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研究生: 陳思穎
Chen, Szu-Ying
論文名稱: 以亞硫酸鹽定序法標定人類胰臟癌細胞株中NSUN2轉甲基酶對RNA的修飾位點
RNA bisulfite sequencing of NSUN2 specific sites in pancreatic cancer cell lines
指導教授: 黃柏憲
Huang, Po-Hsien
學位類別: 碩士
Master
系所名稱: 醫學院 - 生物化學暨分子生物學研究所
Department of Biochemistry and Molecular Biology
論文出版年: 2020
畢業學年度: 108
語文別: 英文
論文頁數: 61
中文關鍵詞: 胰臟癌mRNANSUN2轉甲基酶5-甲基胞嘧啶修飾RNA亞硫酸鹽定序法
外文關鍵詞: Pancreatic cancer, mRNA, NSUN2, 5-methylcytosine modification, RNA bisulfite sequencing
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  • 胰臟癌在美國以及台灣分別為二零一九年預期之第四名及第八名癌症死亡原因,其五年存活率僅有百分之九,由於預後極差而促使許多科學家致力於研究胰臟癌的成因。轉譯後的修飾於編碼和非編碼RNA上在疾病發展中所造成的影響是有著必然的貢獻,而近年來有許多研究指出這些轉譯後的化學修飾帶有著潛在的調控角色,而其中可逆的mRNA甲基化修飾被認為是有可能具有細微調控的能力。有研究發現老鼠中NOP2/Sun RNA methyltransferase family member 2 (NSUN2) 轉甲基酶的突變會導致神經發展障礙;而在乳癌中則發現過表達的NSUN2轉甲基酶,並且與癌症的進程有關。然而,在胰臟癌中尚未清楚研究探討NSUN2轉甲基酶的作用特徵及角色,因此本研究使用亞硫酸鹽反應作用於RNA上並搭配次世代定序來分析胰臟癌細胞株中NSUN2轉甲基酶的修飾位點。目前初步測定的數據中,發現在分別表現shScramble 與shNSUN2的BxPC-3細胞株中,定位出的六個5-甲基胞嘧啶修飾位點,有四個都位在HAT1基因的mRNA上。在探測癌細胞的常規功能性測試中,卻發現單獨降低NSUN2轉甲基酶表現量在BxPC-3細胞株中,對於細胞生長、細胞型態及gemcitabine化療藥物敏感性沒有顯著影響,顯示NSUN2在BxPC-3細胞株的生長率、型態控制,與gemcitabine作用機制中,可能扮演次要調控角色。

    Pancreatic cancer is the estimated fourth leading cause of cancer death in the U.S. and the eighth in Taiwan in 2019. The poor prognosis of a five-year survival rate of only 9% prompts scientists to investigate the mechanisms of tumorigenesis. The contributions of post-transcriptional modifications in coding and noncoding RNA to disease pathogenesis are an indispensable factor. Accumulated studies indicate that among these underlying chemical modifications, the reversible messenger RNA (mRNA) methylation by NOP2/Sun RNA methyltransferase family member 2 (NSUN2) has the potential to be a fine-tuning regulator. Although reported mutations of Nsun2 lead to neurodevelopmental disorders in mice; and the overexpression of NSUN2 associates with breast cancer and cancer progression, the dynamic feature of NSUN2 in pancreatic cancer is still unknown. In this pilot study, we utilized RNA bisulfite sequencing to analyze NSUN2 target sites in mRNA of pancreatic cancer cell lines. From the preliminary data, a total of 6 candidate m5C sites were identified in the BxPC-3 cells stably expressing the shNSUN2 and the scramble control. 4 out of all 6 m5C sites were all located in the HAT1 gene. The phenotypic response of NSUN2 knockdown showed that NSUN2 has little effect on cell growth, morphology and gemcitabine sensitivity. Our result suggested that NSUN2 has a subtle role in cell proliferation, morphology and gemcitabine sensitivity in BxPC-3.

    摘要 I Abstract II Acknowledgement III Table of content IV I. Introduction 1 1. Pancreatic cancer 1 1.1. Pancreatic cancer epidemiology 2 1.2. Pancreatic cancer diagnosis and treatment 3 2. Epitranscriptome 4 3. RNA modifications 5 3.1. 5-Methylcytosine (m5C) 6 3.2. m5C methyltransferase 8 3.3. NOP2/SUN domain family, member 2 (NSUN2) 9 4. Detection of 5-methylcytosine 10 5. Bioinformatics analysis 11 II. Hypothesis and specific Aims 12 III. Materials and Methods 13 1. Materials 13 1.1. Cell culture 13 1.2. Primer sequences 13 1.3. shRNA plasmids and target sequences 14 2. Methods 14 2.1. Lentiviral transduction 14 2.2. Total RNA extraction 15 2.3. qPCR analysis 15 2.4. Protein extraction and western blotting 15 2.5. mRNA enrichment 16 2.6. Bisulfite treatment 17 2.7. Library preparation and sequencing 17 2.8. Analysis of sequencing reads 19 2.9. Proliferation assay 19 2.10. Gemcitabine sensitivity assay 19 2.11. MTT assay 20 IV. Results 21 1. Establishment of RNA bisulfite sequencing procedures, quality control steps, and data analysis workflow. 21 2. Small scale analysis showed complete bisulfite conversion of unmethylated cytosines. 23 3. The functional analysis of NSUN2 in human pancreatic cancer cell lines. 24 V. Discussion 26 VI. Conclusions 30 VII. References 31 VIII. Figures 42 Figure 1. Schematic workflow of RNA bisulfite sequencing and downstream analysis. 42 Figure 2. Quantification of shRNA knockdown efficiency by western blot and qPCR. 44 Figure 3. Assessment of total RNA quality after extraction. 46 Figure 4. The elimination of ribosomal RNA after purification of poly(A) RNA. 48 Figure 5. Size distribution of bisulfite-treated poly(A) RNA in a range of around 200 to 500 nucleotides. 50 Figure 6. Quality and size distribution assessment of the Bisulfite-treated poly(A)-RNA libraries. 52 Figure 7. Cytosine conversion status of the spike-in control sequence. 53 Figure 8. The effects of NSUN2 on cell morphology, proliferation and Gemcitabine sensitivity. 55 IX. Tables 56 X. Appendix 61

    1 Kaur, S., Baine, M. J., Jain, M., Sasson, A. R. & Batra, S. K. Early diagnosis of pancreatic cancer: challenges and new developments. Biomark Med 6, 597-612, doi:10.2217/bmm.12.69 (2012).
    2 Feldmann, G., Beaty, R., Hruban, R. H. & Maitra, A. Molecular genetics of pancreatic intraepithelial neoplasia. J Hepatobiliary Pancreat Surg 14, 224-232, doi:10.1007/s00534-006-1166-5 (2007).
    3 Hackeng, W. M., Hruban, R. H., Offerhaus, G. J. A. & Brosens, L. A. A. Surgical and molecular pathology of pancreatic neoplasms. Diagn Pathol 11, 47-47, doi:10.1186/s13000-016-0497-z (2016).
    4 Collisson, E. A. et al. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nature Medicine 17, 500-503, doi:10.1038/nm.2344 (2011).
    5 Moffitt, R. A. et al. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nature Genetics 47, 1168, doi:10.1038/ng.3398
    https://www.nature.com/articles/ng.3398#supplementary-information (2015).
    6 Bailey, P. et al. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature 531, 47, doi:10.1038/nature16965
    https://www.nature.com/articles/nature16965#supplementary-information (2016).
    7 Bray, F. et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: a cancer journal for clinicians 68, 394-424, doi:10.3322/caac.21492 (2018).
    8 Ferlay, J., Partensky, C. & Bray, F. More deaths from pancreatic cancer than breast cancer in the EU by 2017. Acta Oncologica 55, 1158-1160, doi:10.1080/0284186X.2016.1197419 (2016).
    9 Siegel, R. L., Miller, K. D. & Jemal, A. Cancer statistics, 2019. CA: a cancer journal for clinicians 69, 7-34, doi:10.3322/caac.21551 (2019).
    10 Rawla, P., Sunkara, T. & Gaduputi, V. Epidemiology of Pancreatic Cancer: Global Trends, Etiology and Risk Factors. World J Oncol 10, 10-27, doi:10.14740/wjon1166 (2019).
    11 Jemal, A. et al. Cancer Statistics, 2009. CA: a cancer journal for clinicians 59, 225-249, doi:10.3322/caac.20006 (2009).
    12 Midha, S., Chawla, S. & Garg, P. K. Modifiable and non-modifiable risk factors for pancreatic cancer: A review. Cancer Letters 381, 269-277, doi:https://doi.org/10.1016/j.canlet.2016.07.022 (2016).
    13 Rebours, V. et al. Obesity and Fatty Pancreatic Infiltration Are Risk Factors for Pancreatic Precancerous Lesions (PanIN). Clinical Cancer Research 21, 3522, doi:10.1158/1078-0432.CCR-14-2385 (2015).
    14 Dobbins, M., Decorby, K. & Choi, B. C. K. The Association between Obesity and Cancer Risk: A Meta-Analysis of Observational Studies from 1985 to 2011. ISRN Prev Med 2013, 680536-680536, doi:10.5402/2013/680536 (2013).
    15 Zheng, W. & Lee, S.-A. Well-Done Meat Intake, Heterocyclic Amine Exposure, and Cancer Risk. Nutrition and Cancer 61, 437-446, doi:10.1080/01635580802710741 (2009).
    16 Larsson, S. C., Bergkvist, L. & Wolk, A. Consumption of sugar and sugar-sweetened foods and the risk of pancreatic cancer in a prospective study. The American journal of clinical nutrition 84, 1171-1176, doi:10.1093/ajcn/84.5.1171 (2006).
    17 Wang, Y.-T., Gou, Y.-W., Jin, W.-W., Xiao, M. & Fang, H.-Y. Association between alcohol intake and the risk of pancreatic cancer: a dose-response meta-analysis of cohort studies. BMC Cancer 16, 212-212, doi:10.1186/s12885-016-2241-1 (2016).
    18 Ansary-Moghaddam, A. et al. The effect of modifiable risk factors on pancreatic cancer mortality in populations of the Asia-Pacific region. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 15, 2435-2440, doi:10.1158/1055-9965.epi-06-0368 (2006).
    19 El-Serag, H. B. et al. Risk of hepatobiliary and pancreatic cancers after hepatitis C virus infection: A population-based study of U.S. veterans. Hepatology (Baltimore, Md.) 49, 116-123, doi:10.1002/hep.22606 (2009).
    20 Andreotti, G. & Silverman, D. T. Occupational risk factors and pancreatic cancer: a review of recent findings. Molecular carcinogenesis 51, 98-108, doi:10.1002/mc.20779 (2012).
    21 Brotherton, L., Welton, M. & Robb, S. W. Racial disparities of pancreatic cancer in Georgia: a county-wide comparison of incidence and mortality across the state, 2000-2011. Cancer medicine 5, 100-110, doi:10.1002/cam4.552 (2016).
    22 Wolpin, B. M. et al. Pancreatic cancer risk and ABO blood group alleles: results from the pancreatic cancer cohort consortium. Cancer research 70, 1015-1023, doi:10.1158/0008-5472.can-09-2993 (2010).
    23 Yeo, T. P. Demographics, Epidemiology, and Inheritance of Pancreatic Ductal Adenocarcinoma. Seminars in Oncology 42, 8-18, doi:https://doi.org/10.1053/j.seminoncol.2014.12.002 (2015).
    24 Midha, S. et al. Genetically Determined Chronic Pancreatitis but not Alcoholic Pancreatitis Is a Strong Risk Factor for Pancreatic Cancer. Pancreas 45, 1478-1484, doi:10.1097/mpa.0000000000000684 (2016).
    25 Batabyal, P., Vander Hoorn, S., Christophi, C. & Nikfarjam, M. Association of diabetes mellitus and pancreatic adenocarcinoma: a meta-analysis of 88 studies. Annals of surgical oncology 21, 2453-2462, doi:10.1245/s10434-014-3625-6 (2014).
    26 Blackford, A. et al. Genetic mutations associated with cigarette smoking in pancreatic cancer. Cancer research 69, 3681-3688, doi:10.1158/0008-5472.can-09-0015 (2009).
    27 Shi, C., Hruban, R. H. & Klein, A. P. Familial pancreatic cancer. Archives of pathology & laboratory medicine 133, 365-374, doi:10.1043/1543-2165-133.3.365 (2009).
    28 Castillo, C. F.-d. Clinical manifestations, diagnosis, and staging of exocrine pancreatic cancer. UpToDate. Waltham, MA: UpToDate Inc. (2019).
    29 Howlader N, N. A., Krapcho M, Garshell J, Neyman N, Altekruse SF, Kosary CL, Yu M, Ruhl J, Tatalovich Z, Cho H, Mariotto A, Lewis DR, Chen HS, Feuer EJ, Cronin KA SEER Cancer Statistics Review, 1975-2010, National Cancer Institute. Bethesda, MD, https://seer.cancer.gov/archive/csr/1975_2010/. (2013).
    30 Locker, G. Y. et al. ASCO 2006 update of recommendations for the use of tumor markers in gastrointestinal cancer. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 24, 5313-5327, doi:10.1200/jco.2006.08.2644 (2006).
    31 Cwik, G., Wallner, G., Skoczylas, T., Ciechanski, A. & Zinkiewicz, K. Cancer antigens 19-9 and 125 in the differential diagnosis of pancreatic mass lesions. Archives of surgery (Chicago, Ill. : 1960) 141, 968-973; discussion 974, doi:10.1001/archsurg.141.10.968 (2006).
    32 Baine, M. J. et al. Differential gene expression analysis of peripheral blood mononuclear cells reveals novel test for early detection of pancreatic cancer. Cancer Biomark 11, 1-14, doi:10.3233/CBM-2012-0260 (2011).
    33 Mayerle, J. et al. Metabolic biomarker signature to differentiate pancreatic ductal adenocarcinoma from chronic pancreatitis. Gut 67, 128-137, doi:10.1136/gutjnl-2016-312432 (2018).
    34 Shimizu, H. et al. Identification of epigenetically silenced genes in human pancreatic cancer by a novel method "microarray coupled with methyl-CpG targeted transcriptional activation" (MeTA-array). Biochemical and biophysical research communications 411, 162-167, doi:10.1016/j.bbrc.2011.06.121 (2011).
    35 Liu, R. et al. Serum microRNA expression profile as a biomarker in the diagnosis and prognosis of pancreatic cancer. Clinical chemistry 58, 610-618, doi:10.1373/clinchem.2011.172767 (2012).
    36 Princivalle, A., Monasta, L., Butturini, G., Bassi, C. & Perbellini, L. Pancreatic ductal adenocarcinoma can be detected by analysis of volatile organic compounds (VOCs) in alveolar air. BMC Cancer 18, 529, doi:10.1186/s12885-018-4452-0 (2018).
    37 Chu, L. C., Goggins, M. G. & Fishman, E. K. Diagnosis and Detection of Pancreatic Cancer. The Cancer Journal 23, 333-342, doi:10.1097/ppo.0000000000000290 (2017).
    38 Hajatdoost, L., Sedaghat, K., Walker, E. J., Thomas, J. & Kosari, S. Chemotherapy in Pancreatic Cancer: A Systematic Review. Medicina (Kaunas) 54, 48, doi:10.3390/medicina54030048 (2018).
    39 Ghosn, M. et al. Where does chemotherapy stands in the treatment of ampullary carcinoma? A review of literature. World J Gastrointest Oncol 8, 745-750, doi:10.4251/wjgo.v8.i10.745 (2016).
    40 You, J. S. & Jones, P. A. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22, 9-20, doi:10.1016/j.ccr.2012.06.008 (2012).
    41 Silverman, B. R. & Shi, J. Alterations of Epigenetic Regulators in Pancreatic Cancer and Their Clinical Implications. International journal of molecular sciences 17, doi:10.3390/ijms17122138 (2016).
    42 McCleary-Wheeler, A. L. et al. Insights into the epigenetic mechanisms controlling pancreatic carcinogenesis. Cancer letters 328, 212-221, doi:10.1016/j.canlet.2012.10.005 (2013).
    43 Paradise, B. D., Barham, W. & Fernandez-Zapico, M. E. Targeting Epigenetic Aberrations in Pancreatic Cancer, a New Path to Improve Patient Outcomes? Cancers 10, 128, doi:10.3390/cancers10050128 (2018).
    44 Jones, P. A., Issa, J.-P. J. & Baylin, S. Targeting the cancer epigenome for therapy. Nature Reviews Genetics 17, 630, doi:10.1038/nrg.2016.93 (2016).
    45 Zhou, Q., Zhou, Y., Liu, X. & Shen, Y. GDC-0449 improves the antitumor activity of nano-doxorubicin in pancreatic cancer in a fibroblast-enriched microenvironment. Sci Rep 7, 13379-13379, doi:10.1038/s41598-017-13869-0 (2017).
    46 Nguyen, A. H. et al. Histone deacetylase inhibitors provoke a tumor supportive phenotype in pancreatic cancer associated fibroblasts. Oncotarget 8, 19074-19088, doi:10.18632/oncotarget.13572 (2017).
    47 Yamamoto, K. et al. Stromal remodeling by the BET bromodomain inhibitor JQ1 suppresses the progression of human pancreatic cancer. Oncotarget 7, 61469-61484, doi:10.18632/oncotarget.11129 (2016).
    48 Mathison, A. et al. Combined AURKA and H3K9 Methyltransferase Targeting Inhibits Cell Growth By Inducing Mitotic Catastrophe. Mol Cancer Res 15, 984-997, doi:10.1158/1541-7786.MCR-17-0063 (2017).
    49 Egger, G., Liang, G., Aparicio, A. & Jones, P. A. Epigenetics in human disease and prospects for epigenetic therapy. Nature 429, 457-463, doi:10.1038/nature02625 (2004).
    50 Jones, P. A. & Baylin, S. B. The fundamental role of epigenetic events in cancer. Nature Reviews Genetics 3, 415-428, doi:10.1038/nrg816 (2002).
    51 Kulis, M. & Esteller, M. in Advances in Genetics Vol. 70 (eds Zdenko Herceg & Toshikazu Ushijima) 27-56 (Academic Press, 2010).
    52 Rodríguez-Paredes, M. & Esteller, M. Cancer epigenetics reaches mainstream oncology. Nature Medicine 17, 330-339, doi:10.1038/nm.2305 (2011).
    53 Biswas, S. & Rao, C. M. Epigenetic tools (The Writers, The Readers and The Erasers) and their implications in cancer therapy. European Journal of Pharmacology 837, 8-24, doi:https://doi.org/10.1016/j.ejphar.2018.08.021 (2018).
    54 Boccaletto, P. et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Research 46, D303-D307, doi:10.1093/nar/gkx1030 (2018).
    55 Martinez, N. M. & Gilbert, W. V. Pre-mRNA modifications and their role in nuclear processing. Quant Biol 6, 210-227, doi:10.1007/s40484-018-0147-4 (2018).
    56 Liu, N. et al. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518, 560-564, doi:10.1038/nature14234 (2015).
    57 Jonkhout, N. et al. The RNA modification landscape in human disease. Rna 23, 1754-1769, doi:10.1261/rna.063503.117 (2017).
    58 Du, H. et al. YTHDF2 destabilizes m(6)A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex. Nat Commun 7, 12626, doi:10.1038/ncomms12626 (2016).
    59 Wang, X. et al. N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell 161, 1388-1399, doi:10.1016/j.cell.2015.05.014 (2015).
    60 Alarcon, C. R. et al. HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events. Cell 162, 1299-1308, doi:10.1016/j.cell.2015.08.011 (2015).
    61 Dai, D., Wang, H., Zhu, L., Jin, H. & Wang, X. N6-methyladenosine links RNA metabolism to cancer progression. Cell Death & Disease 9, 124, doi:10.1038/s41419-017-0129-x (2018).
    62 Wei, W., Ji, X., Guo, X. & Ji, S. Regulatory Role of N6-methyladenosine (m6A) Methylation in RNA Processing and Human Diseases. Journal of Cellular Biochemistry 118, 2534-2543, doi:10.1002/jcb.25967 (2017).
    63 Cui, Q. et al. m(6)A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells. Cell reports 18, 2622-2634, doi:10.1016/j.celrep.2017.02.059 (2017).
    64 Li, X. et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nature Chemical Biology 12, 311, doi:10.1038/nchembio.2040
    https://www.nature.com/articles/nchembio.2040#supplementary-information (2016).
    65 Dominissini, D. et al. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441-446, doi:10.1038/nature16998 (2016).
    66 Zhao, Y. et al. m1A Regulated Genes Modulate PI3K/AKT/mTOR and ErbB Pathways in Gastrointestinal Cancer. Transl Oncol 12, 1323-1333, doi:10.1016/j.tranon.2019.06.007 (2019).
    67 Carlile, T. M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143-146, doi:10.1038/nature13802 (2014).
    68 Schwartz, S. et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159, 148-162, doi:10.1016/j.cell.2014.08.028 (2014).
    69 Motorin, Y., Lyko, F. & Helm, M. 5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic acids research 38, 1415-1430, doi:10.1093/nar/gkp1117 (2010).
    70 Chan, C. T. Y. et al. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS genetics 6, e1001247-e1001247, doi:10.1371/journal.pgen.1001247 (2010).
    71 Jenner, L. B., Demeshkina, N., Yusupova, G. & Yusupov, M. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nature structural & molecular biology 17, 555-560, doi:10.1038/nsmb.1790 (2010).
    72 Auxilien, S., Guérineau, V., Szweykowska-Kulińska, Z. & Golinelli-Pimpaneau, B. The human tRNA m (5) C methyltransferase Misu is multisite-specific. RNA biology 9, 1331-1338, doi:10.4161/rna.22180 (2012).
    73 Agris, P. F. Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO reports 9, 629-635, doi:10.1038/embor.2008.104 (2008).
    74 Schaefer, M. et al. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes & Development 24, 1590-1595, doi:10.1101/gad.586710 (2010).
    75 Tuorto, F. et al. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nature structural & molecular biology 19, 900-905, doi:10.1038/nsmb.2357 (2012).
    76 Haag, S. et al. NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. RNA (New York, N.Y.) 21, 1532-1543, doi:10.1261/rna.051524.115 (2015).
    77 Li, J. et al. Archaeal NSUN6 catalyzes m5C72 modification on a wide-range of specific tRNAs. Nucleic acids research 47, 2041-2055, doi:10.1093/nar/gky1236 (2019).
    78 Schosserer, M. et al. Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nature Communications 6, 6158, doi:10.1038/ncomms7158 (2015).
    79 Gigova, A., Duggimpudi, S., Pollex, T., Schaefer, M. & Kos, M. A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability. Rna 20, 1632-1644, doi:10.1261/rna.043398.113 (2014).
    80 Sergiev, P. V., Aleksashin, N. A., Chugunova, A. A., Polikanov, Y. S. & Dontsova, O. A. Structural and evolutionary insights into ribosomal RNA methylation. Nature Chemical Biology 14, 226-235, doi:10.1038/nchembio.2569 (2018).
    81 Salditt-Georgieff, M. et al. Methyl labeling of HeLa cell hnRNA: a comparison with mRNA. Cell 7, 227-237, doi:10.1016/0092-8674(76)90022-2 (1976).
    82 Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Research 40, 5023-5033, doi:10.1093/nar/gks144 (2012).
    83 Amort, T. et al. Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain. Genome Biology 18, 1, doi:10.1186/s13059-016-1139-1 (2017).
    84 Legrand, C. et al. Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs. Genome research 27, 1589-1596, doi:10.1101/gr.210666.116 (2017).
    85 Yang, X. et al. 5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Research 27, 606, doi:10.1038/cr.2017.55
    https://www.nature.com/articles/cr201755#supplementary-information (2017).
    86 Chen, X. et al. 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nature Cell Biology 21, 978-990, doi:10.1038/s41556-019-0361-y (2019).
    87 Yang, Y. et al. RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay. Molecular Cell 75, 1188-1202.e1111, doi:https://doi.org/10.1016/j.molcel.2019.06.033 (2019).
    88 Chi, L. & Delgado-Olguín, P. Expression of NOL1/NOP2/sun domain (Nsun) RNA methyltransferase family genes in early mouse embryogenesis. Gene Expression Patterns 13, 319-327, doi:https://doi.org/10.1016/j.gep.2013.06.003 (2013).
    89 Bohnsack, K. E., Höbartner, C. & Bohnsack, M. T. Eukaryotic 5-methylcytosine (m⁵C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease. Genes 10, 102, doi:10.3390/genes10020102 (2019).
    90 Bourgeois, G. et al. Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120. PloS one 10, e0133321-e0133321, doi:10.1371/journal.pone.0133321 (2015).
    91 Cheng, J. X. et al. RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. Nature communications 9, 1163-1163, doi:10.1038/s41467-018-03513-4 (2018).
    92 Van Haute, L. et al. Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3. Nature Communications 7, 12039, doi:10.1038/ncomms12039 (2016).
    93 Trixl, L. et al. RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity. Cellular and molecular life sciences : CMLS 75, 1483-1497, doi:10.1007/s00018-017-2700-0 (2018).
    94 Metodiev, M. D. et al. NSUN4 is a dual function mitochondrial protein required for both methylation of 12S rRNA and coordination of mitoribosomal assembly. PLoS genetics 10, e1004110-e1004110, doi:10.1371/journal.pgen.1004110 (2014).
    95 Aguilo, F. et al. Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α. Cell reports 14, 479-492, doi:10.1016/j.celrep.2015.12.043 (2016).
    96 Goll, M. G. et al. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science (New York, N.Y.) 311, 395-398, doi:10.1126/science.1120976 (2006).
    97 Frye, M. & Watt, F. M. The RNA Methyltransferase Misu (NSun2) Mediates Myc-Induced Proliferation and Is Upregulated in Tumors. Current Biology 16, 971-981, doi:https://doi.org/10.1016/j.cub.2006.04.027 (2006).
    98 Okamoto, M. et al. Frequent Increased Gene Copy Number and High Protein Expression of tRNA (Cytosine-5-)-Methyltransferase (NSUN2) in Human Cancers. DNA and Cell Biology 31, 660-671, doi:10.1089/dna.2011.1446 (2011).
    99 Gao, Y. et al. NOP2/Sun RNA methyltransferase 2 promotes tumor progression via its interacting partner RPL6 in gallbladder carcinoma. Cancer Sci 110, 3510-3519, doi:10.1111/cas.14190 (2019).
    100 Yi, J. et al. Overexpression of NSUN2 by DNA hypomethylation is associated with metastatic progression in human breast cancer. Oncotarget 8, 20751-20765, doi:10.18632/oncotarget.10612 (2017).
    101 Blanco, S. et al. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. The EMBO Journal 33, 2020-2039, doi:10.15252/embj.201489282 (2014).
    102 Hussain, S. et al. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell reports 4, 255-261, doi:10.1016/j.celrep.2013.06.029 (2013).
    103 Yuan, S. et al. Methylation by NSun2 represses the levels and function of microRNA 125b. Molecular and cellular biology 34, 3630-3641, doi:10.1128/MCB.00243-14 (2014).
    104 Tang, H. et al. NSun2 delays replicative senescence by repressing p27 (KIP1) translation and elevating CDK1 translation. Aging 7, 1143-1158, doi:10.18632/aging.100860 (2015).
    105 Li, Q. et al. NSUN2-Mediated m5C Methylation and METTL3/METTL14-Mediated m6A Methylation Cooperatively Enhance p21 Translation. J Cell Biochem 118, 2587-2598, doi:10.1002/jcb.25957 (2017).
    106 Xing, J. et al. NSun2 Promotes Cell Growth via Elevating Cyclin-Dependent Kinase 1 Translation. Molecular and cellular biology 35, 4043-4052, doi:10.1128/MCB.00742-15 (2015).
    107 Edelheit, S., Schwartz, S., Mumbach, M. R., Wurtzel, O. & Sorek, R. Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m(5)C within Archaeal mRNAs. PLoS Genetics 9, e1003602, doi:10.1371/journal.pgen.1003602 (2013).
    108 Schaefer, M., Pollex, T., Hanna, K. & Lyko, F. RNA cytosine methylation analysis by bisulfite sequencing. Nucleic Acids Research 37, e12-e12, doi:10.1093/nar/gkn954 (2009).
    109 Hussain, S., Aleksic, J., Blanco, S., Dietmann, S. & Frye, M. Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biology 14, 215-215, doi:10.1186/gb4143 (2013).
    110 Khoddami, V. & Cairns, B. R. Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nature biotechnology 31, 458-464, doi:10.1038/nbt.2566 (2013).
    111 Trixl, L. & Lusser, A. The dynamic RNA modification 5-methylcytosine and its emerging role as an epitranscriptomic mark. Wiley Interdiscip Rev RNA 10, e1510-e1510, doi:10.1002/wrna.1510 (2019).
    112 Rieder, D., Amort, T., Kugler, E., Lusser, A. & Trajanoski, Z. meRanTK: methylated RNA analysis ToolKit. Bioinformatics 32, 782-785, doi:10.1093/bioinformatics/btv647 (2015).
    113 Liang, F. et al. BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data. Computational biology and chemistry 65, 173-177, doi:10.1016/j.compbiolchem.2016.09.003 (2016).
    114 Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357-360, doi:10.1038/nmeth.3317 (2015).
    115 Deer, E. L. et al. Phenotype and genotype of pancreatic cancer cell lines. Pancreas 39, 425-435, doi:10.1097/MPA.0b013e3181c15963 (2010).
    116 Jin, S.-G., Kadam, S. & Pfeifer, G. P. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic acids research 38, e125-e125, doi:10.1093/nar/gkq223 (2010).
    117 Huber, S. M. et al. Formation and abundance of 5-hydroxymethylcytosine in RNA. Chembiochem : a European journal of chemical biology 16, 752-755, doi:10.1002/cbic.201500013 (2015).
    118 Fu, L. et al. Tet-mediated formation of 5-hydroxymethylcytosine in RNA. J Am Chem Soc 136, 11582-11585, doi:10.1021/ja505305z (2014).
    119 Sun, Z. et al. Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells. Epigenomics 11, 439-453, doi:10.2217/epi-2018-0169 (2018).
    120 Huang, T., Chen, W., Liu, J., Gu, N. & Zhang, R. Genome-wide identification of mRNA 5-methylcytosine in mammals. Nature structural & molecular biology 26, 380-388, doi:10.1038/s41594-019-0218-x (2019).
    121 Blanco, S. et al. The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate. PLoS Genetics 7, e1002403, doi:10.1371/journal.pgen.1002403 (2011).
    122 Ramanathan, M., Porter, D. F. & Khavari, P. A. Methods to study RNA-protein interactions. Nature methods 16, 225-234, doi:10.1038/s41592-019-0330-1 (2019).
    123 Kim, S. T. et al. Impact of <em>KRAS</em> Mutations on Clinical Outcomes in Pancreatic Cancer Patients Treated with First-line Gemcitabine-Based Chemotherapy. Molecular Cancer Therapeutics 10, 1993, doi:10.1158/1535-7163.MCT-11-0269 (2011).
    124 Zhao, H. et al. ROS/KRAS/AMPK Signaling Contributes to Gemcitabine-Induced Stem-like Cell Properties in Pancreatic Cancer. Mol Ther Oncolytics 14, 299-312, doi:10.1016/j.omto.2019.07.005 (2019).

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