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Eunice Kennedy Shriver National Institute of Child Health and Human Development - Program in Cellular Regulation and Metabolism
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Yun-Bo Shi

The Section on Molecular Morphogenesis, headed by Yun-Bo Shi, studies the gene-regulatory mechanisms controlled by thyroid hormone (TH) receptor (TR) that establish the developmental program of metamorphosis. The laboratory recently showed that the level of TR-binding coactivators regulates the rate of metamorphosis progression, and they revealed the origin of the TH-induced adult intestinal epithelial stem cells. The group also showed that a TH-induced matrix metalloproteinase regulates apoptosis via two different mechanisms in different organs during metamorphosis.

Publications

Original Papers

1. Cimino, G., Shi, Y.-B., and Hearst, J. E. (1986) Wavelength dependence for the photoreversal of a psoralen-DNA crosslink. Biochem. 25, 3013-3020.

2. Shi, Y.-B., and Hearst, J. E. (1986) Thermostability of double-stranded deoxyribonucleic acids: effects of covalent additions of a psoralen. Biochem. 25, 5895-5902.

3. Shi, Y.-B., and Hearst, J. E. (1987) Wavelength dependence for the photoreactions of DNA-psoralen monoadducts (1): photoreversal of monoadducts. Biochem. 26, 3786-3792.

4. Shi, Y.-B., and Hearst, J. E. (1987) Wavelength dependence for the photoreactions of DNA-psoralen monoadducts (2): photocrosslinking of monoadducts. Biochem. 26, 3792-3798.

5. Shi, Y.-B., Gamper, H., and Hearst, J. E. (1987) The effects of covalent additions of a psoralen on transcription by E. coli RNA polymerase. Nucleic Acids Res. 15, 6843-6854.

6. Shi, Y.-B., Gamper, H., Van Houten, B., and Hearst, J. E. (1988) Interaction of E. coli RNA polymerase with DNA in an elongation complex arrested at a specific psoralen crosslink site. J. Mol. Biol. 199, 277-293.

7. Shi, Y.-B., Gamper, H., and Hearst, J. E. (1988) Interaction of T7 RNA polymerase with DNA in an elongation complex arrested at a specific psoralen site. J. Biol. Chem. 263, 527-534.

8. Shi, Y.-B., Spielmann, H. P., and Hearst, J. E. (1988) Base catalyzed reversal of a psoralen-DNA crosslink. Biochem. 27, 5174-5178.

9. Shi, Y.-B., Griffith, J., Gamper, H., and Hearst, J. E. (1988) Evidence for structural deformation of the DNA helix by a psoralen diadduct but not by a monoadduct. Nucleic Acid Res. 16, 8945 8952.

10. Shi, Y.-B., and Brown, D. D. (1990) Developmental and thyroid hormone-dependent regulation of pancreatic genes in Xenopus laevis. Genes and Development. 4, 1107-1113.

11. Yaoita, Y., Shi, Y.-B., and Brown, D. D. (1990) Xenopus laevis a and b thyroid hormone receptors. Proc. Natl. Acad. Sci. USA. 87, 7090-7094.

12. Shi, Y.-B., Yaoita, Y., and Brown, D. D. (1992) Genomic organization and alternative promoter usage of the thyroid hormone receptor b genes in Xenopus laevis. J. Biol. Chem. 267, 733-738.

13. Shi, Y.-B., and Brown, D. D. (1993) The earliest changes in gene expression in tadpole intestine induced by thyroid hormone. J. Biol. Chem. 268, 20312-20317.

14. Shi, Y.-B., and Hayes, W. P. (1994) Thyroid hormone dependent regulation of intestinal fatty acid-binding protein gene during amphibian metamorphosis. Dev. Biol. 161, 48-58.

15. Shi, Y.-B., and Liang, V. C.-T. (1994) Cloning and characterization of the ribosomal protein L8 gene from Xenopus laevis. Biochimica et Biophysica Acta. 1217, 227-228.

16. Patterton, D., and Shi, Y.-B. (1994) Thyroid hormone-dependent differential regulation of multiple arginase genes during amphibian metamorphosis. J. Biol. Chem. 269, 25328-25334.

17. Shi, Y.-B., Liang, V. C.-T., Parkison, C., and Cheng, S.-Y. (1994) Tissue-dependent developmental expression of a cytosolic thyroid hormone binding protein gene in Xenopus: Its role in the regulation of amphibian metamorphosis. FEBS Letters. 355, 61-64.

18. Ranjan, M., Wong, J., and Shi, Y.-B. (1994) Transcriptional repression of Xenopus TRb gene is mediated by a thyroid hormone response element located near the start site. J. Biol. Chem. 269, 24699-24705.

19. Ishizuya-Oka, A., Shimozawa, A., Takeda, H., and Shi, Y.-B. (1994) Cell-specific and spatio-temporal expression of intestinal fatty acid-binding protein gene in the small intestine during amphibian metamorphosis. Roux's Archives of Dev. Biol. 204, 150-155.

20. Patterton, D., Hayes, W. P., and Shi, Y.-B. (1995) Transcriptional activation of the matrix metalloproteinase gene stromelysin-3 coincides with thyroid hormone-induced cell death during frog metamorphosis. Dev. Biol. 167, 252-262.

21. Stolow, M. A., and Shi, Y.-B. (1995) Xenopus sonic hedgehog as a potential morphogen during embryogenesis and thyroid hormone-dependent metamorphosis. Nuc. Acids Res. 23, 2555-2562.

22. Wong, J., and Shi, Y.-B. (1995) Coordinated regulation of and transcriptional activation by Xenopus thyroid hormone and retinoid X receptors. J. Biol. Chem. 270, 18479-18483.

23. Wong, J., Shi, Y.-B., and Wolffe, A. P. (1995) A role for nucleosome assembly in both silencing and activation of the Xenopus TRbA gene by the thyroid hormone receptor. Genes and Development, 9, 2696-2711.

24. Ishizuya-Oka, A., Ueda, S. , and Shi, Y.-B. (1996) Transient expression of stromelysin-3 mRNA in the amphibian small intestine during metamorphosis. Cell Tissue Res. 283, 325-329.

25. Puzianowska-Kuznicka, M., and Shi, Y.-B. (1996) Nuclear factor I as a potential regulator during post-embryonic organ development. J. Biol. Chem. 271, 6273-6282.

26. Stolow, M. A., Bauzon, D. D., Li, J., Sedgwick, T., Liang, V. C.-T., Sang, Q. A., and Shi, Y.-B. (1996) Identification and characterization of a novel collagenase in Xenopus laevis: Possible roles during frog development. Mol. Biol. of the Cell. 7, 1471-1483.

27. Puzianowska-Kuznicka, M., Wong, J., Kanamori, A., and Shi, Y.-B. (1996) Functional characterization of a mutant thyroid hormone receptor in Xenopus laevis. J. Biol. Chem. 271, 33394-33403.

28. Ishizuya-Oka, A., Stolow, M. A., Ueda, S., and Shi, Y.-B. (1997) Temporal and spatial expression of an intestinal Na+/PO4^3 cotransporter correlates with epithelial transformation during thyroid hormone-dependent frog metamorphosis.+ _Developmental Genetics. 20, 53-66. (Cover photo).

29. Shi, Y.-B., and Ishizuya-Oka, A. (1997) Auto-activation of Xenopus TRb genes correlates with larval epithelial apoptosis and adult cell proliferation. J. of Biomed. Science. 4, 9-18.

30. Denver, R. J., Pavgi, S., and Shi, Y.-B. (1997) Thyroid hormone-dependent gene expression program for Xenopus neural development. J. Biol. Chem. 272, 8179-8188.

31. Wong, J., Shi, Y.-B., and Wolffe, A. P. (1997) Determinants of chromatin disruption and transcriptional regulation instigated by the thyroid hormone receptor: Hormone regulated chromatin disruption is not sufficient transcriptional activation. EMBO J. 16, 3158-3171.

32. Ishizuya-Oka, A., Ueda, S., and Shi, Y.-B. (1997) Temporal and spatial regulation of a putative transcriptional repressor implicates a role during thyroid hormone-dependent organ transformation. Developmental Genetics. 20, 329-337.

33. Su, Y., Shi, Y., and Shi, Y.-B. (1997) Cyclosporin A but not FK506 inhibits thyroid hormone-induced apoptosis in Xenopus tadpole intestinal epithelium. The FASEB J. 11, 559-565.

34. Puzianowska-Kuznicka, M., Damjanovski, S., and Shi, Y.-B. (1997) Both TR and RXR are required to efficiently mediate the effects of thyroid hormone on embryonic development and specific gene regulation in Xenopus laevis. Mol. Cell. Biol. 17, 4738-4749.

35. Su, Y., Shi, Y., Stolow, M. A., and Shi, Y.-B. (1997) Thyroid hormone induces apoptosis in primary cell cultures of tadpole intestine: Cell type specificity and effects of extracellular matrix. J. Cell Biol. 139, 1533-1543.

36. Wong, J., Li, Q., Levi, B.-Z., Shi, Y.-B., and Wolffe, A. P. (1997) Structural and functional features of a specific nucleosome containing a recognition element for the thyroid hormone receptor. EMBO J. 16, 7130-7145.

37. Liang, V. C.-T., Sedgwick, T., and Shi, Y.-B. (1997) Characterization of the Xenopus homolog of an immediate early gene associated with cell activation: Sequence analysis and regulation of its expression by thyroid hormone during amphibian metamorphosis. Cell Research 7, 179-193.

38. Ishizuya-Oka, A., Ueda, S., Damjanovski, S., Li, Q., Liang, V. C.-T., and Shi, Y.-B. (1997) Anteroposterior gradient of epithelial transformation during amphibian intestinal remodeling: Immunohistochemical detection of intestinal fatty acid-binding protein. Dev. Biol. 192, 149-161.

39. Wong, J., Patterton, D., Imhof, D., Guschin, D., Shi, Y.-B., and Wolffe, A. P. (1998) Distinct requirements for chromatin assembly in transcriptional repression by thyroid hormone receptor and histone deacetylase. EMBO J. 17, 520-534.

40. Minucci, S., Wong J., Blanco, J., Shi, Y.-B., Wolffe, A. P., and Ozato, K. (1998). Retinoid receptor induced alteration of the chromatin assembled on a ligand responsive promoter in Xenopus oocytes. Molecular Endocrinology 12, 315-324.

41. Gao, X., Sedgwick, T., and Shi, Y.-B., Evans, T. (1998). Distinct functions are implicated for the GATA-4/5/6 transcription factors in the regulation of intestine epithelial cell differentiation. Mol. Cell. Biol. 18, 2901-2911.

42. Wong, J., Liang, V. C.-T., Sachs, L. M., and Shi, Y.-B. (1998). Transcription from the thyroid hormone dependent promoter of Xenopus laevis TRbA gene requires a novel upstream element and the initiator but not a TATA box. J. Biol. Chem. 273, 14186-14193.

43. Li, J., Liang, V. C.-T., Sedgwick, T., Wong, J., and Shi, Y.-B. (1998). Unique organization and involvement of GAGA factors in the transcirptional regulation of the Xenopus stromelysin-3 gene. Nuc. Acids Res. 26, 3018-3025.

44. Torrents, D., Estevez, R., Pineda, M., Fernandez, E., Lloberas, J., Shi, Y.-B., Zorzano, A., and Palacin, M. (1998). Identification of a new cDNA (y+LAT-1) that co-expresses system y+L activity with 4F2hc in oocytes: A candidate gene for Lysinuric Protein Intolerance. J. Biol. Chem. 273, 32437-32445.

45. Damjanovski, S., Ishizuya-Oka, A., and Shi, Y.-B. (1999) Spatial and temporal regulation of collagenases-3, -4, and stromelysin-3 implicate distinct functions in apoptosis and tissue remodeling during frog metamorphosis. Cell Research, 9, 91-105.

46. Vermaak, D., Wade, P. A., Jones, P. L., Shi, Y.-B., and Wolffe, A. P. (1999) Functional analysis of the SIN3-histone deacetylase RPD3-RbAp48-histone H4 connection in the Xenopus oocyte. Mol. Cell. Biol. 19, 5847-5860.

47. Ritchie, J. W. A., Peter, G. J., Shi, Y.-B., and Taylor, P. M. (1999) Thyroid hormone transport by 4F2hc-IU12 heterodimers expressed in Xenopus oocytes_._ J. Endocrinology. 163, R5-R9..

48. Damjanovski, S., Puzianowska-Kuznicka, M., Ishizuya-Oka, A., and Shi, Y.-B. (2000) Differential regulation of three thyroid hormone-responsive matrix metalloproteinase genes implicates distinct functions during frog embryogenesis. FASEB J. 14, 503-510.

49. Ishizuya-Oka, A., Li, Q., Amano, T., Damjanovski, S., Ueda, S., and Shi, Y.-B. (2000) Requirement for matrix metalloproteinase stromelysin-3 in cell migration and apoptosis during tissue remodeling. J. Cell Biol. 150, 1177-1188.

50. Urnov, F.D., Yee, J., Collingwood, T.N., Bauer, A, Beug, H., Shi, Y.-B., and Wolffe, A. P. (2000). Targeting of N-CoR-HDAC3 by the oncoprotein v-ErbA yields a chromatin infrastructure-dependent transcriptional repression pathway. EMBO J. 19, 4074-4090.

51. Sachs, L.M. and Shi, Y.-B. (2000) Targeted chromatin binding and histone acetylation in vivo by thyroid hormone receptor during amphibian development. PNAS 97, 13138-13143.

52. Damjanovski, S., Sachs, L.M. and Shi, Y.-B. (2000) Multiple stage-dependent roles for histone deacetylases during amphibian embryogenesis: Implications for the involvement of extracellular matrix remodeling. Int. J. of Dev. Biol. 44, 769-776..

53. Hsia, S.-C. V, Wang, H, and Shi, Y.-B. (2001) Involvement of Chromatin and Histone Acetylation in the Regulation of HIV-LTR by Thyroid Hormone Receptor. Cell Research, 11. 8-16.

54. Damjanovski, S., Amano, T., Li, Q., Pei, D., and Shi, Y.-B. (2001) Overexpression of Matrix Metalloproteinases Leads to Lethality in Transgenic Xenopus Laevis: Implications for Tissue-Dependent Functions of Matrix Metalloproteinases during Late Embryonic development. Dev. Dynamics 221, 37-47.

55. Jones, P. L., Sachs, L. M., Rouse, N., Wade, P. A, and Shi, Y.-B. (2001) Multiple N-CoR complexes contain distinct histone deacetylases. J. Biol. Chem. 276, 8807-8811.

56. Sachs, L.M., Amano, T., Rouse, N, and Shi, Y.-B. (2001) Involvement of histone deacetylase at two distinct steps in gene regulation during intestinal development in Xenopus laevis. Dev. Dynamics 222, 280-291_._

57. Sachs, L.M., Amano, T., and Shi, Y.-B. (2001) An essential role of histone deacetylases in postembryonic organ transformations in Xenopus laevis. International Journal of Molecular Medicine 8, 595-601.

58. Ishizuya-Oka, A., Ueda, S., Inokuchi, T., Amano, T., Damjanovski, S, Stolow, M., and Shi, Y.-B. (2001) Thyroid hormone-induced expression of Sonic hedgehog correlates with adult epithelial development during remodeling of the Xenopus stomach and intestine. Differentiation, 69, 27-37.

59. Amano, T., Leu, K., Yoshizato, K., and Shi, Y.-B. (2002) Thyroid hormone regulation of a transcriptional coactivator in Xenopus laevis: Implication for a role in postembryonic tissue remodeling. Dev. Dynamics 223, 526-535.

60. Fu, L., Buchholz, D., and Shi, Y.-B. (2002) A novel double promoter approach for identification of transgenic animals: a tool for in vivo analysis of gene function and development of gene-based therapies. Molecular Reproduction and Development 62, 470-476.

61. Seo, Y.-W., Sanyal, S., Kim, H.-J., Won, D. H., An, J.-Y., Amano, T., Zavacki, A. M., Kwon, H.-B., Shi, Y.-B., Kim, W.-S., Kang, H.-J., Moore, D. D., and Choi, H.-S. (2002). FOR, a Novel Orphan Nuclear Receptor Related to Farnesoid X Receptor. J. Biol. Chem. 277, 17836-17844.

62. Hsia, V. S.-C., and Shi, Y.-B. (2002) Chromatin Disruption and Histone Acetylation in the Regulation of HIV-LTR by Thyroid Hormone Receptor. Mol. Cell. Biol. 22, 4043-4052.

63. Sachs, L.M., Jones, P. L., Havis, E., Rouse, N, Demeneix, B. A., and Shi, Y.-B. (2002). N-CoR recruitment by unliganded thyroid hormone receptor in gene repression during Xenopus laevis development. Mol. Cell. Biol. 22, 8527-8538.

64. Ritchie, J.W.A., Shi, Y.-B. , Hayashi, Y., Baird, F.E., Muchekehu, R.W., Christie, G.R., and Taylor, P.M. (2003). A role for thyroid hormone transporters in transcriptional regulation by thyroid hormone receptors. Mol. Endocrinol. 17, 653-661.

65. Tomita, A., Buchholz, D. R., Obata, K., and Shi, Y.-B. (2003) Fusion protein of retinoic acid receptor a with promyelocytic leukemia protein or promyelocytic leukemia zinc-finger protein recruits N-CoR-TBLR1 corepressor complex to repress transcription in vivo. J. Biol. Chem. 278(33), 30788-30795.

66. Buchholz, D. R., Hsia, V. S.-C., Fu, L., and Shi, Y.-B. (2003) A dominant negative thyroid hormone receptor blocks amphibian metamorphosis by retaining corepressors at target genes. Mol. Cell. Biol. 23, 6750-6758.

67. Paul, B. D., and Shi, Y.-B. (2003) Distinct expression profiles of transcriptional coactivators for thyroid hormone receptors during Xenopus laevis metamorphosis. Cell Research 13, 459-464+.+

68. Buchholz, D. R., Fu, L., and Shi, Y.-B. (2004) Cryopreservation of Xenopus transgenic lines. Molecular Reproduction and Development. 67, 65-69+.+

69. Buchholz, D. R., Ishizuya-Oka, A., and Shi, Y.-B. (2004) Spatial and temporal expression pattern of a novel gene in the frog Xenopus laevis: correlations with adult intestinal epithelial differentiation during metamorphosis. Mechanisms of Development: Gene Expression Patterns 4 (3), 321-328.

70. Tomita, A., Buchholz, D. R., and Shi, Y.-B. (2004) Recruitment of N-CoR/SMRT-TBLR1 corepressor complex by unliganded thyroid hormone receptor for gene repression during frog development. Mol. Cell. Biol. 24, 3337-3346.

71. Amano, T, Fu, L., Sahu, S., Markey, M., and Shi, Y.-B. (2004) Substrate specificity of Xenopus matrix metalloproteinase stromelysin-3. International Journal of Molecular Medicine 14, 233-239.

72. Buchholz, D. R., Tomita, A., Fu, L., Paul, B. D., and Shi, Y.-B. (2004) Transgenic analysis reveals that thyroid hormone receptor is sufficient to mediate the thyroid hormone signal in frog metamorphosis. Mol. Cell. Biol. 24, 9026-9037.

73. Paul, B. D., Fu, L., Buchholz, D. R., and Shi, Y.-B. (2005) Coactivator recruitment is essential for liganded thyroid hormone receptor to initiate amphibian metamorphosis. Mol. Cell. Biol. 25, 5712-5724. (With cover photo for vol. 25 (21)).

74. Amano, T., Kwak, O., Fu, L., Marshak, A., and Shi, Y.-B. (2005) The matrix metalloproteinase stromelysin-3 cleaves laminin receptor at two distinct sites between the transmembrane domain and laminin binding sequence within the extracellular domain. Cell Research 15, 150-159.

75. Fu, L., Ishizuya-Oka, A., Buchholz, D. R., Amano, T., and Shi, Y.-B. (2005) A causative role of stromelysin-3 in ECM remodeling and epithelial apoptosis during intestinal metamorphosis in Xenopus laevis. J. Biol. Chem. 280, 27856-65.

76. Amano, T., Fu, L., Marshak, A., Kwak, O., and Shi, Y.B. (2005) Spatio-temporal regulation and cleavage by matrix metalloproteinase stromelysin-3 implicate a role for laminin receptor in intestinal remodeling during Xenopus laevis metamorphosis. Dev. Dynamics. 234, 190-200.

77. Paul, B. D., Buchholz, D. R., Fu, L., and Shi, Y.-B. (2005) Tissue- and gene-specific recruitment of steroid receptor coactivator-3 by thyroid hormone receptor during development. J. Biol. Chem. 280 (29), 27165-27172. JBC Paper of the Week.

78. Wang, G.-P., Song, E.-Q., Xie, H.-Y., Zhang, Z.-L., Tian, Z.-Q., Zuo, C., Pang, D.-W., Wu, D.-C., and Shi, Y.-B. (2005) Biofunctionalization of fluorescent-magnetic-bifunctional nanospheres and their applications. Chem. Commun. 34, 4276 – 4278.

79. Buchholz, D. R., Paul, B. D., and Shi, Y.-B. (2005) Gene-specific changes in promoter occupancy by thyroid hormone receptor during frog metamorphosis: Implications for developmental gene regulation. J. Biol. Chem. 280(50), 41222-8.

80. Ikuzawa, M., Shimizu, K., Yasumasu, S., Iuchi, I., Shi, Y.-B., and Ishizuya-Oka, A. (2005) Thyroid hormone-induced expression of a bZip-containing transcription factor activates epithelial cell proliferation during Xenopus larval-to-adult intestinal remodeling. Dev. Genes Evol. 216(3), 109-18.

81. Hasebe, T., Hartman, R., Matsuda, H., and Shi, Y.-B. (2006) Spatial and temporal expression profiles suggest the involvement of gelatinase A and membrane type 1 matrix metalloproteinase in amphibian metamorphosis. Cell and Tissue Research 324(1), 105-16.

82. Fu, L., Tomita, A., Wang, H., Buchholz, D.R., and Shi, Y.-B. (2006) Transcriptional regulation of the Xenopus laevis stromelysin-3 gene by thyroid hormone is mediated by a DNA element in the first intron. J. Biol. Chem. 281(25), 16870-8.

83. Guo, M.-X., Wang, D., Shao, H.-J., Qiu, H.-L., Lu, X., Zhao, Z.-Z., Zhu, C.-G., Shi, Y.-B., and Li, W.-X. (2006) Transcription of Human Zinc Finger 268 Gene Requires an Intragenic Promoter Element. J. Biol. Chem. 281(34), 24623-36.

84. Hasebe, T., Hartman, R., Fu, L., Amano, T., and Shi, Y.-B. (2007) Evidence for a cooperative role of gelatinase A and membrane type-1 matrix metalloproteinase during Xenopus laevis development. Mechanisms of Development. 124(1), 11-22.

85. Buchholz, D.R., Heimeier, R.A., Das, B., Washington, T., and Shi, Y.B. (2007) Pairing morphology with gene expression in thyroid hormone-induced intestinal remodeling and identification of a core set of TH-induced genes across tadpole tissues. Dev. Biol. 303, 576-590.

86. Paul, B. D., Buchholz, D. R., Fu, L., and Shi, Y.-B. (2007) SRC-p300 coactivator complex is required for thyroid hormone induced amphibian metamorphosis. J. Biol. Chem. 282, 7472-7481.

87. Matsuda, H., Paul, B. D., Choi, C. Y., and Shi, Y.-B. (2007) Contrasting effects of two alternative splicing forms of coactivator-associated arginine methyltransferase 1 on thyroid hormone receptor-mediated transcription in Xenopus laevis. Mol. Endocrinology. 21(5), 1082-94.

88. Sato, Y., Buchholz, D. R., Paul, B. D., and Shi, Y.B. (2007) A role of unliganded thyroid hormone receptor in postembryonic development in Xenopus laevis. Mechanisms of Development. 124, 476-488.

89. Song, E. Q., Wang, G. P., Xie, H. Y., Zhang, Z. L., Hu, J., Peng, J., Wu, D. C., Shi, Y.B., and Pang, D. W. (2007) Visual Recognition and Efficient Isolation of Apoptotic Cells with Fluorescent-Magnetic-Biotargeting Multifunctional Nanospheres. Clinical Chemistry. 53, 2177-2185.

90. Heimeier, R.A., Hsia, V. S.-C., and Shi, Y.-B. (2008) Participation of BAF57 and BRG1-Containing Chromatin Remodeling Complexes in Thyroid Hormone-Dependent Gene Activation during Vertebrate Development. Mol. Endo. 22(5), 1065-77.

91. Wang, D., Guo, M.-X., Hu, H.-M., Zhao, Z.-Z., Qiu, H.-L., Shao, H.-J., Zhu, C.-G., Lu, X., Shi, Y.-B., and Li, W.-X. (2008) Human T-cell leukemia virus type 1 oncoprotein tax represses ZNF268 expression through CREB/ATF pathway. J. Biol. Chem. 283(24),16299-308.

92. Hasebe, T., Kajita, M., Shi, Y.-B., and Ishizuya-Oka, A. (2008) Thyroid hormone-upregulated hedgehog interacting protein is involved in larval-to-adult intestinal remodeling by regulating sonic hedgehog signaling pathway in Xenopus laevis. Dev. Dyn. . 237(10), 3006-3015.

93. Wang, X., Matsuda, H., and Shi, Y.B. (2008) Developmental regulation and function of thyroid hormone receptors and 9-cis retinoic acid receptors during Xenopus tropicalis metamorphosis. Endocrinology. 149(11), 5610-5618.

94. Fiorentino, M., Fu, L., and Shi, Y.-B. (2009) Mutational analysis of the cleavage of the cancer-associated laminin receptor by stromelysin-3 reveals the contribution of flanking sequences to site recognition and cleavage efficiency. International Journal of Molecular Medicine. 23, 389-397.

95. Matsuda, H., Paul, B. D., Choi, C. Y., Hasebe, T., and Shi, Y.B. (2009) Novel functions of protein arginine methyltransferase 1 in thyroid hormone receptor-mediated transcription and in the regulation of metamorphic rate in Xenopus laevis. Mol. Cell. Biol. 29, 745-757.

96. Sato, Y., Ding, A., Heimeier, R. A., Yousef, A. F., Mymryk, J. S., Walfish, P. G., and Shi, Y.-B. (2009) The adenoviral E1A protein displaces corepressors and relieves gene repression by unliganded thyroid hormone receptors in vivo. Cell Res. 19, 783-792.

97. Fu, L., Das, B., Mathew, S., and Shi, Y.-B. (2009) Genome-wide identification of Xenopus matrix metalloproteinases: conservation and unique duplications in amphibians. BMC Genomics. 10, 81 (1-18).

98. Wang, D., Xia, X., Lu, Y., Oetting, A., Walker, R.L., Zhu, Y., Meltzer, P., Cole, P.A., Shi, Y.-B., P. Yen (2009) Negative Regulation of TSHa Target Gene by Thyroid Hormone Involves Histone Acetylation and Corepressor Complex Dissociation. Mol. Endocrinol. 23(5), 600-9.

99. Heimeier, R.A., Das, B., Buchholz, D.R., and Shi, Y.-B. (2009) The xenoestrogen bisphenol A inhibits postembryonic vertebrate development by antagonizing gene regulation by thyroid hormone. Endocrinology. 150(6), 2964-73. Featured in Endocrine News (May, 2009). 

100. Song, E.-Q., Zhang, Z.-L., Luo, Q.-Y., Wen, L., Shi, Y.-B., and Pang, D.-W. (2009) Tumor Cell Targeting Using Folate-Conjugated Fluorescent Quantum Dots And Receptor-Mediated Endocytosis. Clinical Chemistry. 55(5), 955-63.

101. Ishizuya-Oka, A., Hasebe, T., Buchholz, D. R., Kajita, M., Fu, L., and Shi, Y.-B. (2009) The origin of the adult intestinal stem cells induced by thyroid hormone in Xenopus laevis. The FASEB J. 23(8), 2568-75.

102. Mathew, S., Fu, L., Fiorentino, M., Matsuda, H., Das, B., and Shi, Y.-B. (2009) Differential regulation of cell type specific apoptosis by stromelysin-3: A potential mechanism via the cleavage of the laminin receptor during tail resorption in Xenopus laevis. J. Biol. Chem. 284(27), 18545-56.

103. Das, B., Heimeier, R.A., Buchholz, D.R., and Shi, Y.B. (2009) Identification of direct thyroid hormone response genes reveals the earliest gene regulation programs during frog metamorphosis_._ J. Biol. Chem. 284, 34167-34178.

104. Wang, Y., Mukhopadhyay, D., Mathew, S., Hasebe, T., Heimeier, R., Azuma, Y., Kolli, N., Shi, Y.-B., Wilkinson, K.D., and Dasso, M. (2009) Identification and Developmental Expression of Xenopus laevis SUMO Proteases. PLoS One 4: e8462, 1-10.

105. Heimeier, R.A., Das, B., Buchholz, D.R., Fiorentino. M., and Shi, Y.-B. (2010) Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult. Genome Biology, 11:R55, 1-20.

106. Yi, H., Xue, L., Guo, M.-X., Ma, J., Zeng, Y., Wang, W., Cai, J.-Y., Hu, H.-M., Shu, H.-B., Shi, Y.-B.*, and Li, W.-X*. (2010) Gene Expression Atlas for Human Embryogenesis.  FASEB J. 24, 3341-3350 (*Corresponding Authors)

107. Sun, G., Hasebe, T., Fujimoto, K., Lu, R., Fu, L., Matsuda, H., Kajita, M., Ishizuya-Oka, A., and Shi, Y.-B. (2010) Spatio-temporal expression profile of stem cell-associated gene LGR5 in the intestine during thyroid hormone-dependent metamorphosis in Xenopus laevis. PLoS One, 5: e13605, 1-9.

108. Matsuda, H., and Shi, Y.B. (2010) An essential and evolutionarily conserved role of protein arginine methyltransferase 1 for adult intestinal stem cells during postembryonic development. Stem Cells 28, 2073-2083.

109. Hasebe, T., Buchholz, D.R., Shi, Y.-B., and Ishizuya-Oka, A. (2011) Epithelial-connective tissue interactions induced by thyroid hormone receptor are essential for adult stem cell development in the Xenopus laevis intestine. Stem Cells 29 (1), 154-61

110. Sato, Y., Heimeier, R.A., Li, C., Deng, C., and Shi, Y.-B. (2011) Extracellular domain of CD98hc is required for early murine development. Cell & Bioscience 1:7, 1-12.

111. Song, E.-Q., Hu, J., Wen, C.-Y., Tian, Z.-Q., Yu, X., Zhang, Z.-L., Shi, Y.-B., and Pang, D.-W. (2011) Fluorescent-Magnetic-Biotargeting Multifunctional Nanobioprobes for Detecting and Isolating Multiple Types of Tumor Cells. ACS Nano. 5(2), 761-70

112. Matsuura, K., Fujimoto, K., Fu, L., and Shi, Y.-B. (2012) Liganded thyroid hormone receptor induces nucleosome removal and histone modifications to activate transcription during larval intestinal cell death and adult stem cell development. Endocrinology 153, 961-972

113. Helbing, C.C., Wagner, M.J., Pettem, K., Johnston, J., Heimeier, R.A., Veldhoen, N., Jirik, F.R., Shi, Y.-B., and Browder, L.W. (2012) Modulation of thyroid hormone-dependent gene expression in Xenopus laevis by INhibitor of Growth (ING) proteins. PLoS One. In press

114. Hasebe, T., Kajita, M., Fu, L., Shi, Y.B., and Ishizuya-Oka, A. (2012) Thyroid hormone-induced Sonic hedgehog signal up-regulates its own pathway in a paracrine manner in the Xenopus laevis intestine during metamorphosis. Dev Dyn. 241, 403-414

115. Fujimoto, K., Matsuura, K., Hu-Wang, E., Lu, R., and Shi, Y.-B. (2012) Thyroid hormone activates protein arginine methyltransferase 1 expression by directly inducing c-Myc transcription during Xenopus intestinal stem cell development. J. Biol. Chem. 287, 10039-10050

116. Fu, L., Sun, G., Fiorentino, M., and Shi, Y.-B. (2012) Characterization of Xenopus Tissue Inhibitor of Metalloproteinases-2: A role in regulating matrix metalloproteinase activity during development. PLoS One, 7: e36707, 1-8

117. Fujimoto, K., Matsuura, K., Das, B., Fu, L., and Shi, Y.-B. (2012) Direct activation of Xenopus iodotyrosine deiodinase by thyroid hormone receptor in the remodeling intestine during amphibian metamorphosis. Endocrinology in press.

118. Sterling, J., Fu, L., Matsuura, K., and Shi, Y.-B. (2012) Cytological and morphological analyses reveal distinct features of intestinal development during Xenopus tropicalis metamorphosis. PLoS One in press.

119. Matsuura, K., Fujimoto, K., Das, B., Fu, L., Lu, C.D., and Shi, Y.-B. (2012) Histone H3K79 methyltransferase Dot1L is directly activated by thyroid hormone receptor during Xenopus metamorphosis. Cell & Bioscience 2:25, 1-10.

Reviews

1. Shi, Y.-B. (1994) Molecular biology of amphibian metamorphosis: A new approach to an old problem. Trends in Endocrinol. Metabolism. 5, 14-20.

2. Shi, Y.-B., and Ishizuya-Oka, A. (1996) Biphasic intestinal development in amphibians: Embryogenesis and remodeling during metamorphosis. Current Topics in Developmental Biology. 32, 205-235.

3. Shi, Y.-B., Stolow, M. A., Puzianowska-Kuznicka, M., and Wong, J. (1996) Les genes de la metamorphose. La Recherche. 286, 58-64.

4. Shi, Y.-B., Wang, R.-X., and Shi, Y.-F. (1996) Apoptosis: The molecular mechanism. Life Sciences. 8 (3), 8-12.

5. Shi, Y.-B., Wong, J., Puzianowska-Kuznicka, M., and Stolow, M. A. (1996) Tadpole competence and tissue-specific temporal regulation of amphibian metamorphosis: Roles of thyroid hormone and its receptors. BioEssays. 18, 391-399.

6. Shi, Y.-B., Wong, J., Puzianowska-Kuznicka, M. (1996) Thyroid hormone receptors: Mechanisms of transcriptional regulation and roles during frog development. J. Biomedical Science. 3, 307-318.

7. Stolow, M. A., Ishizuya-Oka, A., Su, Y., and Shi, Y.-B. (1997) Gene regulation by thyroid hormone during amphibian metamorphosis: Implications on the role of cell-cell and cell-extracellular matrix interactions. American Zoologist. 37, 195-207.

8. Shi, Y.-B. (1997) Cell-cell and cell-ECM interactions in epithelial apoptosis and cell renewal during frog intestinal development. Cell Biochemistry and Biophysics. 27, 179-202.

9. Wolffe, A. P., Wong, J., Li, Q., Levi, B.-Z., and Shi, Y.-B. (1997) Three steps in the regulation of transcription by the thyroid hormone receptor: establishment of a repressive chromatin, disruption of chromatin and transcriptional activation. Biochem. Soc. Transactions 25, 612-615.

10. Shi, Y.-B., Su, Y., Li, Q., and Damjanovski, S. (1998) Auto-regulation of thyroid hormone receptor genes during Metamorphosis: Roles in apoptosis and cell proliferation. Int. J. of Dev. Biol. 42, 107-116

11. Shi, Y.-B., Sachs, L. M., Jones, P. L., Li, Q., and Ishizuya-Oka, A. (1998) Thyroid hormone regulation of Xenopus laevis metamorphosis: Function of TRs and roles of ECM remodeling. Wound Repair and Regeneration. 6, 314-322.

12. Shi, Y.-B., Li, Q., Damjanovski, S., Amano, T., and Ishizuya-Oka, A. (1998) Regulation of apoptosis during development: Input from the extracellular matrix. International Journal of Molecular Medicine 2, 273-282.

13. Wade, P. A., Jones, P. L., Vermaak, D., Veenstra, G. J. C., Imhof, A., Sera, T., Tse, C., Ge, H., Shi, Y.-B., Hansen, J. C., and Wolffe, A. P. (1998) Histone deacetylase directs the dominant silencing of transcription in chromatin: Association with MeCP2 and the Mi-2 chromodomain SWI/SNF ATPase. Cold Spring Harbor Symp. Quant. Biol. .63, 435-445.

14. Wolffe, A. P., and Shi, Y.-B. (1999) A hypothesis for the transcriptional control of amphibian metamorphosis by the thyroid hormone receptor. American Zool. 39, 807-817.

15. Su, Y., Damjanovski, S., Shi, Y., and Shi, Y.-B. (1999) Molecular and cellular basis of tissue remodeling during amphibian metamorphosis. Histology and histopathology. 14, 175-183.

16. Ishizuya-Oka, S., and Shi, Y.-B. (1999). Molecular mechanisms of amphibian intestinal remodeling: Functional implications of thyroid hormone response genes. Protein, Nucleic Acid, and Enzyme. 44, 2060-2068.

17. Li, Q., Sachs, L., Shi, Y.-B., and Wolffe, A. P. (1999) Modification of chromatin structure by the thyroid hormone receptor. Trends in Endocrinol. Metabolism. 10, 157-164.

18. Sachs, L. M., Damjanovski, S., Jones, P.L., Li, Q., Amano, T., Ueda, S., Shi, Y.-B., and Ishizuya-Oka, S. (2000). Dual function of thyroid hormone receptors during Xenopus development. Comparative Biochemistry and Physiology, Part B. Biochemistry and Molecular Biology. 126, 199-211.

19. Wolffe, A. P., Collingwood, T., Li, Q., Yee, J., Urnov, F., and Shi, Y.-B. (2000) Thyroid hormone receptor, v-erbA, and chromatin. Vitamins and Hormones 58, 449-492.

20. Damjanovski, S., Amano, T., Li, Q., Ueda, S., Shi, Y.-B., and Ishizuya-Oka, A. (2000) Role of ECM remodeling in thyroid hormone-dependent apoptosis during anuran metamorphosis. Annals of New York Academy of Sciences. 926, 180-191.

21. Sachs, L. M., Jones, P. L., Hsia, V. S.-C., and Shi, Y.-B. (2000) Chromatin remodeling and developmental gene regulation by thyroid hormone receptor. Gene Ther Mol Biol 5, 101-109.

22. Shi, Y.-B., and Ishizuya-Oka, S. (2001). Thyroid hormone regulation of apoptotic tissue remodeling: Implications from molecular analysis of amphibian metamorphosis. Progress in Nucleic Acid Research and Molecular Biology. 65, 53-100.

23. Shi, Y.-B., Fu, L. Hsia, V. S.-C., Tomita, A., and Buchholz, D. (2001). Thyroid hormone regulation of apoptotic tissue remodeling during anuran metamorphosis. Cell Research 11, 245-252.

24. Shi, Y.-B., Ritchie, J., and Taylor, P. M. (2002). Complex regulation of thyroid hormone action: Multiple opportunities for pharmacological intervention. Pharmacology & Therapeutics. 94, 235-51.

25. Hsia, V. S.-C., Tomita, A., Obata, K., Paul, B., Buchholz, D., and Shi, Y.-B. (2003). Role of chromatin disruption and histone acetylation in thyroid hormone receptor action: Implications in the regulation of HIV-1 LTR. Histology and histopathology. 8, 323-331.

26. Wei, L., and Shi, Y.-B. (2005) Matrix metalloproteinase stromelysin-3 in development and pathogenesis. Histology and histopathology. 20, 177-85.

27. Ishizuya-Oka, A, and Shi, Y.-B. (2005) Molecular mechanisms for thyroid hormone-induced remodeling in the amphibian digestive tract: A model for studying organ regeneration. Dev. Growth Differ. 47 (9), 601-607.

28. Buchholz, D. R., Paul, B. D., Fu, L., and Shi, Y.-B. (2006) Molecular and developmental analyses of thyroid hormone receptor function in Xenopus laevis, the African clawed frog. General and Comparative Endocrinology. 145, 1-19. (Cover photo).

29. Stewart, D., Tomita, A., Shi, Y.-B., and J. Wong. (2006) Chromatin Immunoprecipitation for studying transcriptional regulation in Xenopus oocytes and tadpoles. Methods Mol Biol. 322, 165-81. (In Xenopus Protocols: Cell Biology and Signal Transdution (Ed. Liu, J.). Humana Press, Inc., Totowa, NJ.)

30. Fu, L., Hasebe, T., Ishizuya-Oka, A., and Shi, Y.-B. (2007) Roles of matrix metalloproteinases and ECM remodeling during thyroid hormone-dependent intestinal metamorphosis in Xenopus laevis. Organogenesis. 3, 14-19.

31. Ishizuya-Oka, A, and Shi, Y.B. (2007) Regulation of Adult Intestinal Epithelial Stem Cell Development by Thyroid hormone during Xenopus laevis Metamorphosis. Dev. Dyn. 236, 3358-3368.

32. Shi, Y.-B., Fu, L., Hasebe, T., Ishizuya-Oka, A. (2007). Regulation of ECM remodeling and cell fate determination by matrix metalloproteinase stromelysin-3 during thyroid hormone-dependent postembryonic development. Pharmacology & Therapeutics. 116, 391-400.

33. Ishizuya-Oka, A, and Shi, Y.B. (2008) Thyroid-hormone regulation of stem cell development during intestinal remodeling. Molecular and Cellular Endocrinology. 288, 71-78.

34. Shi, Y.-B. (2009) Dual functions of thyroid hormone receptors in vertebrate development: the roles of histone-modifying cofactor complexes (The 2008 Van Meter Award Prize Lecture and Review). Thyroid. 19, 987-999. (Cover photo).

35. Ishizuya-Oka, A., Hasebe, T., and Shi, Y.-B. (2009) Apoptosis in amphibian organs during metamorphosis. Apoptosis. 15, 350-364.

36. Das, B. Matsuda, H., Fujimoto, K., Sun, G.H., Matsuura, K., and Shi, Y.-B. (2010) Molecular and genetic studies suggest that thyroid hormone receptor is both necessary and sufficient to mediate the developmental effects of thyroid hormone.General and Comparative Endocrinology. 168, 174-180.

37. Heimeier, R.A., and Shi, Y.B. (2010) Amphibian metamorphosis as a model for studying both the morphological effects and the underlying molecular basis of endocrine disruptors on vertebrate development: A case study with the xenoestrogen bisphenol A. General and Comparative Endocrinology. 168, 181-189.

38. Mathew, S., Fu, L., Hasebe, T., Ishizuya-Oka, A., and Shi, Y.-B. (2010) Tissue-dependent induction of apoptosis by matrix metalloproteinase stromelysin-3 during amphibian metamorphosis. Birth Defects Research Part C: Embryo Today. 90(1), 55-66.

39. Shi, Y.-B., Hasebe, T., Fu, L., Fujimoto, K., and Ishizuya-Oka, A. (2011) The development of the adult intestinal stem cells: Insights from studies on thyroid hormone-dependent amphibian metamorphosis. Cell & Bioscience 1:30, 1-9.

40. Xue, L., Yi, H., Huang, Z., Shi, Y.-B.,* and Li, W.-X*. (2011) Global Gene Expression during the Human Organogenesis: From Transcription Profiles to Function Predictions. Int. J. Biol. Sci. 7, 1068-1076. (*Corresponding Authors)

41. Gimaldi, A., Buisine, N., Miller, T., Shi, Y.-B., and Sachs, M. L. (2012) Mechanisms of thyroid hormone receptor action during development: Insights from amphibian. Biochimica et Biophysica Acta. In press.

42. Sun, G., and Shi, Y.-B. (2012) Thyroid hormone regulation of adult intestinal stem cell development: Mechanisms and evolutionary conservations. Int. J. Biol. Sci. . In press

Book Chapters and Others

1. Shi, Y.-B., Lipson, S. E., Chi, D. Y., Spielmann, H. P., Monforte, J. A., and Hearst, J. E. (1990) Applications of psoralens as probes of nucleic acid structure and function. In Bio-organic photochemistry: Photochemistry and the nucleic acid. (Ed. Morrison, H.) 1, 341-378. John Wiley & Sons, Inc. New York.

2. Shi, Y.-B. (1996) Thyroid hormone-regulated early and late genes during amphibian metamorphosis. In Metamorphosis: Post-embryonic reprogramming of gene expression in amphibian and insect cells. (Eds. L. I. Gilbert, J. R. Tata, and B. G. Atkinson). pp. 505-538. Academic Press, New York.

3. Kiang, J. G., and Shi, Y.-B. (1996) Commentary: The Third Annual Joint Scientific Symposium of NIH/FDA CAA and Washington DC Chapter of SCBA: Advances in Biological Sciences. J. Biomedical Science. 3, 133.

4. Shi, Y.-B., and Ishizuya-Oka, A. (1997) Activation of matrix metalloproteinase genes during thyroid hormone-induced apoptotic tissue remodeling. In Programmed Cell Death. (Eds. Y.-B. Shi, Y. Shi, Y. Xu, and D. Scott). pp. 13-26. Plenum Publishing Corp., New York.

5. Shi, Y.-B., and Sang, Q. A. (1998) Collagenase 4 (Xenopus). In Handbook of proteolytic enzymes (Eds. A. J. Barrett, N. D. Rawlings, and J. F. Woessner). pp 1170-1172. Academic Press, New York.

6. Shi, Y.-B.(2000) Temporal and spatial regulation of apoptosis in tissue remodeling: Implications from molecular studies of amphibian development. In Cell Biology and Tumor Immunology (Ed. Y.J. Guo). pp 49-58. Military Medical Science Publication Co., Beijing.

7. Damjanovski, S., Sachs, L.M. and Shi, Y.-B. (2002) Function of thyroid hormone receptors during amphibian development. In Methods in Molecular Biology: Thyroid hormone receptors. Humana Press, Inc., Totowa, NJ. 202, 153-176.

8. Shi, Y.-B. (2002) Roles of matrix metalloproteinases in developmental and pathological processes. In Frontiers of Biotechnology and Pharmaceuticals (Eds. Guo, M., Chen, S., Reiner, J., and Zhao, K). Science Press, New York. 3, 46-57.

9. Jones, P. L., and Shi, Y.-B. (2003) N-CoR-HDAC corepressor complexes: Roles in transcriptional regulation by nuclear hormone receptors. In Current Topics in Microbiology and Immunology: Protein Complexes that Modify Chromatin (Ed. Workman, J. L.). Springer-Verlag, Berlin. 274, 237-268.

10. Amano, T., Fu, L., Ishizuya-Oka, A., and Shi, Y.-B. (2003) Thyroid hormone induced apoptosis during amphibian metamorphosis. In Molecular Mechanisms of Programmed Cell Death. (Eds. Y. Shi, J. Cidlowski, D. Scott, J. Wu, and Y.-B. Shi). pp. 9-19. Kluwer Academic/Plenum, New York

11. Ishizuya-Oka, A., Amano, T., Fu, L., and Shi, Y.-B. (2004) Regulation of apoptosis by extracellular matrix during postembryonic development in Xenopus laevis. In When cells die II: A comprehensive evaluation of apoptosis and programmed cell death (Eds. Lockshin, R. A., and Zakeri, Z.). John Wiley & Sons, Inc., New York. 123-141.

12. Sang, Q. A., and Shi, Y.-B. (2004) Collagenase 4 (Xenopus). In Handbook of proteolytic enzymes, 2nd Edn. (Eds. A. J. Barrett, N. D. Rawlings, and J. F. Woessner). Academic Press, New York. 494-497.

13. Buchholz, D. R., Paul, B. D., and Shi, Y.-B. (2007) Chromatin immunoprecipitation for in vivo studies of transcriptional regulation during development. In Methods in Signal Transduction: Analysis of Growth Factor Signaling in Embryos (Eds. Whitman, M., and Sater, A. K.) CRC Press, FL. 305-319.

14. Shi, Y.-B. (2011) The right journal for the right time.  Cell & Bioscience 1:1, 1.

15. Ishizuya-Oka, A., and Shi, Y.-B. (2011) Evolutionary insights into postembryonic development of adult intestinal stem cells. Cell & Bioscience 1:37, 1-3.

16. Zhao, K., and Shi, Y.-B. (2012) An anti-cancer Smurf. Cell & Bioscienc e2:10, 1-2

17. Shi, Y.-B. (2012) The 2011 Ming K Jeang Award for Excellence in Cell & Bioscience. Cell & Bioscienc e2:16, 1.

Books

1*. Shi*, Y.-B., Shi, Y., Xu, Y., and Scott, D. (1997) Eds. Programmed Cell Death. 171 pp. Plenum Publishing Corp., New York.

2. Shi, Y.-B. (1999). Amphibian Metamorphosis: From morphology to molecular biology. John Wiley & Sons, Inc., New York.

3. Shi, Y., Cidlowski, J., Scott, D., Wu, J., and Shi, Y.-B. (2003) Eds. Molecular Mechanisms of Programmed Cell Death. Kluwer Academic/Plenum, New York, 229 pp.

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