Dr. Fu's lab

Publications

1985-1989 | 1990-1999 | 2000-2008 | 

1. Fu, X-D., Phillips, N., Jentoft, J., Tuazon, P., Traugh, J., and Leis. J. (1985). Site-specific phosphorylation of avian retrovirus nucleocapsid protein pp12 regulates binding to viral RNA. J. Biol. Chem. 260:9941-9947.

2.Katz, R., Fu, X-D., Tuazon, P., Traugh, J., Skalka, A., and Leis, J. (1986). Expression of the avian retrovirus nucleocapsid protein, pp12, in E. coli: Bacterially produced protein has biochemical properties identical to unphosphorylated viral protein. Gene 50:361-369.

3. Fu, X-D., Tuazon, P., Traugh, J., and Leis, L. (1988). Site-directed mutagenesis of the avian retrovirus nucleocapsid protein, pp12, at serine 40, the primary site of phosphorylation in vivo. J. Biol. Chem. 263:2134-2139.

4. Fu, X-D., Katz, R., Skalka, A., and Leis, J. (1988). Site-directed mutagenesis of the avian retrovirus nucleocapsid protein, pp12: Mutation which affects RNA binding in vitro blocks viral replication. J. Biol. Chem. 263:2140-2145.

5. Jentoft, J., Smith, L., Fu, X-D., Johnson, M., and Leis, J. (1988). Conserved cysteine and histidine residues of the AMV nucleocapsid protein are essential for viral replication, but are not zinc-binding fingers. Proc. Natl. Acad. Sci. USA 85:7094-7098.

6. Leis, J., Phillips, N., Fu, X-D., Tuazon, P., and Traugh, J. (1989). Phosphorylation of the avian retrovirus matrix protein by Ca++-phospholipid-dependent protein kinase. Eur. J. Biochem. 179:415-422.

7. Goto, T. and Fu, X-D. (1990). Spliceosome. Cell Technology (Japan) 9(9):75-82.

8. Fu, X-D. and Maniatis, T. (1990). Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343:437-441.

9. Fu, X-D., Katz, R., Skalka, A. M., and Maniatis, T. (1991). The role of branchpoint and 3'-exon sequences in the control of balanced splicing of retrovirus RNA. Genes Dev. 5:211-220.

10. Spector, D., Fu, X-D., and Maniatis, T. (1991). Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J. 10:3467-3481.

11. Fu, X-D. and Maniatis, T. (1992). The mammalian splicing factor SC35 mediates specific interactions between U1 and U2 snRNPs at the 3' splice site. Proc. Natl. Acad. Sci. USA 89:1725-1729.

12. Fu, X-D. and Maniatis, T. (1992). Isolation of a cDNA that encodes the mammalian splicing factor SC35. Science 256:535-538.

13. Fu, X-D. , Mayeda, A., Maniatis, T., and Krainer, A. R. (1992). General splicing factors SF2 and SC35 have equivalent activities in vitro, and both affect alternative 5' and 3' splice site selection. Proc. Natl. Acad. Sci. USA 89:11224-11228.

14. Fu, X-D. (1993). Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365:82-85.

15. Imai, H., Chan, E. K. L., Kiyosawa, K. Fu, X-D., and Tan, E. M. (1993). Novel nuclear autoantigen with splicing factor motifs identified with antibody from hepatocellular carcinoma. J. Clinical Investigation, 92:2419-2426.

16. Gui, J-F., Lane, W. S., and Fu, X-D. (1994). A serine kinase regulates the intracellular localization of splicing factors during the cell cycle. Nature 369:678-682.

17. Gui, J-F., Tronchere, H., Chandler, S., and Fu, X-D. (1994). Purification and characterization of a kinase specific for the serine and arginine-rich pre-mRNA splicing factors. Proc. Natl. Acad. Sci. USA 91:10824-10828.

18. Bouck, J., Fu, X-D., Skalka, A. M., and Katz, R. A. (1995). Genetic selection for balanced splicing: Novel regulation involving the second step can be mediated by transitions in the polypyrimidine tract. Mol. Cell. Biol. 15:2663-2670.

19. Bermingham, J. R., Arden, K. C., Naumova, A. K., Sapienza, C., Viars, C. S., Fu, X-D., Khotz, J., Manely, J. L., and Rosenfeld, M. G. (1995). Chromosomal localization of mouse and human genes encoding the splicing factors ASF/SF2 (Sfrs1) and SC35 (Sfrs2). Genomics 29:70-79.

20. Malatesta, M., Zancamaro, C., Tamburini, M., Martin, T. E., Fu, X-D., Vogel, P., and Fakan, S. (1995). Novel nuclear ribonucleoprotein structural components in the dormouse adrenal cortex during hibernation. Chromosoma 104:121-128.

21. Fu, X-D. (1995). The superfamily of arginine/serine-rich splicing factors. RNA 1:663-680.

22. Kopecny, V., Biggiogera, M., Laurincik, J., Pivko, J., Grafenau, P., Martin, T. F., Fu, X-D., and Fakan, S. (1996). Fine structural cytochemical and immunocytochemical analysis of nucleic acids and ribonucleoprotein distribution in nuclei of pig oocytes and early preimplantation embryos. Chromosoma 104:561-574.

23. Yeakley, J. M., Morfin, J-P., Rosenfeld, M. G., and Fu, X-D. (1996). A complex of nuclearproteins mediates SR protein binding to a purine-rich splicing enhancer. Proc. Natl. Acad. Sci. USA 93:7582-7587.

24. Tamburini, M., Malatesta, M., Zancanaro, C., Martin, T. E., Fu, X-D., Vogel, P., and Fakan, S. (1996). Dense granular bodies: a novel nucleoplasmic structure in hibernating dormice. Histochem. Cell. Biol. 106:581-586.

25. Colwill, K., Feng, L. L., Yeakley, J. M., Gish, G. D., Caceres, J. F., Pawson, T., and Fu, X-D. (1996). SRPK1 and Clk/Sty protein kinases show distinct substrate specificities for Serine/Arginine-rich splicing factors. J. Biol. Chem. 271:24569-24575.

26. Chandler, S. D., Mayeda, A., Yeakley, J. M., Krainer, A. R., and Fu, X-D. (1997). RNA splicing specificity determined by the coordinated action of the RNA recognition motifs in SR proteins. Proc. Natl. Acad. Sci. USA. 94:3596-3601.

27. Tronchere, H., Wang, J. and Fu, X-D. (1997). A protein related to U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA. Nature 388:397-400.

28. Wang, H-Y., Lin, W., Dyck, J. A., Yeakley, J. M., Songyang, Z., Cantley, L. C., and Fu, X-D. (1998). SRPK2: A differentially expressed SR protein-specific kinase involved in mediating the interaction and localization of pre-mRNA splicing factors in mammalian cells. J. Cell Biol. 140:737-750.

29. Bouck, J., Fu, X-D., Skalka, A. M., and Katz, R. (1998). Role of the constitutive splicing U2AF65 and SAP49 in suboptimal RNA splicing of novel retroviral mutants. J. Biol. Chem. 273:15169-15176.

30. Cmarko, D., Verschure, P. J., Martin, T. E., Dahmus, M. E., Krause, S., Fu, X-D., van Driel, R., and Fakan, S. (1999). Ultrastructural analysis of transcription and splicing in the cell nucleus after BrUTP-microinjection. Mol. Biol. Cell. 10:211-223.

31. Mayeda, A., Screaton, G. R., Chandler, S. D., Fu, X-D., and Krainer, A. R. (1999). Substrate Specificities of SR proteins in constitutive splicing are determined by their RRMs and composite exonic elements. Mol. Cell Biol. 19:1853-1863.

32. Wang, H-Y., Arden, K. C., Bermingham, J. R., Viars, C. S., Lin, W., Boyer, A. D., and Fu, X-D. (1999). Localization of serine kinases, SRPK1 (SFRSK1) and SRPK2 (SFRSK2), specific for the SR family of splicing factors in mouse and human chromosomes. Genomics. 57:310-315.

33. Siebel, C. W., Feng,, L., Guthrie, C., and Fu, X-D. (1999). Conservation in budding yeast of a kinase specific for SR splicing factors. Proc. Natl. Acad. Sci. USA. 96:5440-5445.

34. Yeakley, J. M., Tronchère, H., Olesen, J., Dyck, J. A., Wang, H-Y., and Fu, X-D. (1999). Phosphorylation regulates in vivo interaction and molecular targeting of serine/arginine-rich pre-mRNA splicing factors. J. Cell Biol. 145:447-455.

35. Yun, C. Y. and Fu, X-D. (2000). Conserved SR protein kinase functions in regulated nuclear import and its action is counteracted by arginine methylation in Saccharomyces cerevisiae. J. Cell Biol. 150:707-717.

36. Nolen, B., Yun, C. Y., Wong, C. F., McCammon, A., Fu, X-D., and Ghosh, G. (2001). The structure of Sky1p reveals a novel mechanism for constitutive activity. Nature Struc. Biol. 8:176-183.

37. Wang, H-Y., Xu, X., Ding, J-H., Bermingham, J. R., and Fu, X-D. (2001). SC35 plays a role in T cell development and alternative splicing of CD45. Mole. Cell 7:331-342.

38. Dagher, S. F. and Fu, X-D. (2001). Evidence for a role of Sky1p-mediated phosphorylation in 3’ splice site recognition involving both Prp8 and Prp17/Slu4. RNA 7:1284-1297.

39. Yeakley, J. M., Fan, J-B., Doucet, D., Luo, L., Wickham, E., Ye, Z., Chee, M., and Fu, X-D. (2002). Profiling alternative splicing on fiber-optic arrays. Nature Biotech. 20:353-358.

40. Cmarko, D., Bøe, S-O., Scassellati, C., Szilvay, A. M., Davanger, S., Fu, X-D., Haukenes, G., Kalland, K. H., and Fakan, S. (2002). Rev inhibition strongly affects intracellular distribution of HIV-1 RNAs. J. Virology 76:10473-10484.

41. Yun, C. Y., Velazquez-Dones, A. L., Lyman, S. K., and Fu, X-D. (2003). Phosphorylation dependent and independent nuclear import of RS domain-containing splicing factors and regulators. J. Biol. Chem. 278:18050-18055.

42. Aubol, B. E., Chakrabarty, S., Ngo, J., Shaffer, J., Nolen, B., Fu, X-D., Ghosh, G., and Adams, J. A. (2003). Splicing factor ASF/SF2 is phosphorylated processively by the protein kinase SRPK1. Proc. Natl. Acad. Sci. USA. 100:12601-12606.

43. Zheng, C. L., Nair, T. M., Gribskov, M, Kwon, Y-S., Li, H-R., and Fu, X-D. (2004). A database designed to computationally aid an experimental approach to alternative splicing. Pacific Symp. Biocomputing 2004 Altman, R. B.; Dunker, A. K., Hunter, L., Jung, T. A., and Klein, T. E. eds. Published by World Scientific. pp78-88.

44. Ding, J-H., Xu, X., Yang, D., Chu, P-S., Dalton, N., Ye, Z, Chen, P., Xiao, R-P., Ross Jr. J., Chen, J., and Fu, X-D. (2004). Dilated cardiomyopathy caused by tissue-specific ablation of SC35 in the heart. EMBO J. 23:885-896.

45. Fan, J-B., Yeakley, J. M., Bibikova, M., Chudin, E., Wickham, E., Chen, J., Doucet, D., Rigault, P., Shen, R., McBride, C., Li, H-R., Fu, X-D., Oliphant, A., Barker, D. L., and Chee, M. S. (2004). A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 14:878-885.

46. Feingold,E. and ENCODE consortium members. (2004). The ENCyclopedia Of DNA Elements) Project. Science 306:636-640.

47. Fu, X-D. (2004). Towards a splicing code. Cell 119:736-738.

48. Kwon, Y-S., Li, H-R., and Fu, X-D. (2004). Large-scale analysis of mRNA splice variants by microarray. Handbook of RNA Biochemistry, (ed. R. K Hartmann, A. Bindereif, A. Schon, E. Westhof), Wiley-Vch Verlag GmbH & Co. KgaA, Weinheim. pp655-663.

49. Xu, X., Yang, D., Ding, J-H., Wang, W., Chu, P-H., Dalton, N. D., Wang, H-Y., Bermingham, Jr., J. R., Ye, Z., Liu, F., Rosenfeld, M. G., Manley, J. L., Ross Jr. J., Chen, J., Xiao, R-P., Cheng, H., and Fu, X-D. (2005). ASF/SF2-regulated postnatal reprogramming of CaMKII? alternative splicing modulates excitation-contraction coupling in cardiac muscle. Cell 120:59-72.

50. Zheng, Y., Fu, X-D., and Ou, J. (2005). Suppression of hepatitis B virus replication by SRPK1 and SRPK2 via a pathway independent of the phosphorylation of the viral core protein. Virology 342:150-158.

51. Ngo, J. Chakrabarti, S., Velazquez-Dones, A., Ding, J-H., Nolen, B., Aubol, B. E., Adams, J., Fu, X-D., and Ghosh, G. (2005). Interplay between SRPK and Clk/Sty kinases in the phosphorylation of splicing ASF/SF2 is regulated by a docking motif in ASF/SF2. Mole Cell 20:77-89.

52. Zheng, C. L., Kwon, Y-S., Li, H-R., Zhang, K., Coutinho-Mansfield, G., Yang, C., Nair, T., Gribskov, M., and Fu, X-D. (2005). MAASE: An alternative splicing database designed for supporting splicing microarray applications. RNA 11:1767-1776.

53. Zheng, C. L., Fu, X-D., and Gribskov, M. (2005). Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. RNA 11:1777-1787.

54. Lin, S-R., Xiao, R., Sun, P., Xu, X., and Fu, X-D. (2005). Dephosphorylation dependent sorting of SR proteins during mRNP maturation. Mole Cell 20:413-425.

55. Xu, X. and Fu, X-D. (2005). Conditional knockout mice to study alternative splicing in vivo. Methods 37:387-392.

56. Velazques-Dones, A., Hagopian, J., Aubol, B. E., Ma, C-T., Zhong, X-Y., Zhou, H., Ghosh, G., Fu, X-D., and Adams, J. A. (2005). Mass spectrometric and kinetic analysis of ASF/SF2 phosphorylation by SRPK1 and Clk/Sty. J Biol Chem 280:41761-41768.

57. Ding, J-H., Zhong, X-Y., Hapopian, J., Aubol, B. E., Feramisco, J., Ghosh, G., Zhou, H-L., Adams, J. A., and Fu, X-D. (2006). Regulated cellular partition of SR protein specific kinases in mammalian cells. Mole Biol Cell 17:876-885.

58. Li, H-R., Wang-Rodriguez, J., Nair, M. T., Yeakley, J. M., Kwon, Y-S., Bibikova, M., Zheng, C. K. Zhang.,  T. Downs; Fu, X-D., and Fan, J.B.  (2006). Two-dimensional transcriptome profiling: Identification of novel prostate cancer biomarkers from archived paraffin-embedded specimens. Cancer Res 66:4079-4088.

59. Zhang, C., Li, H-R., Fan, J-B., Wang-Rodriguez, J., Downs, T., Fu, X-D., and Zhang, M. Q. (2006). Profiling alternatively spliced mRNA isoforms for prostate cancer classification.  BMC Bioinformatics 7(1):202.

60. Fu, X-D. (2006). Pre-mRNA splicing in eukaryotic cells. Gene Expression and Regulation. (ed. J. Ma), Current Scientific Frontiers Book, Higher Education Press (Beijing), pp447-467.

61. Kwon, Y-S., Garcia-Bassets, I., Hutt, K., Cheng, C., Jin, M-J., Liu, D-Y., Benner, C., Wang, D., Ye, Z., Bibikova, M., Fan, J-B., Duan, L-X., Glass, C. K., Rosenfeld, M. G., and Fu, X-D. (2007). Sensitive ChIP-DSL technology reveals an extensive ERa binding program on human gene promoters. Proc Natl Acad Sci. USA104:4852-4857.

62. Garcia-Bassets, I., Kwon, Y-S., Telese, F., Prefontaine, G. G., Hutt, K., Cheng, C., Ju, B-G., Ohgi, K. A., Wang, J., Escoubet-Lozach, L., Rose, D., Glass, C. K., Fu, X-D., and Rosenfeld, M. G. (2007). Histone methylation-dependent mechanisms impose ligand-dependency for gene activation by nuclear receptors. Cell 128:505-518.

63. Ngo, J. C., Gullingsrud, J., Giang, K., Yeh, M. J., Fu, X-D., Adams, J. A., McCammon, J. A., and Ghosh, G. (2007).   SR protein kinase 1 is resilient to inactivation.  Structure 15:123-133.

64. Wang, J., Scully, K., Zhu X., Cai, L., Zhang, J., Prefontaine, G., Krones, A., Ohgi, K. A., Zhu P., Garcia-Bassets, I., Liu, F., Taylor, H., Lozach J., Jayes, F. L., Korach, S. K., Glass, C. K., Fu, X-D., and Rosenfeld, M. G. (2007). Opposing LSD1 complexes in pituitary gene activation/repression programs.  Nature (article) 446:882-887.

65. Hu, A. and Fu, X-D. (2007).  Splicing oncogenes.  Nature Struc Mol Biol 14:174-175.

66. Lin, S. and Fu, X-D. (2007). SR proteins and related factors in alternative splicing.  Alternative splicing in the postgenomic era, (ed. B. Blencowe and B. Graveley), Eurekah Bioscience Series 623:107-122.

67. Lukasiewicz, R., Velazquez-Dones, A., Huynh, N., Hagopian, J., Fu, X-D., Adams, J., and Ghosh, G. (2007). Structurally unique yeast and mammalian SR protein kinases catalyze evolutionarily conserved phosphorylation reactions. J Biol Chem 282:23036-23043.

68. Xiao, R., Sun, Ye, Ding, J-H., Lin, S, Rose, D. W., Rosenfeld, M. G, Fu, X-D. and Li, X.  (2007). Splicing regulator SC35 is essential for genomic stability and cell proliferation during mammalian organogenesis. Mol Cell Biol 27:5393-5402.

69. Coutinho-Mansfield, G. C., Xue, Y-C., Zhang, Y., and Fu, X-D. (2007). PTB/nPTB switch: A post-transcriptional mechanism for programming neuronal differentiation.  Genes Dev 21:1573-1577.

70. Ma, C-T., Velazques-Dones, A., Hagopian, J. C., Ghosh, G., Fu, X-D., and Adams, J. A.  (2007).  Ordered multi-site phosphorylation of the splicing factor ASF/SF2 by SRPK1.  J Mol Biol 376:55-68.

71. Ngo, J. C. K., Giang, N., Chakrabarti, S., Ma, C-T., Huynh, N., Hagopian, J. C., Dorrestein, P., Fu, X-D., Adams, J. A., and Ghosh, G.  (2008).  A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by SRPK1.  Mol Cell 29:563-576.

72. Pandit, S., Wang, D., and Fu, X-D. (2008). Functional integration of transcriptional and RNA processing machineries.  Curr Opin Cell Biol 20:253-259.