Please use this identifier to cite or link to this item:
標題: I.參與DNA甲基化之基因定位 II.利用酵母菌雙雜合系統篩選與AtRH57相互作用的蛋白質
I.Gene mapping of genes involving DNA methylation II.Identification of AtRH57-interacting proteins using yeast two-hybrid system
作者: 盧冠宏
Lu, Kuan-Hung
關鍵字: 甲基化;DNA methylation;基因定位;酵母菌雙雜合系統;mapping;yeast two-hybrid system
出版社: 生物科技學研究所
引用: 第一章 Agius F, Kapoor A, Zhu J-K (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proceedings of the National Academy of Sciences of the United States of America 103: 11796-11801 Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, Sikkink K, Chandler VL (2006) An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442: 295-298 Alonso-Blanco C, Aarts MGM, Bentsink L, Keurentjes JJB, Reymond M, Vreugdenhil D, Koornneef M (2009) What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation? Plant Cell 21: 1877-1896 Alonso JM, Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nature Reviews Genetics 7: 524-536 Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen HM, Shinn P, Stevenson DK, Zimmerman J, Barajas P, et al. (2003) Genome-wide Insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657 Amasino R (2010) Seasonal and developmental timing of flowering. Plant Journal 61: 1001-1013 Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJM (2002) HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. Embo Journal 21: 6832-6841 Ausin I, Mockler TC, Chory J, Jacobsen SE (2009) IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nature Structural & Molecular Biology 16: 1325-1327 AzpirozLeehan R, Feldmann KA (1997) T-DNA insertion mutagenesis in Arabidopsis: Going back and forth. Trends in Genetics 13: 152-156 Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19: 137-144 Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363-366 Bies-Etheve N, Pontier D, Lahmy S, Picart C, Vega D, Cooke R, Lagrange T (2009) RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. Embo Reports 10: 649-654 Bird A (2002) DNA methylation patterns and epigenetic memory. Genes & Development 16: 6-21 Borsani O, Zhu JH, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123: 1279-1291 Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314-331 Cao XF, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proceedings of the National Academy of Sciences of the United States of America 99: 16491-16498 Cao XF, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE (2003) Role of the DRM and CMT3 Methyltransferases in RNA-directed DNA methylation. Current Biology 13: 2212-2217 Carmell MA, Xuan ZY, Zhang MQ, Hannon GJ (2002) The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes & Development 16: 2733-2742 Carpenter AE, Sabatini DM (2004) Systematic genome-wide screens of gene function. Nature Reviews Genetics 5: 11-22 Chan SWL, Zilberman D, Xie ZX, Johansen LK, Carrington JC, Jacobsen SE (2004) RNA silencing genes control de novo DNA methylation. Science 303: 1336-1336 Chi X-F, Lou X-Y, Shu Q-Y (2008) Progressive fine mapping in experimental populations: An improved strategy toward positional cloning. Journal of Theoretical Biology 253: 817-823 Chinnusamy V, Zhu J-K (2009) RNA-directed DNA methylation and demethylation in plants. Science in China Series C-Life Sciences 52: 331-343 Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219 Erhard KF, Jr., Stonaker JL, Parkinson SE, Lim JP, Hale CJ, Hollick JB (2009) RNA polymerase IV functions in paramutation in zea mays. Science 323: 1201-1205 Gao Z, Liu H-L, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, et al. (2010) An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465: 106-U118 Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447-1451 Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, Goldberg RB, Fischer RL (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124: 495-506 Gong ZH, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu JK (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111: 803-814 Grewal SIS, Rice JC (2004) Regulation of heterochromatin by histone methylation and small RNAs. Current Opinion in Cell Biology 16: 230-238 Hannon GJ (2002) RNA interference. Nature 418: 244-251 Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, Dunn RM, Schwach F, Doonan JH, Baulcombe DC (2010) The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell 22: 321-334 He X-J, Hsu Y-F, Zhu S, Liu H-L, Pontes O, Zhu J, Cui X, Wang C-S, Zhu J-K (2009) A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes & Development 23: 2717-2722 He X-J, Hsu Y-F, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu H-L, Wang C-S, Jin H, et al. (2009) An effector of RNA-Directed DNA methylation in Arabidopsis Is an ARGONAUTE 4-and RNA-binding protein. Cell 137: 498-508 Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nature Genetics 38: 721-725 Herr AJ, Jensen MB, Dalmay T, Baulcombe DC (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120 Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proceedings of the National Academy of Sciences of the United States of America 93: 7783-7788 Hou X, Li L, Peng Z, Wei B, Tang S, Ding M, Liu J, Zhang F, Zhao Y, et al. (2010) A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis. Plant Journal 63: 880-888 Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D (2009) Genome-Wide Demethylation of Arabidopsis Endosperm. Science 324: 1451-1454 Huang L, Jones AME, Searle I, Patel K, Vogler H, Hubner NC, Baulcombe DC (2009) An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nature Structural & Molecular Biology 16: 91-93 Ishitani M, Xiong LM, Stevenson B, Zhu JK (1997) Genetic analysis of osmotic and cold stress signal transduction in Arabidopsis: Interactions and convergence of abscisic acid-dependent and abscisic acid-independent pathways. Plant Cell 9: 1935-1949 Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiology 129: 440-450 Jones L, Ratcliff F, Baulcombe DF (2001) RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Current Biology 11: 747-757 Jones PA, Takai D (2001) The role of DNA methylation in mammalian epigenetics. Science 293: 1068-1070 Jullien PE, Mosquna A, Ingouff M, Sakata T, Ohad N, Berger F (2008) Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PloS Biology 6: 1693-1705 Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, Matzke AJM (2004) Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Current Biology 14: 801-805 Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJM (2005) Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nature Genetics 37: 761-765 Kanno T, Bucher E, Daxinger L, Huettel B, Boehmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJM (2008) A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nature Genetics 40: 670-675 Kanno T, Bucher E, Daxinger L, Huettel B, Kreil DP, Breinig F, Lind M, Schmitt MJ, Simon SA, et al. (2010) RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. Embo Reports 11: 65-71 Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PloS Biology 5: 479-493 Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H (2007) A novel class of bacteria-induced small RNAs in Arabidopsis. Genes & Development 21: 3123-3134 Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T, Tallon LJ, Feldblyum T, Nierman W, Benito MI, et al. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815 Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics 11: 204-220 Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu J-K, Wohlschlegel JA, Jacobsen SE (2010) A Protein Complex Required for Polymerase V Transcripts and RNA-Directed DNA Methylation in Arabidopsis. Current Biology 20: 951-956 Li CF, Pontes O, El-Shami M, Henderson IR, Bernatavichute YV, Chan SWL, Lagrange T, Pikaard CS, Jacobsen SE (2006) An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell 126: 93-106 Li F, Hu G, Fu Y, Si H, Bai X, Sun Z (2005) Genetic analysis and high-resolution mapping of a premature senescence gene Pse(t) in rice (Oryza sativa L.). Genome 48: 738-746 Li JJ, Yang ZY, Yu B, Liu J, Chen XM (2005) Methylation protects miRNAs and siRNAs from a 3 ''-end uridylation activity in Arabildopsis. Current Biology 15: 1501-1507 Lindroth AM, Cao XF, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080 Lister R, O''Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536 Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322 Liu F, Quesada V, Crevillen P, Baeurle I, Swiezewski S, Dean C (2007) The Arabidopsis RNA-Binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Molecular Cell 28: 398-407 Liu J, He YH, Amasino R, Chen XM (2004) siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes & Development 18: 2873-2878 Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, Wang XZ, Fedak G, Hao S, Liu B (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theoretical and Applied Genetics 109: 200-209 Lu F, Cui X, Zhang S, Liu C, Cao X (2010) JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Research 20: 387-390 Lukowitz W, Gillmor CS, Scheible WR (2000) Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiology 123: 795-805 Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ (2009) RNA-mediated chromatin-based silencing in plants. Current Opinion in Cell Biology 21: 367-376 Matzke MA, Birchler JA (2005) RNAi-mediated pathways in the nucleus. Nature Reviews Genetics 6: 24-35 Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, et al. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5 '' terminal nucleotide. Cell 133: 116-127 Michaels SD, Amasino RM (1998) A robust method for detecting single-nucleotide changes as polymorphic markers by PCR. Plant Journal 14: 381-385 Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, et al. (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133: 128-141 Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marin MI, Martinez-Macias MI, Ariza RR, Roldan-Arjona T (2006) DEMETER and REPRESSOR OFSILENCING 1 encode 5-methylcytosine DNA glycosylases. Proceedings of the National Academy of Sciences of the United States of America 103: 6853-6858 Mosher RA, Schwach F, Studhollme D, Baulcombe DC (2008) PolIVb influences RNA-directed DNA-methylation independently of its role in siRNA biogenesis. Proceedings of the National Academy of Sciences of the United States of America 105: 3145-3150 Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC (2009) Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460: 283-U151 Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant Journal 14: 387-392 Noyer-Weidner M, Trautner TA (1993) Methylation of DNA in prokaryotes. Experientia Supplementum 64: 39-108 Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120: 613-622 Pacurar DI, Pacurar ML, Street N, Bussell JD, Pop TI, Gutierrez L, Bellini C (2012) A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions. Journal of Experimental Botany 63: 2491-2501 Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL (2007) DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences of the United States of America 104: 6752-6757 Peters JL, Cnudde F, Gerats T (2003) Forward genetics and map-based cloning approaches. Trends in Plant Science 8: 484-491 Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS (2006) The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126: 79-92 Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T (2005) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes & Development 19: 2030-2040 Qi Y, Denli AM, Hannon GJ (2005) Biochemical specialization within Arabidopsis RNA silencing pathways. Molecular Cell 19: 421-428 Qi Y, He X, Wang X-J, Kohany O, Jurka J, Hannon GJ (2006) Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443: 1008-1012 Radhamony RN, Prasad AM, Srinivasan R (2005) T-DNA insertional mutagenesis in Arabidopsis: a tool for functional genomics. Electronic Journal of Biotechnology 8: 82-106 Raja P, Wolf JN, Bisaro DM (2010) RNA silencing directed against geminiviruses: Post-transcriptional and epigenetic components. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms 1799: 337-351 Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proceedings of the National Academy of Sciences of the United States of America 97: 5237-5242 Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck AD, Zhu J-K, Hagen G, Guilfoyle TJ, Pasa-Tolic L, et al. (2009) Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II. Molecular Cell 33: 192-203 Ron M, Saez MA, Williams LE, Fletcher JC, McCormick S (2010) Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. Genes & Development 24: 1010-1021 Ronemus MJ, Galbiati M, Ticknor C, Chen JC, Dellaporta SL (1996) Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273: 654-657 Saze H, Scheid OM, Paszkowski J (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nature Genetics 34: 65-69 Schwarz DS, Hutvagner G, Du T, Xu ZS, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208 Sessions A, Burke E, Presting G, Aux G, McElver J, Patton D, Dietrich B, Ho P, Bacwaden J, et al. (2002) A high-throughput Arabidopsis reverse genetics system. Plant Cell 14: 2985-2994 Simonsson S, Gurdon J (2004) DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nature Cell Biology 6: 984-990 Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, Feijo JA, Martienssen RA (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461-472 Smith LM, Pontes O, Searle L, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC (2007) An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 19: 1507-1521 Song JJ, Smith SK, Hannon GJ, Joshua-Tor L (2004) Crystal structure of argonaute and its implications for RISC slicer activity. Science 305: 1434-1437 Sontheimer EJ, Carthew RW (2004) Argonaute journeys into the heart of RISC. Science 305: 1409-1410 Soppe WJJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJM (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Molecular Cell 6: 791-802 Springer PS (2000) Gene traps: Tools for plant development and genomics. Plant Cell 12: 1007-1020 Sridhar VV, Kapoor A, Zhang K, Zhu J, Zhou T, Hasegawa PM, Bressan RA, Zhu J-K (2007) Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature 447: 735-U718 Swiezewski S, Crevillen P, Liu F, Ecker JR, Jerzmanowski A, Dean C (2007) Small RNA-mediated chromatin silencing directed to the 3 '' region of the Arabidopsis gene encoding the developmental regulator, FLC. Proceedings of the National Academy of Sciences of the United States of America 104: 3633-3638 Verdel A, Jia ST, Gerber S, Sugiyama T, Gygi S, Grewal SIS, Moazed D (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303: 672-676 Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, et al. (1995) AFLP - a new technique for DNA-fingerprinting. Nucleic Acids Research 23: 4407-4414 Wang XJ, Gaasterland T, Chua NH (2005) Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biology 6: R30 Wassenegger M (2005) The role of the RNAi machinery in heterochromatin formation. Cell 122: 13-16 Wierzbicki AT, Haag JR, Pikaard CS (2008) Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes. Cell 135: 635-648 Wierzbicki AT, Ream TS, Haag JR, Pikaard CS (2009) RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nature Genetics 41: 630-634 Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic-markers. Nucleic Acids Research 18: 6531-6535 Xie ZX, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PloS Biology 2: 642-652 Yu B, Yang ZY, Li JJ, Minakhina S, Yang MC, Padgett RW, Steward R, Chen XM (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307: 932-935 Zhang H, Zhu J-K (2011) RNA-directed DNA methylation. Current Opinion in Plant Biology 14: 142-147 Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE (2007) Role of RNA polymerase IV in plant small RNA metabolism. Proceedings of the National Academy of Sciences of the United States of America 104: 4536-4541 Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu J-K (2007) The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Current Biology 17: 54-59 Zilberman D, Cao XF, Johansen LK, Xie ZX, Carrington JC, Jacobsen SE (2004) Role of arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology 14: 1214-1220 第二章 陳韻竹 (2011) 阿拉伯芥種子萌發及後萌發時期RNA解旋酶突變株呈現對葡萄糖和離層酸高度敏感之特性. 國立中興大學生物科技學研究所碩士論文 Aregger R, Klostermeier D (2009) The DEAD box helicase YxiN maintains a closed conformation during ATP hydrolysis. Biochemistry 48: 10679-10681 Aubourg S, Kreis M, Lecharny A (1999) The DEAD box RNA helicase family in Arabidopsis thaliana. Nucleic Acids Research 27: 628-636 Ballut L, Marchadier B, Baguet A, Tomasetto C, Seraphin B, Le Hir H (2005) The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nature Structural & Molecular Biology 12: 861-869 Banroques J, Doere M, Dreyfus M, Linder P, Tanner NK (2010) Motif III in superfamily 2 "helicases" helps convert the binding energy of ATP into a high-affinity RNA binding site in the yeast DEAD-box protein Ded1. J Mol Biol 396: 949-966 Behm-Ansmant I, Kashima I, Rehwinkel J, Sauliere J, Wittkopp N, Izaurralde E (2007) mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons. Federation of European Biochemical Societies Letters 581: 2845-2853 Bernstein J, Patterson DN, Wilson GM, Toth EA (2008) Characterization of the essential activities of Saccharomyces cerevisiae Mtr4p, a 3 ''-> 5 '' helicase partner of the nuclear exosome. Journal of Biological Chemistry 283: 4930-4942 Berthelot K, Muldoon M, Rajkowitsch L, Hughes J, McCarthy JEG (2004) Dynamics and processivity of 40S ribosome scanning on mRNA in yeast. Molecular Microbiology 51: 987-1001 Bizebard T, Ferlenghi I, Iost I, Dreyfus M (2004) Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases. Biochemistry 43: 7857-7866 Bleichert F, Baserga SJ (2007) The long unwinding road of RNA helicases. Molecular Cell 27: 339-352 Bohnsack MT, Kos M, Tollervey D (2008) Quantitative analysis of snoRNA association with pre-ribosomes and release of snR30 by Rok1 helicase. Embo Reports 9: 1230-1236 Brogna S, Wen J (2009) Nonsense-mediated mRNA decay (NMD) mechanisms. Nature Structural & Molecular Biology 16: 107-113 Brueckner A, Polge C, Lentze N, Auerbach D, Schlattner U (2009) Yeast Two-Hybrid, a Powerful Tool for Systems Biology. International Journal of Molecular Sciences 10: 2763-2788 Cartier G, Lorieux F, Allemand F, Dreyfus M, Bizebard T (2010) Cold adaptation in DEAD-box proteins. Biochemistry 49: 2636-2646 Caruthers JM, McKay DB (2002) Helicase structure and mechanism. Current Opinion in Structural Biology 12: 123-133 Chan CC, Dostie J, Diem MD, Feng WQ, Mann M, Rappsilber J, Dreyfuss G (2004) eIF4A3 is a novel component of the exon junction complex. Rna-a Publication of the Rna Society 10: 200-209 Charollais J, Dreyfus M, Iost I (2004) CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Research 32: 2751-2759 Charollais J, Pflieger D, Vinh J, Dreyfus M, Iost I (2003) The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli. Molecular Microbiology 48: 1253-1265 Chen Y, Potratz JP, Tijerina P, Del Campo M, Lambowitz AM, Russell R (2008) DEAD-box proteins can completely separate an RNA duplex using a single ATP. Proceedings of the National Academy of Sciences of the United States of America 105: 20203-20208 Chi W, He B, Mao J, Li Q, Ma J, Ji D, Zou M, Zhang L (2012) The function of RH22, a DEAD RNA helicase, in the biogenesis of the 50S ribosomal subunits of Arabidopsis chloroplasts. Plant Physiology 158: 693-707 Coller JM, Tucker M, Sheth U, Valencia-Sanchez MA, Parker R (2001) The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. Rna-a Publication of the Rna Society 7: 1717-1727 Cordin O, Banroques J, Tanner NK, Linder P (2006) The DEAD-box protein family of RNA helicases. Gene 367: 17-37 Cordin O, Tanner NK, Doere M, Linder P, Banroques J (2004) The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity. Embo Journal 23: 2478-2487 de la Cruz J, Kressler D, Linder P (1999) Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends in Biochemical Sciences 24: 192-198 de la Cruz J, Kressler D, Tollervey D, Linder P (1998) Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3 '' end formation of 5.8S rRNA in Saccharomyces cerevisiae. Embo Journal 17: 1128-1140 Endoh H, Maruyama K, Masuhiro Y, Kobayashi Y, Goto M, Tai H, Yanagisawa J, Metzger D, Hashimoto S, et al. (1999) Purification and identification of p68 RNA helicase acting as a transcriptional coactivator specific for the activation function 1 of human estrogen receptor alpha. Molecular and Cellular Biology 19: 5363-5372 Fairman-Williams ME, Guenther U-P, Jankowsky E (2010) SF1 and SF2 helicases: family matters. Current Opinion in Structural Biology 20: 313-324 Ferraiuolo MA, Lee CS, Ler LW, Hsu JL, Costa-Mattioli M, Luo MJ, Reed R, Sonenberg N (2004) A nuclear translation-like factor elF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proceedings of the National Academy of Sciences of the United States of America 101: 4118-4123 Fromont-Racine M, Senger B, Saveanu C, Fasiolo F (2003) Ribosome assembly in eukaryotes. Gene 313: 17-42 Fukada M, Kawachi H, Fujikawa A, Noda M (2005) Yeast substrate-trapping system for isolating substrates of protein tyrosine phosphatases: Isolation of substrates for protein tyrosine phosphatase receptor type z. Methods 35: 54-63 Gillian AL, Svaren J (2004) The Ddx20/DP103 dead box protein represses transcriptional activation by Egr2/Krox-20. Journal of Biological Chemistry 279: 9056-9063 Gong ZZ, Dong CH, Lee H, Zhu JH, Xiong LM, Gong DM, Stevenson B, Zhu JK (2005) A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. Plant Cell 17: 256-267 Gorbalenya AE, Koonin EV (1993) Helicases - amino-acid-sequence comparisons and structure-function-relationships. Current Opinion in Structural Biology 3: 419-429 Granneman S, Baserga SJ (2004) Ribosome biogenesis: of knobs and RNA processing. Experimental Cell Research 296: 43-50 Grifo JA, Abramson RD, Satler CA, Merrick WC (1984) RNA-stimulated atpase activity of eukaryotic initiation-factors. Journal of Biological Chemistry 259: 8648-8654 Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD, De La Cruz EM (2010) Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proceedings of the National Academy of Sciences of the United States of America 107: 4046-4050 Hilbert M, Karow AR, Klostermeier D (2009) The mechanism of ATP-dependent RNA unwinding by DEAD box proteins. Biological Chemistry 390: 1237-1250 Hodge CA, Colot HV, Stafford P, Cole CN (1999) Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells. Embo Journal 18: 5778-5788 Houseley J, LaCava J, Tollervey D (2006) RNA-quality control by the exosome. Nature Reviews Molecular Cell Biology 7: 529-539 Huang CK, Huang LF, Huang JJ, Wu SJ, Yeh CH, Lu CA (2010) A DEAD-box protein, AtRH36, is essential for female gametophyte development and is involved in rRNA biogenesis in Arabidopsis. Plant Cell Physiol 51: 694-706 Huang TS, Wei T, Laliberte JF, Wang A (2010) A host RNA helicase-like protein, AtRH8, interacts with the potyviral genome-linked protein, VPg, associates with the virus accumulation complex, and is essential for infection. Plant Physiology 152: 255-266 Isken O, Maquat LE (2008) The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nature Reviews Genetics 9: 699-712 Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proceedings of the National Academy of Sciences of the United States of America 98: 4569-4574 Jamieson DJ, Beggs JD (1991) A suppressor of yeast spp81/ded1 mutations encodes a very similar putative atp-dependent rna helicase. Molecular Microbiology 5: 805-812 Jankowsky E (2011) RNA helicases at work: binding and rearranging. Trends in Biochemical Sciences 36: 19-29 Kammel C, Thomaier M, Sorensen BB, Schubert T, Laengst G, Grasser M, Grasser KD (2013) Arabidopsis DEAD-box RNA helicase UAP56 interacts with both RNA and DNA as well as with mRNA export factors. PloS One 8 Kant P, Kant S, Gordon M, Shaked R, Barak S (2007) STRESS RESPONSE SUPPRESSOR1 and STRESS RESPONSE SUPPRESSOR2, two DEAD-box RNA helicases that attenuate Arabidopsis responses to multiple abiotic stresses. Plant Physiology 145: 814-830 Kim JS, Kim KA, Oh TR, Park CM, Kang H (2008) Functional characterization of DEAD-box RNA helicases in Arabidopsis thaliana under abiotic stress conditions. Plant and Cell Physiology 49: 1563-1571 Kos M, Tollervey D (2005) The putative RNA helicase Dbp4p is required for release of the U14 snoRNA from preribosomes in Saccharomyces cerevisiae. Molecular Cell 20: 53-64 Kossen K, Uhlenbeck OC (1999) Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Nucleic Acids Research 27: 3811-3820 Kressler D, Linder P, de la Cruz J (1999) Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Molecular and Cellular Biology 19: 7897-7912 Kressler D, Hurt E, Bassler J (2010) Driving ribosome assembly. Biochim Biophys Acta 1803: 673-683 Lamm GM, Nicol SM, FullerPace FV, Lamond AI (1996) p72: A human nuclear DEAD box protein highly related to p68. Nucleic Acids Research 24: 3739-3747 Liang X-h, Fournier MJ (2006) The helicase Has1p is required for snoRNA release from pre-rRNA. Molecular and Cellular Biology 26: 7437-7450 Libri D, Graziani N, Saguez C, Boulay J (2001) Multiple roles for the yeast SUB2/yUAP56 gene in splicing. Genes & Development 15: 36-41 Linder P (2003) Yeast RNA helicases of the DEAD-box family involved in translation initiation. Biology of the Cell 95: 157-167 Linder P (2006) DEAD-box proteins: a family affair--active and passive players in RNP-remodeling. Nucleic Acids Research 34: 4168-4180 Linder P, Lasko P (2006) Bent out of shape: RNA unwinding by the DEAD-Box helicase vasa. Cell 125: 219-221 Linder P, Jankowsky E (2011) From unwinding to clamping - the DEAD box RNA helicase family. Nature Reviews Molecular Cell Biology 12: 505-516 Linder P, Lasko PF, Ashburner M, Leroy P, Nielsen PJ, Nishi K, Schnier J, Slonimski PP (1989) Birth of the D-E-A-D box. Nature 337: 121-122 Lindqvist L, Imataka H, Pelletier J (2008) Cap-dependent eukaryotic initiation factor-mRNA interactions probed by cross-linking. RNA 14: 960-969 Liu F, Putnam A, Jankowsky E (2008) ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding. Proceedings of the National Academy of Sciences of the United States of America 105: 20209-20214 Liu HH, Liu J, Fan SL, Song MZ, Han XL, Liu F, Shen FF (2008) Molecular cloning and characterization of a salinity stress-induced gene encoding DEAD-box helicase from the halophyte Apocynum venetum. Journal of Experimental Botany 59: 633-644 Liu ZR (2002) p68 RNA helicase is an essential human splicing factor that acts at the U1 snRNA-5 '' splice site duplex. Molecular and Cellular Biology 22: 5443-5450 Luking A, Stahl U, Schmidt U (1998) The protein family of RNA helicases. Critical Reviews in Biochemistry and Molecular Biology 33: 259-296 Lykke-Andersen S, Brodersen DE, Jensen TH (2009) Origins and activities of the eukaryotic exosome. Journal of Cell Science 122: 1487-1494 Marintchev A, Edmonds KA, Marintcheva B, Hendrickson E, Oberer M, Suzuki C, Herdy B, Sonenberg N, Wagner G (2009) Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation. Cell 136: 447-460 Marsden S, Nardelli M, Linder P, McC

基因沉默發生原因可分成PTGS(post-transcriptional gene silencing)以及TGS(transcriptional gene silencing)。PTGS主要是由RNAi所造成而TGS是藉由DNA甲基化或組蛋白修飾所影響。先前實驗室利用已知參與基因沉默的突變株ros1為背景,利用T-DNA插入建立雙重突變株庫,在ros1的背景下篩選能回復的突變株。該突變株發生突變的基因即可能為影響基因沉默的重要因子。目前已篩選出兩個突變株rgs838-1及rgs3956-1。由於rgs838-1及rgs3956-1突變株中受到T-DNA插入而破壞的基因並非真正影響基因沉默的位置。因此需藉由基因定位(gene mapping)方式進行突變點的定位。利用SSLP、INDEL與CAPS等不同類型分子標誌來定位選殖。經突變株的定位分析,rgs838-1可能的突變位置已縮小至3號染色體CAPS分子標誌PERL0615887 與PERL0616720之間; rgs3956-1可能的突變位置也縮小至2號染色體CAPS分子標誌PERL0307259與PERL0308446之間。未來將增擴大篩選族群及找到新的分子標誌來定位rgs838-1及rgs3956-1的突變位點。


rh57-1是對葡萄糖高敏感之突變株。AtRH57為DEAD box RNA 解螺旋酶一員。AtRH57主要表現於細胞核與核仁中,推測可能和核糖體的生合成有關。為了進一步釐清AtRH57扮演的角色,利用酵母菌雙雜交系統(yeast-two-hybrid system)篩選與AtRH57進行交互作用蛋白質。將AtRH57構築於酵母菌表達載體內,在此同時,以三週齡全株阿拉伯芥構築cDNA基因庫並得到3×106個轉形株(transformant)。以AtRH57作為釣餌蛋白質篩選阿拉伯芥cDNA基因庫,有12顆菌落可在缺乏histidine培養基中生長且具有β-galactosidase活性。最後篩選到1個可與AtRH57專一性交互作用的蛋白質,此蛋白為protein N-terminal glutamine amidohydrolase (At2g41760)。將完整此蛋白質與AtRH57進一步測試,並沒有專一性的交互作用。由於第一次沒有成功篩選到與AtRH57有交互作用蛋白質,所以再次進行一次大規模酵母菌轉形。這此酵母菌轉形效率比第一次高出三倍,以AtRH57作為釣餌蛋白質篩選阿拉伯芥cDNA基因庫,有276顆菌落可在缺乏histidine培養基中生長且具有β-galactosidase活性。最後篩選到8個可與AtRH57專一性交互作用,蛋白為OBE1 (AT3G07780)、MED31 (AT5G19910)、Aluminium induced protein with YGL and LRDR motifs (AT4G27450)、Haloacid dehalogenase-like hydrolase (HAD) superfamily protein (AT5G36790)、ETC2 (At2g30420)、proline-rich family protein (AT2G40070)以及2個unknown function (AT5G15120、AT1G25400)。這些可能與AtRH57相互作用的蛋白質將進一步鑑定。

Chapter 1
Gene mapping of genes involving DNA methylation

Gene silencing is divided into two types: PTGS (post-transcriptional gene silencing) and TGS (transcriptional gene silencing). PTGS is elicited by RNAi (RNA interference) while the TGS is caused by either DNA methylation or histone modification. It is known that ros1 causes transcriptional gene silencing. In order to screen ros1 suppressed gene, a T-DNA-mutagenized ros1 population was generated and screened. Two mutants rgs838-1 and rgs3956-1 were identified, but T-DNA mutated genes did not suppress silencing. Suggesting that gene silencing is caused bu other gene. Therefore, gene mapping was used to identify the gene that suppressed silencing in rgs838-1 and rgs3956-1 mutants. SSLP, INDEL and CAPS markers were used for the positional cloning. Gene mapping localized rgs838-1 to chromosome 3 in between the CAPS markers PERL0615887 and PERL0616720 while rgs3956-1 to the bottom of chromosome 2 in between the CAPS markers PERL0307259 and PERL0308446. Further gene mapping is needed done by enlarging population and finding new molecular markers to identify genes involving DNA methylation.

Chapter 2
Identification of AtRH57-interacting proteins using
yeast two-hybrid system

rh57-1 is a glucose hypersensitive mutant. AtRH57 to encodes a member of DEAD box RNA helicase. Because AtRH57 protein was localized in the nucleus and nucleolus, it suggests, the protein is possibly involved in ribosome biogenesis. To further explore the role of AtRH57, yeast two-hybrid analysis was used to identify the potential proteins that may interact with AtRH57. A cDNA library was constructed from mRNA isolated from 3-week-old Arabidopsis plants and 3×106 transformants were generated from the library. Using AtRH57 as a bait to screen Arabidopsis cDNA library by yeast two-hybrid, we identified 12 colonies can grew up on minimal medium minus histidine and displayed β-galactosidase activity. Of these, only one interacted with AtRH57 is a protein named N-terminal glutamine amidohydrolase (At2g41760). However, when tested with entire protein, no specific interaction with AtRH57 occurred. Therefore, a screening with large-scale library transformation was examined. The transformation efficiency of secondary screening is three times higher than the previous screening. We identified 276 colonies that grew up on minimal medium minus histidine and displayed β-galactosidase activity. Of these, only eight interacted with AtRH57 is protein named OBE1 (AT3G07780)、MED31 (AT5G19910)、Aluminium induced protein with YGL and LRDR motifs (AT4G27450)、Haloacid dehalogenase-like hydrolase (HAD) superfamily protein (AT5G36790)、ETC2 (At2g30420)、proline-rich family protein (AT2G40070) and unknown function (AT5G15120、AT1G25400).The investigating these potential AtRH57 interacting proteins is currently in program.
其他識別: U0005-2407201316273600
Appears in Collections:生物科技學研究所

Show full item record

Google ScholarTM


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.