmic location of the FER tyrosine kinase. Mol. Cell. Biol., 11, 1180–1183. · DOI
- Derry, J.J., Richard, S., Carvajal, H.V., YE, X., Vasioukhin, V., Cochrane, A.W., Chen, T. and Tyner, A.L. (2000) Sik (BRK) phosphorylates Sam68 in the nucleus and negatively regulates its RNA binding ability. Mol. Cell. Biol., 20, 6114–6126. · DOI
- Zhang, J., Berenstein, E.H., Evans, R.L. and Siraganian, R.P. (1996) Transfection of Syk protein tyrosine kinase reconstitutes high affinity IgE receptor-mediated degranulation in a Syk-negative variant of rat basophilic leukemia RBL-2H3 cells. J. Exp. Med., 184, 71–79. · DOI
- König, H., Ponta, H. and Herrlich, P. (1998) Coupling of signal transduction to alternative pre-mRNA splicing by a composite splice regulator. EMBO J., 17, 2904–2913. · DOI
- Jumaa, H. and Nielsen, P.J. (1997) The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation. EMBO J., 16, 5077–5085. · DOI
Cited by
YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs
Roundtree, I. A., Luo, G.-Z., Zhang, Z., Wang, X., Zhou, T., Cui, Y., Sha, J., Huang, X., Guerrero, L., Xie, P., et al. (2017) · eLife · doi:10.7554/elife.31311 · Cited by 1,256
Self-citation
Metadata
- Authors
- Rafalska, I., Zhang, Z., Benderska, N., Wolff, H., Hartmann, A. M., Brack-Werner, R., & Stamm, S.
- Venue
- Human Molecular Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-06-02
- Volume
- 13
- Issue
- 15
- Pages
- 1535-1549
- ISSN
- 1460-2083
- 0964-6906
- Cited by
- 54
- References
- 2
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.