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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 吳君泰(June-Tai Wu) | |
dc.contributor.author | Yi-Jyun Chen | en |
dc.contributor.author | 陳怡君 | zh_TW |
dc.date.accessioned | 2021-06-15T11:30:27Z | - |
dc.date.available | 2018-08-26 | |
dc.date.copyright | 2016-08-26 | |
dc.date.issued | 2016 | |
dc.date.submitted | 2016-08-17 | |
dc.identifier.citation | 1. Varga-Weisz, P., ATP-dependent chromatin remodeling factors: nucleosome shufflers with many missions. Oncogene, 2001. 20(24): p. 3076-85.
2. Vignali, M., et al., ATP-dependent chromatin-remodeling complexes. Mol Cell Biol, 2000. 20(6): p. 1899-910. 3. Narlikar, G.J., R. Sundaramoorthy, and T. Owen-Hughes, Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes. Cell, 2013. 154(3): p. 490-503. 4. Jenuwein, T. and C.D. Allis, Translating the histone code. Science, 2001. 293(5532): p. 1074-80. 5. Bannister, A.J. and T. Kouzarides, Regulation of chromatin by histone modifications. Cell Res, 2011. 21(3): p. 381-95. 6. Strahl, B.D. and C.D. Allis, The language of covalent histone modifications. Nature, 2000. 403(6765): p. 41-5. 7. Zhang, Y. and D. Reinberg, Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev, 2001. 15(18): p. 2343-60. 8. Eberharter, A. and P.B. Becker, Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep, 2002. 3(3): p. 224-9. 9. Rice, J.C., et al., Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell, 2003. 12(6): p. 1591-8. 10. Zhang, Y., Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev, 2003. 17(22): p. 2733-40. 11. Verdone, L., M. Caserta, and E. Di Mauro, Role of histone acetylation in the control of gene expression. Biochem Cell Biol, 2005. 83(3): p. 344-53. 12. Osley, M.A., A.B. Fleming, and C.F. Kao, Histone ubiquitylation and the regulation of transcription. Results Probl Cell Differ, 2006. 41: p. 47-75. 13. Banerjee, T. and D. Chakravarti, A peek into the complex realm of histone phosphorylation. Mol Cell Biol, 2011. 31(24): p. 4858-73. 14. Rossetto, D., N. Avvakumov, and J. Cote, Histone phosphorylation: a chromatin modification involved in diverse nuclear events. Epigenetics, 2012. 7(10): p. 1098-108. 15. Cao, J. and Q. Yan, Histone ubiquitination and deubiquitination in transcription, DNA damage response, and cancer. Front Oncol, 2012. 2: p. 26. 16. Karmodiya, K., et al., H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics, 2012. 13: p. 424. 17. Vakoc, C.R., et al., Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol, 2006. 26(24): p. 9185-95. 18. Kuo, M.H. and C.D. Allis, Roles of histone acetyltransferases and deacetylases in gene regulation. Bioessays, 1998. 20(8): p. 615-26. 19. de Ruijter, A.J., et al., Histone deacetylases (HDACs): characterization of the classical HDAC family. Biochem J, 2003. 370(Pt 3): p. 737-49. 20. Klose, R.J. and Y. Zhang, Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol, 2007. 8(4): p. 307-18. 21. Musselman, C.A., et al., Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol, 2012. 19(12): p. 1218-27. 22. Mujtaba, S., L. Zeng, and M.M. Zhou, Structure and acetyl-lysine recognition of the bromodomain. Oncogene, 2007. 26(37): p. 5521-7. 23. Zeng, L. and M.M. Zhou, Bromodomain: an acetyl-lysine binding domain. FEBS Lett, 2002. 513(1): p. 124-8. 24. Bannister, A.J., et al., Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature, 2001. 410(6824): p. 120-4. 25. Jacobs, S.A. and S. Khorasanizadeh, Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science, 2002. 295(5562): p. 2080-3. 26. Nielsen, P.R., et al., Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature, 2002. 416(6876): p. 103-7. 27. Yap, K.L. and M.M. Zhou, Structure and mechanisms of lysine methylation recognition by the chromodomain in gene transcription. Biochemistry, 2011. 50(12): p. 1966-80. 28. Zhang, Y., It takes a PHD to interpret histone methylation. Nat Struct Mol Biol, 2006. 13(7): p. 572-4. 29. Sanchez, R. and M.M. Zhou, The PHD finger: a versatile epigenome reader. Trends Biochem Sci, 2011. 36(7): p. 364-72. 30. Yun, M., et al., Readers of histone modifications. Cell Res, 2011. 21(4): p. 564-78. 31. Suganuma, T., S.G. Pattenden, and J.L. Workman, Diverse functions of WD40 repeat proteins in histone recognition. Genes Dev, 2008. 22(10): p. 1265-8. 32. Xu, C. and J. Min, Structure and function of WD40 domain proteins. Protein Cell, 2011. 2(3): p. 202-14. 33. Huang, Y., et al., Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science, 2006. 312(5774): p. 748-51. 34. Rogne, M., et al., The KH-Tudor domain of a-kinase anchoring protein 149 mediates RNA-dependent self-association. Biochemistry, 2006. 45(50): p. 14980-9. 35. Brent, M.M. and R. Marmorstein, Ankyrin for methylated lysines. Nat Struct Mol Biol, 2008. 15(3): p. 221-2. 36. Collins, R.E., et al., The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat Struct Mol Biol, 2008. 15(3): p. 245-50. 37. Bittencourt, D., et al., Role of distinct surfaces of the G9a ankyrin repeat domain in histone and DNA methylation during embryonic stem cell self-renewal and differentiation. Epigenetics Chromatin, 2014. 7: p. 27. 38. Vezzoli, A., et al., Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nat Struct Mol Biol, 2010. 17(5): p. 617-9. 39. Wu, H., et al., Structural and histone binding ability characterizations of human PWWP domains. PLoS One, 2011. 6(6): p. e18919. 40. Qin, S. and J. Min, Structure and function of the nucleosome-binding PWWP domain. Trends Biochem Sci, 2014. 39(11): p. 536-47. 41. Wang, G.G., C.D. Allis, and P. Chi, Chromatin remodeling and cancer, Part I: Covalent histone modifications. Trends Mol Med, 2007. 13(9): p. 363-72. 42. Struhl, K., Histone acetylation and transcriptional regulatory mechanisms. Genes Dev, 1998. 12(5): p. 599-606. 43. Wang, X., et al., Acetylation increases the alpha-helical content of the histone tails of the nucleosome. J Biol Chem, 2000. 275(45): p. 35013-20. 44. Brower-Toland, B., et al., Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J Mol Biol, 2005. 346(1): p. 135-46. 45. Lee, J.Y. and T.H. Lee, Effects of histone acetylation and CpG methylation on the structure of nucleosomes. Biochim Biophys Acta, 2012. 1824(8): p. 974-82. 46. Henikoff, S., Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet, 2008. 9(1): p. 15-26. 47. Rocha, W. and A. Verreault, Clothing up DNA for all seasons: Histone chaperones and nucleosome assembly pathways. FEBS Lett, 2008. 582(14): p. 1938-49. 48. Chakravarthy, S., et al., Structure and dynamic properties of nucleosome core particles. FEBS Lett, 2005. 579(4): p. 895-8. 49. Luger, K., Dynamic nucleosomes. Chromosome Res, 2006. 14(1): p. 5-16. 50. Korber, P. and P.B. Becker, Nucleosome dynamics and epigenetic stability. Essays Biochem, 2010. 48(1): p. 63-74. 51. Andrews, A.J. and K. Luger, Nucleosome structure(s) and stability: variations on a theme. Annu Rev Biophys, 2011. 40: p. 99-117. 52. Zentner, G.E. and S. Henikoff, Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol, 2013. 20(3): p. 259-66. 53. Scharf, A.N., T.K. Barth, and A. Imhof, Establishment of histone modifications after chromatin assembly. Nucleic Acids Res, 2009. 37(15): p. 5032-40. 54. Wirbelauer, C., O. Bell, and D. Schubeler, Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias. Genes Dev, 2005. 19(15): p. 1761-6. 55. Chen, P., et al., H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev, 2013. 27(19): p. 2109-24. 56. Kamakaka, R.T. and S. Biggins, Histone variants: deviants? Genes Dev, 2005. 19(3): p. 295-310. 57. Ausio, J., Histone variants--the structure behind the function. Brief Funct Genomic Proteomic, 2006. 5(3): p. 228-43. 58. Bonenfant, D., et al., Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry. Mol Cell Proteomics, 2006. 5(3): p. 541-52. 59. Boulard, M., et al., Histone variant nucleosomes: structure, function and implication in disease. Subcell Biochem, 2007. 41: p. 71-89. 60. Weber, C.M. and S. Henikoff, Histone variants: dynamic punctuation in transcription. Genes Dev, 2014. 28(7): p. 672-82. 61. Venkatesh, S. and J.L. Workman, Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol, 2015. 16(3): p. 178-89. 62. Zhong, C.X., et al., Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell, 2002. 14(11): p. 2825-36. 63. Mendiburo, M.J., et al., Drosophila CENH3 is sufficient for centromere formation. Science, 2011. 334(6056): p. 686-90. 64. Ravi, M., et al., Meiosis-specific loading of the centromere-specific histone CENH3 in Arabidopsis thaliana. PLoS Genet, 2011. 7(6): p. e1002121. 65. Unni, E., et al., Stage-specific distribution of the spermatid-specific histone 2B in the rat testis. Biol Reprod, 1995. 53(4): p. 820-6. 66. Zalensky, A.O., et al., Human testis/sperm-specific histone H2B (hTSH2B). Molecular cloning and characterization. J Biol Chem, 2002. 277(45): p. 43474-80. 67. Li, A., et al., Characterization of nucleosomes consisting of the human testis/sperm-specific histone H2B variant (hTSH2B). Biochemistry, 2005. 44(7): p. 2529-35. 68. Cedar, H. and Y. Bergman, Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet, 2009. 10(5): p. 295-304. 69. Illingworth, R.S. and A.P. Bird, CpG islands--'a rough guide'. FEBS Lett, 2009. 583(11): p. 1713-20. 70. Deaton, A.M. and A. Bird, CpG islands and the regulation of transcription. Genes Dev, 2011. 25(10): p. 1010-22. 71. Jones, P.A., Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet, 2012. 13(7): p. 484-92. 72. Vaissiere, T., C. Sawan, and Z. Herceg, Epigenetic interplay between histone modifications and DNA methylation in gene silencing. Mutat Res, 2008. 659(1-2): p. 40-8. 73. Kondo, Y., Epigenetic cross-talk between DNA methylation and histone modifications in human cancers. Yonsei Med J, 2009. 50(4): p. 455-63. 74. Rose, N.R. and R.J. Klose, Understanding the relationship between DNA methylation and histone lysine methylation. Biochim Biophys Acta, 2014. 1839(12): p. 1362-72. 75. Law, J.A. and S.E. Jacobsen, Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet, 2010. 11(3): p. 204-20. 76. Jin, B., Y. Li, and K.D. Robertson, DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer, 2011. 2(6): p. 607-17. 77. Ooi, S.K., et al., DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature, 2007. 448(7154): p. 714-7. 78. Lande-Diner, L. and H. Cedar, Silence of the genes--mechanisms of long-term repression. Nat Rev Genet, 2005. 6(8): p. 648-54. 79. Mikkelsen, T.S., et al., Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 2007. 448(7153): p. 553-60. 80. Nuyt, A.M. and M. Szyf, Developmental programming through epigenetic changes. Circ Res, 2007. 100(4): p. 452-5. 81. Gabory, A., L. Attig, and C. Junien, Developmental programming and epigenetics. Am J Clin Nutr, 2011. 94(6 Suppl): p. 1943S-1952S. 82. Hassa, P.O. and M.O. Hottiger, An epigenetic code for DNA damage repair pathways? Biochem Cell Biol, 2005. 83(3): p. 270-85. 83. Dinant, C., A.B. Houtsmuller, and W. Vermeulen, Chromatin structure and DNA damage repair. Epigenetics Chromatin, 2008. 1(1): p. 9. 84. Rossetto, D., et al., Epigenetic modifications in double-strand break DNA damage signaling and repair. Clin Cancer Res, 2010. 16(18): p. 4543-52. 85. Lahtz, C. and G.P. Pfeifer, Epigenetic changes of DNA repair genes in cancer. J Mol Cell Biol, 2011. 3(1): p. 51-8. 86. Lennartsson, A. and K. Ekwall, Histone modification patterns and epigenetic codes. Biochim Biophys Acta, 2009. 1790(9): p. 863-8. 87. Villar-Garea, A., L. Israel, and A. Imhof, Analysis of histone modifications by mass spectrometry. Curr Protoc Protein Sci, 2008. Chapter 14: p. Unit 14 10. 88. Britton, L.M., et al., Breaking the histone code with quantitative mass spectrometry. Expert Rev Proteomics, 2011. 8(5): p. 631-43. 89. Simon, J.A. and R.E. Kingston, Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol, 2009. 10(10): p. 697-708. 90. Young, M.D., et al., ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res, 2011. 39(17): p. 7415-27. 91. Lewis, E.B., A gene complex controlling segmentation in Drosophila. Nature, 1978. 276(5688): p. 565-70. 92. Levine, S.S., et al., The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. Mol Cell Biol, 2002. 22(17): p. 6070-8. 93. Buchenau, P., et al., The distribution of polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing. J Cell Biol, 1998. 141(2): p. 469-81. 94. Bracken, A.P. and K. Helin, Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer, 2009. 9(11): p. 773-84. 95. Sauvageau, M. and G. Sauvageau, Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. Cell Stem Cell, 2010. 7(3): p. 299-313. 96. Steffen, P.A. and L. Ringrose, What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nat Rev Mol Cell Biol, 2014. 15(5): p. 340-56. 97. Beuchle, D., G. Struhl, and J. Muller, Polycomb group proteins and heritable silencing of Drosophila Hox genes. Development, 2001. 128(6): p. 993-1004. 98. Schuettengruber, B., et al., Genome regulation by polycomb and trithorax proteins. Cell, 2007. 128(4): p. 735-45. 99. Schuettengruber, B., et al., Trithorax group proteins: switching genes on and keeping them active. Nat Rev Mol Cell Biol, 2011. 12(12): p. 799-814. 100. Ringrose, L. and R. Paro, Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development, 2007. 134(2): p. 223-32. 101. Boyer, L.A., et al., Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature, 2006. 441(7091): p. 349-53. 102. Lee, T.I., et al., Control of developmental regulators by Polycomb in human embryonic stem cells. Cell, 2006. 125(2): p. 301-13. 103. Maurange, C. and R. Paro, A cellular memory module conveys epigenetic inheritance of hedgehog expression during Drosophila wing imaginal disc development. Genes Dev, 2002. 16(20): p. 2672-83. 104. Buszczak, M. and A.C. Spradling, Searching chromatin for stem cell identity. Cell, 2006. 125(2): p. 233-6. 105. Bracken, A.P., et al., Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev, 2006. 20(9): p. 1123-36. 106. Muller, P., et al., Identification of JAK/STAT signalling components by genome-wide RNA interference. Nature, 2005. 436(7052): p. 871-5. 107. Classen, A.K., et al., A tumor suppressor activity of Drosophila Polycomb genes mediated by JAK-STAT signaling. Nat Genet, 2009. 41(10): p. 1150-5. 108. Pasini, D., A.P. Bracken, and K. Helin, Polycomb group proteins in cell cycle progression and cancer. Cell Cycle, 2004. 3(4): p. 396-400. 109. Valk-Lingbeek, M.E., S.W. Bruggeman, and M. van Lohuizen, Stem cells and cancer; the polycomb connection. Cell, 2004. 118(4): p. 409-18. 110. Zhou, W., et al., Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation. Mol Cell, 2008. 29(1): p. 69-80. 111. Schwartz, Y.B. and V. Pirrotta, A new world of Polycombs: unexpected partnerships and emerging functions. Nat Rev Genet, 2013. 14(12): p. 853-64. 112. Wang, H., et al., Role of histone H2A ubiquitination in Polycomb silencing. Nature, 2004. 431(7010): p. 873-8. 113. Min, J., Y. Zhang, and R.M. Xu, Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev, 2003. 17(15): p. 1823-8. 114. Bernstein, E., et al., Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol Cell Biol, 2006. 26(7): p. 2560-9. 115. Kaustov, L., et al., Recognition and specificity determinants of the human cbx chromodomains. J Biol Chem, 2011. 286(1): p. 521-9. 116. Wang, R., et al., Polycomb group targeting through different binding partners of RING1B C-terminal domain. Structure, 2010. 18(8): p. 966-75. 117. Vandamme, J., et al., Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. Mol Cell Proteomics, 2011. 10(4): p. M110 002642. 118. Gao, Z., et al., PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol Cell, 2012. 45(3): p. 344-56. 119. Cao, R., et al., Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science, 2002. 298(5595): p. 1039-43. 120. Czermin, B., et al., Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell, 2002. 111(2): p. 185-96. 121. Muller, J., et al., Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell, 2002. 111(2): p. 197-208. 122. Kuzmichev, A., et al., Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev, 2002. 16(22): p. 2893-905. 123. Nekrasov, M., et al., Pcl-PRC2 is needed to generate high levels of H3-K27 trimethylation at Polycomb target genes. EMBO J, 2007. 26(18): p. 4078-88. 124. Cao, R., et al., Role of hPHF1 in H3K27 methylation and Hox gene silencing. Mol Cell Biol, 2008. 28(5): p. 1862-72. 125. Sarma, K., et al., Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo. Mol Cell Biol, 2008. 28(8): p. 2718-31. 126. Savla, U., et al., Recruitment of Drosophila Polycomb-group proteins by Polycomblike, a component of a novel protein complex in larvae. Development, 2008. 135(5): p. 813-7. 127. Barski, A., et al., High-resolution profiling of histone methylations in the human genome. Cell, 2007. 129(4): p. 823-37. 128. Gilchrist, D.A., et al., Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks. Genes Dev, 2012. 26(9): p. 933-44. 129. Wu, J.Q. and M. Snyder, RNA polymerase II stalling: loading at the start prepares genes for a sprint. Genome Biol, 2008. 9(5): p. 220. 130. Stock, J.K., et al., Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat Cell Biol, 2007. 9(12): p. 1428-35. 131. Birve, A., et al., Su(z)12, a novel Drosophila Polycomb group gene that is conserved in vertebrates and plants. Development, 2001. 128(17): p. 3371-9. 132. Katz, A., et al., FIE and CURLY LEAF polycomb proteins interact in the regulation of homeobox gene expression during sporophyte development. Plant J, 2004. 37(5): p. 707-19. 133. Katoh-Fukui, Y., et al., Male-to-female sex reversal in M33 mutant mice. Nature, 1998. 393(6686): p. 688-92. 134. Whitcomb, S.J., et al., Polycomb Group proteins: an evolutionary perspective. Trends Genet, 2007. 23(10): p. 494-502. 135. Gonzalez, I., R. Simon, and A. Busturia, The Polyhomeotic protein induces hyperplastic tissue overgrowth through the activation of the JAK/STAT pathway. Cell Cycle, 2009. 8(24): p. 4103-11. 136. Martinez, A.M. and G. Cavalli, The role of polycomb group proteins in cell cycle regulation during development. Cell Cycle, 2006. 5(11): p. 1189-97. 137. Piunti, A., et al., Polycomb proteins control proliferation and transformation independently of cell cycle checkpoints by regulating DNA replication. Nat Commun, 2014. 5: p. 3649. 138. Zeidler, M., et al., The Polycomb group protein EZH2 impairs DNA repair in breast epithelial cells. Neoplasia, 2005. 7(11): p. 1011-9. 139. Vissers, J.H., M. van Lohuizen, and E. Citterio, The emerging role of Polycomb repressors in the response to DNA damage. J Cell Sci, 2012. 125(Pt 17): p. 3939-48. 140. Yang, Q., et al., The Polycomb Group Protein EZH2 Impairs DNA Damage Repair Gene Expression in Human Uterine Fibroids. Biol Reprod, 2016. 94(3): p. 69. 141. Mahmoudi, T. and C.P. Verrijzer, Chromatin silencing and activation by Polycomb and trithorax group proteins. Oncogene, 2001. 20(24): p. 3055-66. 142. Francis, N.J., R.E. Kingston, and C.L. Woodcock, Chromatin compaction by a polycomb group protein complex. Science, 2004. 306(5701): p. 1574-7. 143. Grau, D.J., et al., Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge. Genes Dev, 2011. 25(20): p. 2210-21. 144. Schwartz, Y.B., et al., Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet, 2006. 38(6): p. 700-5. 145. Kohler, C. and L. Hennig, Regulation of cell identity by plant Polycomb and trithorax group proteins. Curr Opin Genet Dev, 2010. 20(5): p. 541-7. 146. Prezioso, C. and V. Orlando, Polycomb proteins in mammalian cell differentiation and plasticity. FEBS Lett, 2011. 585(13): p. 2067-77. 147. Sparmann, A. and M. van Lohuizen, Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer, 2006. 6(11): p. 846-56. 148. Rajasekhar, V.K. and M. Begemann, Concise review: roles of polycomb group proteins in development and disease: a stem cell perspective. Stem Cells, 2007. 25(10): p. 2498-510. 149. Arisan, S., et al., Increased expression of EZH2, a polycomb group protein, in bladder carcinoma. Urol Int, 2005. 75(3): p. 252-7. 150. Bracken, A.P., et al., EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J, 2003. 22(20): p. 5323-35. 151. Raman, J.D., et al., Increased expression of the polycomb group gene, EZH2, in transitional cell carcinoma of the bladder. Clin Cancer Res, 2005. 11(24 Pt 1): p. 8570-6. 152. Weikert, S., et al., Expression levels of the EZH2 polycomb transcriptional repressor correlate with aggressiveness and invasive potential of bladder carcinomas. Int J Mol Med, 2005. 16(2): p. 349-53. 153. Sanchez-Beato, M., et al., Variability in the expression of polycomb proteins in different normal and tumoral tissues. A pilot study using tissue microarrays. Mod Pathol, 2006. 19(5): p. 684-94. 154. Bachmann, I.M., et al., EZH2 expression is associated with high proliferation rate and aggressive tumor subgroups in cutaneous melanoma and cancers of the endometrium, prostate, and breast. J Clin Oncol, 2006. 24(2): p. 268-73. 155. Kleer, C.G., et al., EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci U S A, 2003. 100(20): p. 11606-11. 156. Kirmizis, A., S.M. Bartley, and P.J. Farnham, Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol Cancer Ther, 2003. 2(1): p. 113-21. 157. Raaphorst, F.M., et al., Poorly differentiated breast carcinoma is associated with increased expression of the human polycomb group EZH2 gene. Neoplasia, 2003. 5(6): p. 481-8. 158. van Kemenade, F.J., et al., Coexpression of BMI-1 and EZH2 polycomb-group proteins is associated with cycling cells and degree of malignancy in B-cell non-Hodgkin lymphoma. Blood, 2001. 97(12): p. 3896-901. 159. D'Costa, A., et al., The Drosophila ramshackle gene encodes a chromatin-associated protein required for cell morphology in the developing eye. Mech Dev, 2006. 123(8): p. 591-604. 160. Chen, W.Y., et al., Intellectual disability-associated dBRWD3 regulates gene expression through inhibition of HIRA/YEM-mediated chromatin deposition of histone H3.3. EMBO Rep, 2015. 161. Kondo, S. and N. Perrimon, A genome-wide RNAi screen identifies core components of the G(2)-M DNA damage checkpoint. Sci Signal, 2011. 4(154): p. rs1. 162. Field, M., et al., Mutations in the BRWD3 gene cause X-linked mental retardation associated with macrocephaly. Am J Hum Genet, 2007. 81(2): p. 367-74. 163. Moazed, D. and P.H. O'Farrell, Maintenance of the engrailed expression pattern by Polycomb group genes in Drosophila. Development, 1992. 116(3): p. 805-10. 164. Kennison, J.A., The Polycomb and trithorax group proteins of Drosophila: trans-regulators of homeotic gene function. Annu Rev Genet, 1995. 29: p. 289-303. 165. Ali, J.Y. and W. Bender, Cross-regulation among the polycomb group genes in Drosophila melanogaster. Mol Cell Biol, 2004. 24(17): p. 7737-47. 166. Fang, M., et al., Drosophila ptip is essential for anterior/posterior patterning in development and interacts with the PcG and trxG pathways. Development, 2009. 136(11): p. 1929-38. 167. Schwartz, Y.B. and V. Pirrotta, Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet, 2007. 8(1): p. 9-22. 168. van Steensel, B. and S. Henikoff, Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol, 2000. 18(4): p. 424-8. 169. Tokimasa, S., et al., Lack of the Polycomb-group gene rae28 causes maturation arrest at the early B-cell developmental stage. Exp Hematol, 2001. 29(1): p. 93-103. 170. Sawa, M., et al., BMI-1 is highly expressed in M0-subtype acute myeloid leukemia. Int J Hematol, 2005. 82(1): p. 42-7. 171. Nakahata, S., et al., Alteration of enhancer of polycomb 1 at 10p11.2 is one of the genetic events leading to development of adult T-cell leukemia/lymphoma. Genes Chromosomes Cancer, 2009. 48(9): p. 768-76. 172. Boultwood, J., et al., Frequent mutation of the polycomb-associated gene ASXL1 in the myelodysplastic syndromes and in acute myeloid leukemia. Leukemia, 2010. 24(5): p. 1062-5. 173. Carbuccia, N., et al., Mutual exclusion of ASXL1 and NPM1 mutations in a series of acute myeloid leukemias. Leukemia, 2010. 24(2): p. 469-73. 174. Reichert, H. and B. Bello, Hox genes and brain development in Drosophila. Adv Exp Med Biol, 2010. 689: p. 145-53. 175. Sprecher, S.G., et al., Hox gene cross-regulatory interactions in the embryonic brain of Drosophila. Mech Dev, 2004. 121(6): p. 527-36. 176. Sandoval, J., et al., RNAPol-ChIP: a novel application of chromatin immunoprecipitation to the analysis of real-time gene transcription. Nucleic Acids Res, 2004. 32(11): p. e88. 177. Sun, H., et al., Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Res, 2011. 39(1): p. 190-201. 178. Zeitlinger, J., et al., RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet, 2007. 39(12): p. 1512-6. 179. Hendrix, D.A., et al., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci U S A, 2008. 105(22): p. 7762-7. 180. Southall, T.D., et al., Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells. Dev Cell, 2013. 26(1): p. 101-12. 181. Ping, Y.H. and T.M. Rana, DSIF and NELF interact with RNA polymerase II elongation complex and HIV-1 Tat stimulates P-TEFb-mediated phosphorylation of RNA polymerase II and DSIF during transcription elongation. J Biol Chem, 2001. 276(16): p. 12951-8. 182. Wu, C.H., et al., NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev, 2003. 17(11): p. 1402-14. 183. Aida, M., et al., Transcriptional pausing caused by NELF plays a dual role in regulating immediate-early expression of the junB gene. Mol Cell Biol, 2006. 26(16): p. 6094-104. 184. Lee, C., et al., NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol Cell Biol, 2008. 28(10): p. 3290-300. 185. Adelman, K. and J.T. Lis, Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet, 2012. 13(10): p. 720-31. 186. Yamaguchi, Y., H. Shibata, and H. Handa, Transcription elongation factors DSIF and NELF: promoter-proximal pausing and beyond. Biochim Biophys Acta, 2013. 1829(1): p. 98-104. 187. Mandal, S.S., et al., Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc Natl Acad Sci U S A, 2004. 101(20): p. 7572-7. 188. Gilchrist, D.A., et al., NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev, 2008. 22(14): p. 1921-33. 189. Muller-McNicoll, M. and K.M. Neugebauer, How cells get the message: dynamic assembly and function of mRNA-protein complexes. Nat Rev Genet, 2013. 14(4): p. 275-87. 190. Sims, R.J., 3rd, R. Belotserkovskaya, and D. Reinberg, Elongation by RNA polymerase II: the short and long of it. Genes Dev, 2004. 18(20): p. 2437-68. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/49475 | - |
dc.description.abstract | 表觀遺傳調控為控制基因表現的一種方式,可透過改變染色質上核小體的位置、核小體中組蛋白的組成、核小體中組蛋白上的轉譯後修飾及去氧核醣核酸序列中腺嘌呤的甲基化,來達到染色質的狀態改變,影響轉錄因子接近染色質的能力而改變基因表現,進而影響生物體中的細胞型態、細胞分化或不同發展階段的基因調控。其中,可透過加上組蛋白的轉譯後修飾達到抑制基因表現的一種蛋白質複合體Polycomb Group (PcGs) 可專一性地催化H2AK118及H3K27me3此二種抑制性組蛋白密碼,來使其目標基因的表現被抑制。除此之外,PcGs也被發現可調控具有轉錄因子特性的基因、或是參與在訊息傳遞路徑中的部份基因表現。另一方面,核小體中組蛋白變異體的置換亦被視為一種表觀遺傳的調控機制,如組蛋白H3變異體H3.3在染色質上的置換與基因轉錄的區域相關。在實驗室先前的研究中發現,組蛋白變異體的置換存在負向的調控方式,意即H3.3的置換可被dBRWD3 (Drosophila Bromodomain and WD repeat domain containing 3) 透過其伴護蛋白HIRA/YEM的作用來負向調控。而在本研究中,我們透過減少PcGs其中一蛋白質Pc在果蠅幼蟲神經系統中的表現,發現其目標基因Ubx及Antp產生異位基因表現,而此異位基因表現可由減少dBRWD3的表現來達到抑制。而若減少PcGs中的H3K27甲基轉移酶E(z) 的表現,也會產生目標基因的異位表現,同樣地,亦可透過減少dBRWD3的表現來抑制。此外,當我們減少特定的基本轉錄因子 (General transcription factors, e.g. TAF5, TAF7, Cdk7 or CycH) 的表現時,同樣也抑制了由Pc或E(z) 表現量降低導致的異位基因表現。有趣的是,當我們只降低dBRWD3表現量時,Ubx或Antp的原位基因表現卻不受影響,因此,我們好奇降低dBRWD3表現量可達到抑制異位基因表現的分子機制為何。首先,我們著重於dBRWD3是否會對RNA Polymerase II產生影響做探討,利用DamID (DNA Adenine Methylation Identification) 來偵測Pol II在Ubx或Antp上佔據的頻率,發現dBRWD3的表現量降低可能會使Pol II停留在Antp上的啟動子或靠近5’端的區域,而影響基因轉錄初期。接下來,我們想知道dBRWD3表現量降低而抑制異位基因表現的原因,是否是透過補回因PcGs表現量降低導致的抑制性組蛋白密碼缺失,因此我們利用H2AK118ub或H3K27me3的染色質免疫沉澱 (ChIP),發現在降低Pc或E(z) 表現量的同時,再減少dBRWD3的表現時,抑制性組蛋白修飾並未受到影響,因此,其分子機制還有待更多實驗來釐清。而在了解dBRWD3在異位基因表現中扮演之角色的過程中,我們意外發現異位與原位基因表現在表觀遺傳中的不同之處。 | zh_TW |
dc.description.abstract | Epigenetic regulation involves chromatin remodeling, nucleosome assembly, replacement of histone variants and DNA methylation. Histone modification alter the compaction of chromatin, thereby affecting transcription factors binding to gene regions. One of the well-known enzymes that catalyze histone modifications, Polycomb group (PcG) proteins, are reported to write the repressive histone marks, H3K27me3 and H2AK118ub, to keep the targeted gene silenced. On the other hand, the incorporation of histone variants is another regulatory mechanism of epigenetics. In the previous studies, we found that incorporation of histone variants could be regulated negatively. The incorporation of histone 3 variant, H3.3, could be negatively regulated by dBRWD3 (Drosophila Bromodomain and WD repeat domain containing 3) through a HIRA/YEM-dependent pathway. Here, we found when we depleted one of the PcG protein, Pc, in Drosophila larval nervous system, Ubx and Antp, two Hox genes, expressed ectopically (into the brain. Interestingly, this ectopic gene expression could be suppressed by dBRWD3 depletion. dBRWD3 depletion also suppressed the ectopic gene expression caused by the depletion of E(z), encoding the histone methyltransferase that catalyzes the modification of H3K27me3. Moreover, when we depleted the general transcription factors, Cdk7, CycH, TAF5 or TAF7, the ectopic expression of Ubx or Antp was also suppressed. Interestingly, there was no alteration of orthotopic gene expression by dBRWD3 depletion. To dissect the mechanisms underlying the suppression of ectopic gene expression by dBRWD3 depletion. First, we focused on the effect of dBRWD3 on RNA polymerase II. We utilized DamID (DNA adenine methyltransferase identification) to study the frequency of Pol II occupying on the target genes (Ubx, Antp). The results showed that dBRWD3 depletion might maintain Pol II-Dam on promoter and 5' regions of Antp and then affect the initial stage of transcription.. Second, we wondered if the repressive histone mark added by PcGs would be rescued by dBRWD3 depletion. We utilized ChIP of H3K27me3 or H2AK118ub, and found that additional dBRWD3 depletion had no effect on these marks when E(z) or Pc was depleted. In the process to investigate the role of dBRWD3in ectopic gene expression, we unexpectedly provided a new insights into the differences between the ectopic and orthotopic gene expression. | en |
dc.description.provenance | Made available in DSpace on 2021-06-15T11:30:27Z (GMT). No. of bitstreams: 1 ntu-105-R03448013-1.pdf: 6365797 bytes, checksum: 0d54d11543060c27fc20a65b128c7f66 (MD5) Previous issue date: 2016 | en |
dc.description.tableofcontents | 目錄
口試委員會審定書 i Abstract ii 中文摘要 iv Chapter 1 Introduction 1 1.1 Epigenetics 1 1.2 Polycomb Group (PcG) 6 1.3 dBRWD3 9 Chapter 2 Result 11 2.1 The role of dBRWD3 regarding ectopic expression 12 2.2 The mechanism underlying the suppression of ectopic gene expression by dBRWD3 depletion 15 2.3 The role of Nelf-B regarding ectopic expression 20 Chapter 3 Discussion 22 3.1 The difference of detecting Pol II between DamID and ChIP 22 3.2 The differences between ectopic and orthotopic gene expression 23 3.3 The mechanism of dBRWD3 as the suppressor of ectopic gene expression 24 3.4 The role of Nelf-B in ectopic gene expression 25 Materials and Methods 27 Figures 32 Tables 62 Appendix 63 Reference 67 | |
dc.language.iso | en | |
dc.title | dBRWD3 抑制 Polycomb Group 突變導致之異位基因表現 | zh_TW |
dc.title | dBRWD3 suppressed the ectopic gene expression resulted from Polycomb Group mutations | en |
dc.type | Thesis | |
dc.date.schoolyear | 104-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 李秀香(Hsiu-Hsiang Lee),劉雅雯(Ya-Wen Liu),皮海薇(Hai-Wei Pi) | |
dc.subject.keyword | 表觀遺傳學,轉譯,Polycomb Groups,dBRWD3,組蛋白H3.3,異位基因表現, | zh_TW |
dc.subject.keyword | Epigenetics,Transcription,Polycomb Groups,dBRWD3,H3.3,Ectopic gene expression, | en |
dc.relation.page | 79 | |
dc.identifier.doi | 10.6342/NTU201603124 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2016-08-17 | |
dc.contributor.author-college | 醫學院 | zh_TW |
dc.contributor.author-dept | 分子醫學研究所 | zh_TW |
顯示於系所單位: | 分子醫學研究所 |
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