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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 涂世隆(Shih-Long Tu) | |
dc.contributor.author | Chien-Chang Wang | en |
dc.contributor.author | 王健彰 | zh_TW |
dc.date.accessioned | 2021-06-17T07:01:08Z | - |
dc.date.available | 2021-01-20 | |
dc.date.copyright | 2021-01-20 | |
dc.date.issued | 2020 | |
dc.date.submitted | 2021-01-15 | |
dc.identifier.citation | Bertram MJ, Bérubé NG, Hang-Swanson X, Ran Q, Leung JK, Bryce S, Spurgers K, Bick RJ, Baldini A, Ning Y, Clark LJ, Parkinson EK, Barrett JC, Smith JR, Pereira-Smith OM (1999) Identification of a gene that reverses the immortal phenotype of a subset of cells and is a member of a novel family of transcription factor-like genes. Mol Cell Biol 19: 1479-1485 Bertram MJ, Pereira-Smith OM (2001) Conservation of the MORF4 related gene family: identification of a new chromo domain subfamily and novel protein motif. Gene 266: 111-121 Bowman BR, Moure CM, Kirtane BM, Welschhans RL, Tominaga K, Pereira-Smith OM, Quiocho FA (2006) Multipurpose MRG domain involved in cell senescence and proliferation exhibits structural homology to a DNA-interacting domain. Structure 14: 151-158 Brumwell A, Fell L, Obress L, Uniacke J (2020) Hypoxia influences polysome distribution of human ribosomal protein S12 and alternative splicing of ribosomal protein mRNAs. RNA 26: 361-371 Bu Z, Yu Y, Li Z, Liu Y, Jiang W, Huang Y, Dong AW (2014) Regulation of arabidopsis flowering by the histone mark readers MRG1/2 via interaction with CONSTANS to modulate FT expression. PLoS Genet 10: e1004617 Burgess J, Linstead PJ (1981) Studies on the growth and development of protoplasts of the moss, Physcomitrella patens, and its control by light. Planta 151: 331-338 Charron JB, He H, Elling AA, Deng XW (2009) Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21: 3732-3748 Cheng YL, Tu SL (2018) Alternative splicing and cross-talk with light signaling. Plant Cell Physiol 59: 1104-1110 Cui Z, Tong A, Huo Y, Yan Z, Yang W, Yang X, Wang XX (2017) SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis. BMC Biol 15: 80 de Almeida SF, Grosso AR, Koch F, Fenouil R, Carvalho S, Andrade J, Levezinho H, Gut M, Eick D, Gut I, Andrau JC, Ferrier P, Carmo-Fonseca M (2011) Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol 18: 977-983 Godoy Herz MA, Kubaczka MG, Brzyzek G, Servi L, Krzyszton M, Simpson C, Brown J, Swiezewski S, Petrillo E, Kornblihtt AR (2019) Light regulates plant alternative splicing through the control of transcriptional elongation. Mol Cell 73: 1066-1074 Gomez Acuna LI, Fiszbein A Fau - Allo M, Allo M Fau - Schor IE, Schor Ie Fau - Kornblihtt AR, Kornblihtt AR (2013) Connections between chromatin signatures and splicing. WIREs RNA 4: 77-91 Grasser M, Grasser KD (2018) The plant RNA polymerase II elongation complex: A hub coordinating transcript elongation and mRNA processing. Transcription 9: 117-122 Gunderson FQ, Johnson TL (2009) Acetylation by the transcriptional coactivator Gcn5 plays a novel role in co-transcriptional spliceosome assembly. PLoS Genet 5: e1000682 Guo L, J Z, Elling AA, JB C, Deng X (2008) Histone modifications and expression of light-regulated genes in Arabidopsis are cooperatively influenced by changing light conditions. Plant Physiol 147: 2070-2083 Hajheidari M, Koncz C, Eick D (2013) Emerging roles for RNA polymerase II CTD in Arabidopsis. Trends Plant Sci 18: 633-643 Hansen JC, Tse C, Wolffe AP (1998) Structure and function of the core histone N-termini: more than meets the eye. Biochemistry 37: 17637-17641 Hartmann L, Drewe-Boss P, Wiessner T, Wagner G, Geue S, Lee HC, Obermuller DM, Kahles A, Behr J, Sinz FH, Ratsch G, Wachter A (2016) Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in Arabidopsis. Plant Cell 28: 2715-2734 Hsin JP, Manley JL (2012) The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 26: 2119-2137 Jenkins GI, Cove DJ (1983) Phototropism and polarotropism of primary chloronemata of the moss Physcomitrella patens: responses of mutant strains. Planta 159: 432-438 Jenuwein T, Allis CD (2001) Translating the histone code. Science 293: 1074-1080 Kanno T, Lin WD, Fu JL, Chang CL, Matzke AJM, Matzke M (2017) A genetic screen for pre-mRNA splicing mutants of Arabidopsis thaliana identifies putative U1 snRNP components RBM25 and PRP39a. Genetics 207: 1347-1359 Kent WJ (2002) BLAT—The BLAST-like alignment tool. Genome Res 12: 656-664 Kim S, Kim H, Fong N, Erickson B, Bentley DL (2011) Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc Natl Acad Sci U S A 108: 13564-13569 Kornblihtt AR, Schor Ie Fau - Allo M, Allo M Fau - Dujardin G, Dujardin G Fau - Petrillo E, Petrillo E Fau - Munoz MJ, Munoz MJ (2013) Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 14: 153-165 Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Meth 9: 357-359 Lin BY, Shih CJ, Hsieh HY, Chen HC, Tu SL (2019) Phytochrome coordinates with a hnRNP to regulate alternative splicing via an exonic splicing silencer. Plant Physiol 182: 243-254 Liu CY, Lu FL, Cui X, Cao XF (2010) Histone Methylation in Higher Plants. Plant Biol 61: 395-420 Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T (2011) Epigenetics in alternative pre-mRNA splicing. Cell 144: 16-26 Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T (2010) Regulation of alternative splicing by histone modifications. Science 327: 996-1000 Mahrez W, Shin J, Munoz-Viana R, Figueiredo DD, Trejo-Arellano MS, Exner V, Siretskiy A, Gruissem W, Kohler C, Hennig L (2016) BRR2a Affects Flowering Time via FLC Splicing. PLoS Genet 12: e1005924 Mancini E, Sanchez SE, Romanowski A, Schlaen RG, Sanchez-Lamas M, Cerdan PD, Yanovsky MJ (2016) Acute effects of light on alternative splicing in light-grown plants. JPPA 92: 126-133 Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6: 838-849 Martinez E, Palhan VB, Tjernberg A, Lymar ES, Gamper AM, Kundu TK, Chait BT, Roeder RG (2001) Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo. Mol Cell Biol 21: 6782-6795 Mitterer V, Murat G, Rety S, Blaud M, Delbos L, Stanborough T, Bergler H, Leulliot N, Kressler D, Pertschy B (2016) Sequential domain assembly of ribosomal protein S3 drives 40S subunit maturation. Nat Commun 7: 10336 Mittmann F, Brucker G, Zeidler M, Repp A, Abts T, Hartmann E, Hughes J (2004) Targeted knockout in Physcomitrella reveals direct actions of phytochrome in the cytoplasm. Proc Natl Acad Sci U S A 101: 13939-13944 Mockler TC, Yu X, Shalitin D, Parikh D, Michael TP, Liou J, Huang J, Smith Z, Alonso JM, Ecker JR, Chory J, Lin C (2004) Regulation of flowering time in Arabidopsis by K homology domain proteins. Proc Natl Acad Sci U S A 101: 12759-12764 Naftelberg S, Schor IE, Ast G, Kornblihtt AR (2015) Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 84: 165-198 Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N (2019) Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2. Front Plant Sci 10: 1680 Pajoro A, Severing E, Angenent GC, Immink RGH (2017) Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants. Genome Biol 18: 102 Peng M, Li Z, Zhou N, Ma M, Jiang Y, Dong A, Shen WH, Li L (2018) Linking PHYTOCHROME-INTERACTING FACTOR to histone modification in plant shade avoidance. Plant Physiol 176: 1341-1351 Piacentini L, Fanti L, Negri R, Del Vescovo V, Fatica A, Altieri F, Pimpinelli S (2009) Heterochromatin protein 1 (HP1a) positively regulates euchromatic gene expression through RNA transcript association and interaction with hnRNPs in Drosophila. PLoS Genet 5: e1000670 Pradeepa MM, Sutherland HG, Ule J, Grimes GR, Bickmore WA (2012) Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet 8: e1002717 Qi HD, Lin Y, Ren QP, Wang YY, Xiong F, Wang XL (2019) RNA Splicing of FLC Modulates the Transition to Flowering. Front Plant Sci 10: 1625 Shi Z, Fujii K, Kovary KM, Genuth NR, Rost HL, Teruel MN, Barna M (2017) Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. Mol Cell 67: 71-83 e77 Shih CJ, Chen HW, Hsieh HY, Lai YH, Chiu FY, Chen YR, Tu SL (2019) Heterogeneous nuclear ribonucleoprotein H1 coordinates with phytochrome and the U1 snRNP complex to regulate alternative splicing in Physcomitrella patens. Plant Cell 31: 2510-2524 Shikata H, Nakashima M, Matsuoka K, Matsushita T (2012) Deletion of the RS domain of RRC1 impairs phytochrome B signaling in Arabidopsis. Plant Signal Behav 7: 933-936 Sims RJ, 3rd, Millhouse S, Chen CF, Lewis BA, Erdjument-Bromage H, Tempst P, Manley JL, Reinberg D (2007) Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol Cell 28: 665-676 Staiger D, Brown JW (2013) Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell 25: 3640-3656 Takei S, Togo-Ohno M, Suzuki Y, Kuroyanagi H (2016) Evolutionarily conserved autoregulation of alternative pre-mRNA splicing by ribosomal protein L10a. Nucleic Acids Res 44: 5585-5596 Ullah F, Hamilton M, Reddy ASN, Ben-Hur A (2018) Exploring the relationship between intron retention and chromatin accessibility in plants. BMC Genomics 19: 21 Wang YY, Xiong F, Ren QP, Wang XL (2020) Regulation of flowering transition by alternative splicing: the role of the U2 auxiliary factor. J Exp Bot 71: 751-758 Widiez T, Symeonidi A, Luo C, Lam E, Lawton M, Rensing SA (2014) The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress. Plant J 79: 67-81 Wu HP, Su YS, Chen HC, Chen YR, Wu CC, Lin WD, Tu SL (2014) Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome Biol 15: R10 Wu S (2014) Gene expression regulation in photomorphogenesis from the perspective of the central dogma. Annu Rev Plant Biol 65: 311-333 Xin R, Zhu L, Salomé PA, Mancini E, Marshall CM, Harmon FG, Yanovsky MJ, Weigel D, Huq E (2017) SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis. Proc Natl Acad Sci U S A 114: E7018-E7027 Xu Y, Gan ES, Zhou J, Wee WY, Zhang X, Ito T (2014) Arabidopsis MRG domain proteins bridge two histone modifications to elevate expression of flowering genes. Nucleic Acids Res 42: 10960-10974 Young SK, Wek RC (2016) Upstream Open Reading Frames Differentially Regulate Gene-specific Translation in the Integrated Stress Response. J Biol Chem 291: 16927-16935 | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/72572 | - |
dc.description.abstract | 我們以小立碗藓(Physcomitrella patens)為模式植物,研究植物在照到光之後所引發信使核糖核酸前驅物(pre-mRNA)選擇性剪接(alternative splicing, AS)的現象。選擇性剪接可將相同的信使核糖核酸前驅物剪接成不同的信使核糖核酸,此機制可以改變蛋白質組成來調控生長發育各階段的反應。實驗室先前的研究發現植物照到光之後發生頻率最高的選擇性剪接,是內插子保留(intron retention, IR)的現象,而且有很多內插子保留的調控發生在核糖體蛋白(ribosomal proteins)的信使核糖核酸前驅物上。由於過去曾有動物系統的文獻指出轉錄的過程中,信使核糖核酸選擇性剪接伴隨著組蛋白修飾(histone modification)同時進行。我參考動物系統的文獻並加以測試,以暸解植物中信使核糖核酸選擇性剪接的分子調控機制。我的研究發現,小立碗藓照光之後在受光調控而保留內插子的基因座上,組蛋白3第36號離氨酸被加上三個甲基 (H3K36me3)的機制受到調控;小立碗藓的MRG1 (MORF-Related Gene 1, PpMRG1) 蛋白會辨識H3K36me3並參與許多核糖體蛋白信使核糖核酸前驅物的剪接,選擇性保留信使核糖核酸前驅物的內插子。我們也嘗試找出MRG1對植物向光性的影響,發現PpMRG1的突變株對紅光誘導的向光性不敏感。這些結果結合動物系統的研究,我推測在紅光的處理後,H3K36me3的累積在個別基因座的變化,間接影響許多內插子保留現象發生在核糖體蛋白的信使核糖核酸前驅物上,可能使得最終核糖體蛋白結構改變,或使大小次單元的核糖體蛋白重組,而對特定現有的信使核糖核酸進行轉譯,使植物可以快速的對光線的變化作出反應。 | zh_TW |
dc.description.abstract | Plants perceive dynamic light conditions and optimize their growth and development accordingly by mainly regulating gene expression at multiple layers. Alternative splicing (AS), a widespread mechanism in eukaryotes that post-transcriptionally generates two or more mRNAs from the same pre-mRNA, is rapidly controlled by light. However, detailed mechanism of light-regulated AS is still not clear. In this study, I demonstrate that histone 3 lysine 36 trimethylation (H3K36me3) rapidly and differentially responds to light at specific gene loci with light-regulated intron retention (IR) of their transcripts in the moss Physcomitrella patens. However, the level of H3K36me3 following exposure to light is inversely related to that of IR events. P. patens MORF-Related Gene 1 (PpMRG1), a chromatin adaptor, bound with higher affinity to H3K36me3 in light conditions than in darkness and was differentially targeted to gene loci showing light-responsive IR. Transcriptome analysis indicated that PpMRG1 functions in light-mediated splicing regulation. We also found PpMRG1 associated with a hnRNP-K like splicing regulator to potentially control AS. Furthermore, PpMRG1 was also involved in red-light-mediated phototropic responses. my results suggest that light regulates histone methylation, which leads to alterations of AS patterns. The chromatin adaptor PpMRG1 potentially participates in light-mediated AS, revealing that chromatin-coupled regulation of pre-mRNA splicing is an important aspect of the plant’s response to environmental changes. | en |
dc.description.provenance | Made available in DSpace on 2021-06-17T07:01:08Z (GMT). No. of bitstreams: 1 U0001-1301202111321200.pdf: 10897404 bytes, checksum: 75523c3bfd9856dc5b50eaaa052b7e8d (MD5) Previous issue date: 2020 | en |
dc.description.tableofcontents | 1. 中文摘要 1 2. Abstract 2 3. Introduction 3 4. Results 6 4.1. H3K36 is trimethylated in response to RL 6 4.2. IR events and H3K36me3 levels have opposite responses to RL 8 4.3. PpMRG1 differentially associates with H3K36me3 in response to RL 8 4.4. Loss of MRG1 affects RL-responsive IR 10 4.5. PpMRG1 positively regulates phototropic responses in P. patens 12 4.6. A FLK like protein interacts with PpMRG1 13 5. Discussion 14 6. Materials and Methods 18 6.1. Plant materials and growth conditions 18 6.2. Plasmid construction 18 6.3. CRISPR-cas9 mediated mutation 19 6.4. Transformation and generation of knockout and overexpression lines 20 6.5. RT-qPCR analysis 20 6.6. Chromatin immunoprecipitation (ChIP) 21 6.7. Immunoprecipitation 21 6.8. RNA-Seq and Data Analysis 22 6.9. Phototropism Assay 23 6.10. Yeast Two-Hybrid experiment 23 6.11. Accession numbers 24 7. Figures 25 Figure 1. H3K36 trimethylation responds to light. 25 Figure 2. Validation of H3K36me3 enrichment on additional genes by using ChIP-qPCR. 26 Figure 3. Validation of H3K36me3 enrichment on additional genes by using ChIP-qPCR. 27 Figure 4. Light-dependent changes in H3K36me3 enrichment and IR level have opposite patterns. 28 Figure 5. Association of PpMRG1 with histone lysine trimethylations. 29 Figure 6. MRG1 associates with H3K36me3 under light. 30 Figure 7. Validation of PpMRG1 enrichment on additional genes by using ChIP-qPCR. 31 Figure 8. PpMRG1 is involved in RL-regulated IR. 32 Figure 9. Validation of IR pattern in the WT and ppmrg1. 33 Figure 10. Validation of IR pattern in the WT and ppmrg1. 37 Figure 11. PpMRG1 is involved in regulating RL-mediated AltD/A, ES. 38 Figure 12. PpMRG1 functions in RL-dependent phototropic response. 39 Figure 13. Yeast two-hybrid assay to identify PpMRG1 interacting proteins. 40 Figure 14. Sequence alignment of FLKs. 41 Figure 15. Proposed model for chromatin-coupled regulation of AS. 42 Supplemental Figure S1. H3K36 trimethylation responds to light. 43 Supplemental Figure S2. Generation of c-Myc-PpMRG1 transgenic plants by homozygous recombination. 44 Supplemental Figure S3. RL-dependent association of PpMRG1 with H3K36me3. 45 Supplemental Figure S4. Generation of ppmrg1 knock mutant by homozygous recombination. 46 Supplemental Figure S5. Validation of H3K36me3 and PpMRG1 enrichment on additional genes by using ChIP-qPCR. 47 Supplemental Figure S6. Phototropism in the WT and ppmrg1. 49 8. Table 50 Supplemental Table S1. Read mapping statistics of RNA-seq data. 50 Supplemental Table S2. Functional enrichment of IR genes regulated by PpMRG1. 51 Supplemental Table S3. Distribution of bending angles in the WT and ppmrg1. 52 Supplemental Table S4. IDs and annotations of genes used in this study. 53 9. Literature Cited 54 | |
dc.language.iso | en | |
dc.title | PpMRG1藉由辨識H3K36me3參與光調控mRNA選擇性剪接 | zh_TW |
dc.title | PpMRG1 Recognizes H3K36me3 for the Regulation of Light-Responsive Alternative Splicing in Physcomitrella patens | en |
dc.type | Thesis | |
dc.date.schoolyear | 109-1 | |
dc.description.degree | 博士 | |
dc.contributor.coadvisor | 謝旭亮(Hsu-Liang Hsieh) | |
dc.contributor.oralexamcommittee | 吳素幸(Shu-Hsing Wu),陸重安(Chung-An Lu),陳柏仰(Pao-Yang Chen) | |
dc.subject.keyword | 小立碗藓,選擇性剪接,內插子保留,MRG1蛋白,組蛋白修飾, | zh_TW |
dc.subject.keyword | Physcomitrella patens,alternative splicing,intron retention,MRG protein,H3K36me3, | en |
dc.relation.page | 59 | |
dc.identifier.doi | 10.6342/NTU202100051 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2021-01-15 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 植物科學研究所 | zh_TW |
顯示於系所單位: | 植物科學研究所 |
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