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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 | 丁照棣(Chau-Ti Ting) | |
dc.contributor.author | Sung-Ya Lin | en |
dc.contributor.author | 林頌雅 | zh_TW |
dc.date.accessioned | 2021-05-19T17:44:00Z | - |
dc.date.available | 2023-08-18 | |
dc.date.available | 2021-05-19T17:44:00Z | - |
dc.date.copyright | 2018-08-18 | |
dc.date.issued | 2018 | |
dc.date.submitted | 2018-08-15 | |
dc.identifier.citation | Akera T, Chmatal L, Trimm E, Yang K, Aonbangkhen C, Chenoweth DM, Janke C, Schultz RM, Lampson MA. 2017. Spindle asymmetry drives non-Mendelian chromosome segregation. Science 358:668-672.
Andersen PR, Tirian L, Vunjak M, Brennecke J. 2017. A heterochromatin-dependent transcription machinery drives piRNA expression. Nature 549:54-59. Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc Atlan A, Mercot H, Landre C, Montchamp-Moreau C. 1997. The sex-ratio trait in Drosophila simulans: geographical distribution of distortion and resistance. Evolution 51:1886-1895. Bauer H, Schindler S, Charron Y, Willert J, Kusecek B, Herrmann BG. 2012. The nucleoside diphosphate kinase gene Nme3 acts as quantitative trait locus promoting non-Mendelian inheritance. PLoS Genet. 8:e1002567. Bauer H, Veron N, Willert J, Herrmann BG. 2007. The t-complex-encoded guanine nucleotide exchange factor Fgd2 reveals that two opposing signaling pathways promote transmission ratio distortion in the mouse. Genes Dev. 21:143-147. Bauer H, Willert JR, Koschorz B, Herrmann BG. 2005. The t complex-encoded GTPase-activating protein Tagap1 acts as a transmission ratio distorter in mice. Nat. Genet. 37:969-973. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120. Bravo Nunez MA, Nuckolls NL, Zanders SE. 2018. Genetic villains: killer meiotic drivers. Trends Genet. 34:424-433. Camacho JP, Schmid M, Cabrero J. 2011. B chromosomes and sex in animals. Sex Dev. 5:155-166. Cazemajor M, Joly D, Montchamp-Moreau C. 2000. Sex-ratio meiotic drive in Drosophila simulans is related to equational nondisjunction of the Y chromosome. Genetics 154:229-236. Cazemajor M, Landre C, Montchamp-Moreau C. 1997. The sex-ratio trait in Drosophila simulans: genetic analysis of distortion and suppression. Genetics 147:635-642. Chmatal L, Gabriel SI, Mitsainas GP, Martinez-Vargas J, Ventura J, Searle JB, Schultz RM, Lampson MA. 2014. Centromere strength provides the cell biological basis for meiotic drive and karyotype evolution in mice. Curr. Biol. 24:2295-2300. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szczesniak MW, Gaffney DJ, Elo LL, Zhang X, et al. 2016. A survey of best practices for RNA-seq data analysis. Genome Biol. 17:13. Dawe RK, Lowry EG, Gent JI, Stitzer MC, Swentowsky KW, Higgins DM, Ross-Ibarra J, Wallace JG, Kanizay LB, Alabady M, et al. 2018. A kinesin-14 motor activates neocentromeres to promote meiotic drive in maize. Cell 173:1-12. Dermitzakis ET, Masly JP, Waldrip HM, Clark AG. 2000. Non-Mendelian segregation of sex chromosomes in heterospecific Drosophila males. Genetics 154:687-694. Doyen CM, Moshkin YM, Chalkley GE, Bezstarosti K, Demmers JA, Rathke C, Renkawitz-Pohl R, Verrijzer CP. 2013. Subunits of the histone chaperone CAF1 also mediate assembly of protamine-based chromatin. Cell Rep 4:59-65. Ebens AJ, Garren H, Cheyette BN, Zipursky SL. 1993. The Drosophila anachronism locus: a glycoprotein secreted by glia inhibits neuroblast proliferation. Cell 74:15-27. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. Ellis LL, Carney GE. 2010. Mating alters gene expression patterns in Drosophila melanogaster male heads. BMC Genomics 11:558. Findlay GD, Yi XH, MacCoss MJ, Swanson WJ. 2008. Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating. PLoS Biol. 6:1417-1426. Fisher RA. 1930. The genetical theory of natural selection. Clarendon Press, Oxford Fradkin LG, Kamphorst JT, DiAntonio A, Goodman CS, Noordermeer JN. 2002. Genomewide analysis of the Drosophila tetraspanins reveals a subset with similar function in the formation of the embryonic synapse. Proc. Natl. Acad. Sci. USA 99:13663-13668. Fuller, MT. 1993. Spermatogenesis. Cold Spring Harbor Press, Cold Spring Harbor, NY. Ganetzky B. 1977. On the components of segregation distortion in Drosophila melanogaster. Genetics 86:321-355. Gershenson S. 1928. A new sex-ratio abnormality in Drosophila obscura. Genetics 13:488-507. Gracheva E, Dus M, Elgin SC. 2009. Drosophila RISC component VIG and its homolog Vig2 impact heterochromatin formation. PLoS One 4:e6182. Hartl DL. 1974. Genetic dissection of segregation distortion. I. Suicide combinations of SD genes. Genetics 76:477-486. Hatini V, Green RB, Lengyel JA, Bray SJ, DiNardo S. 2005. The drumstick/lines/bowl regulatory pathway links antagonistic Hedgehog and Wingless signaling inputs to epidermal cell differentiation. Genes Dev. 19:709-718. Hauschteckjungen E, Maurer B. 1976. Sperm dysfunction in sex-ratio males of Drosophila subobscura. Genetica 46:459-477. Helleu Q, Gerard PR, Dubruille R, Ogereau D, Prud'homme B, Loppin B, Montchamp-Moreau C. 2016. Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive. Proc. Natl. Acad. Sci. USA 113:4110-4115. Helleu Q, Gerard PR, and Montchamp-Moreau C. 2015. Sex chromosome drive. Cold Spring Harb. Perspect. Biol. 7:a017616. Herrmann BG, Koschorz B, Wertz K, McLaughlin KJ, Kispert A. 1999. A protein kinase encoded by the t complex responder gene causes non-mendelian inheritance. Nature 402:141-146. Hochheimer A, Zhou S, Zheng S, Holmes MC, Tjian R. 2002. TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 420:439-445. Hu W, Jiang ZD, Suo F, Zheng JX, He WZ, Du LL. 2017. A large gene family in fission yeast encodes spore killers that subvert Mendel's law. Elife 6:e26057. Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4:44-57. Iwaki DD, Johansen KA, Singer JB, Lengyel JA. 2001. drumstick, bowl, and lines are required for patterning and cell rearrangement in the Drosophila embryonic hindgut. Dev. Biol. 240:611-626. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14:R36. Kunert N, Marhold J, Kramer K, Lyko F. 2005. Identification and characterization of IPOD, a novel interaction partner of the Dnmt2 DNA methyltransferase in Drosophila. A. Dros. Res. Conf. 46:298A. Kusano A, Staber C, Ganetzky B. 2001. Nuclear mislocalization of enzymatically active RanGAP causes segregation distortion in Drosophila. Dev. Cell 1:351-361. Kusano A, Staber C, Ganetzky B. 2002. Segregation distortion induced by wild-type RanGAP in Drosophila. Proc. Natl. Acad. Sci. USA 99:6866-6870. Kusch T, Florens L, MacDonald WH, Swanson SK, Glaser RL, Yates JR, Abmayr SM, Washburn MP, Workman JL. 2004. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306:2084-2087. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25. Larracuente AM, Presgraves DC. 2012. The selfish segregation distorter gene complex of Drosophila melanogaster. Genetics 192:33-53. Levine MT, McCoy C, Vermaak D, Lee YC, Hiatt MA, Matsen FA, Malik HS. 2012. Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family. PLoS Genet. 8:e1002729. Levy F, Rabel D, Charlet M, Bulet P, Hoffmann JA, Ehret-Sabatier L. 2004. Peptidomic and proteomic analyses of the systemic immune response of Drosophila. Biochimie 86:607-616. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. Lindholm AK, Dyer KA, Firman RC, Fishman L, Forstmeier W, Holman L, Johannesson H, Knief U, Kokko H, Larracuente AM, et al. 2016. The ecology and evolutionary dynamics of meiotic drive. Trends Ecol. Evol. 31:315-326. Lye CM, Naylor HW, Sanson B. 2014. Subcellular localisations of the CPTI collection of YFP-tagged proteins in Drosophila embryos. Development 141:4006-4017. Lyttle TW. 1989. The effect of novel chromosome position and variable dose on the genetic behavior of the Responder (Rsp) element of the Segregation distorter (SD) system of Drosophila melanogaster. Genetics 121:751-763. Lyttle TW. 1991. Segregation distorters. Annu. Rev. Genet. 25:511-557. Mercot H, Atlan A, Jacques M, and Montchamp-Moreau C. 1995a. Sex-ratio distortion in Drosophila simulans: co-occurrence of a meiotic drive and a suppressor of drive. J. Evol. Biol. 8:283-300. Mercot H, Llorente B, Jacques M, Atlan A, Montchampmoreau C. 1995b. Variability within the Seychelles cytoplasmic incompatibility system in Drosophila simulans. Genetics 141:1015-1023. Merrill C, Bayraktaroglu L, Kusano A, Ganetzky B. 1999. Truncated RanGAP encoded by the Segregation Distorter locus of Drosophila. Science 283:1742-1745. Montchamp-Moreau C, Ginhoux V, Atlan A. 2001. The Y chromosomes of Drosophila simulans are highly polymorphic for their ability to suppress sex-ratio drive. Evolution 55:728-737. Montchamp-Moreau C, Ogereau D, Chaminade N, Colard A, Aulard S. 2006. Organization of the sex-ratio meiotic drive region in Drosophila simulans. Genetics 174:1365-1371. Morgan TH, Bridges CB, Sturtevant AH. 1925. The genetics of Drosophila. Bibliogr. Genet. 2:1-262. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5:621-628. Murzina N, Verreault A, Laue E, Stillman B. 1999. Heterochromatin dynamics in mouse cells: Interaction between chromatin assembly factor 1 and HP1 proteins. Mol. Cell 4:529-540. Noguchi T, Koizumi M, Hayashi S. 2011. Sustained elongation of sperm tail promoted by local remodeling of giant mitochondria in Drosophila. Curr. Biol. 21:805-814. Nuckolls NL, Bravo Nunez MA, Eickbush MT, Young JM, Lange JJ, Yu JS, Smith GR, Jaspersen SL, Malik HS, Zanders SE. 2017. wtf genes are prolific dual poison-antidote meiotic drivers. Elife 6:e26033. Pimpinelli S, Dimitri P. 1989. Cytogenetic analysis of segregation distortion in Drosophila melanogaster: the cytological organization of the Responder (Rsp) locus. Genetics 121:765-772. Policansky D, Ellison J. 1970. 'Sex-Ratio' in Drosophila Pseudoobscura: spermiogenic failure. Science 169:888-889. R Core Team. 2017. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Roberts A, Pimentel H, Trapnell C, Pachter L. 2011. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27:2325-2329. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat. Biotechnol. 29:24-26. Ross J, Jiang H, Kanost MR, Wang Y. 2003. Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships. Gene 304:117-131. Samakovlis C, Kylsten P, Kimbrell DA, Engstrom A, Hultmark D. 1991. The andropin gene and its product, a male-specific antibacterial peptide in Drosophila melanogaster. EMBO J. 10:163-169. Sandler L, Carpenter AT. 1972. A note on the chromosomal site of action of SD in Drosophila melanogaster. Ediburgh Symposium on the Genetics of the Spermatozoon, edited by R. A. Beatty and S. Gluecksohn-Waelsch. University of Ediburgh, Edinburgh, Scotland. pp. 247-268. Schimenti J. 2000. Segregation distortion of mouse t haplotypes - the molecular basis emerges. Trends Genet. 16:240-243. Silver LM. 1993. The peculiar journey of a selfish chromosome: mouse t haplotypes and meiotic drive. Trends Genet. 9:250-254. Tao Y, Araripe L, Kingan SB, Ke Y, Xiao H, Hartl DL. 2007a. A sex-ratio meiotic drive system in Drosophila simulans. II: an X-linked distorter. PLoS Biol. 5:e293. Tao Y, Hartl DL, Laurie CC. 2001. Sex-ratio segregation distortion associated with reproductive isolation in Drosophila. Proc. Natl. Acad. Sci. USA 98:13183-13188. Tao Y, Masly JP, Araripe L, Ke Y, Hartl DL. 2007b. A sex-ratio meiotic drive system in Drosophila simulans. I: an autosomal suppressor. PLoS Biol. 5:e292. Tarazona S, Furio-Tari P, Turra D, Pietro AD, Nueda MJ, Ferrer A, Conesa A. 2015. Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic Acids Res. 43:e140. Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A. 2011. Differential expression in RNA-seq: a matter of depth. Genome Res. 21:2213-2223. Thorvaldsdottir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14:178-192. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511-515. Vibranovski MD, Lopes HF, Karr TL, Long MY. 2009. Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes. PLoS Genet. 5:e1000731. Wei KH, Reddy HM, Rathnam C, Lee J, Lin D, Ji S, Mason JM, Clark AG, Barbash DA. 2017. A pooled sequencing approach identifies a candidate meiotic driver in Drosophila. Genetics 206:451-465. Werren JH. 2011. Selfish genetic elements, genetic conflict, and evolutionary innovation. Proc. Natl. Acad. Sci. USA 108(Suppl 2):10863-10870. Werren JH, Nur U, Wu CI. 1988. Selfish genetic elements. Trends Ecol. Evol. 3:297-302. Werren JH, Stouthamer R. 2003. PSR (paternal sex ratio) chromosomes: the ultimate selfish genetic elements. Genetica 117:85-101. Wu CI, Lyttle TW, Wu ML, Lin GF. 1988. Association between a satellite DNA sequence and the Responder of Segregation Distorter in D. melanogaster. Cell 54:179-189. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/7453 | - |
dc.description.abstract | 性別比 (sex-ratio, SR)減數分裂驅動會讓X染色體比Y染色體更容易被傳到下一代,因此造成偏向產生雌性的子代。SR減數分裂驅動曾經在不同的物種中被發現過,但我們對於造成這個現象的分子機制還是不甚瞭解。在擬黃果蠅 (Drosophila simulans)的巴黎SR系統中,有很多參與作用的基因,但至今只有HP1基因家族裡的HP1D2是被確認的。HP1D2在SR品系中有一段chromo shadow domain的缺失,並且表現量較野生型標準品系(ST)低。為了調查HP1D2的基因型和SR現象的關聯性,我做了基因型鑑定,並發現在ST品系內和SR品系內都有基因型差異。這項結果代表只有HP1D2基因型並無法預測SR的現象。為了更系統性地發現其他與SR相關的基因,我比較了ST與SR品系果蠅在精巢基因表現的轉錄體差異。在這些基因之中,有很高比例的多細胞生物生殖與免疫反應相關的基因。我接著做RT-qPCR來確認SR候選基因中的34個基因。雖然有五個基因在三個SR品系中都有較高表現量,包括CG16772、CG15209、Ser7、CG34265和CG43348,但其他有表現差異的基因在不同SR品系中都不同。SR品系的機制和遺傳基礎可能是不一樣的。依照現有的結果,要區分主要機制是殺手-目標驅動 (killer-target drive)或毒藥-解毒劑驅動 (poison-antidote drive)還很困難,但殺手-目標驅動是跟目前結果比較吻合的。如果可以找到Y染色體上的目標,就有可能闡明巴黎SR系統的機制。 | zh_TW |
dc.description.abstract | Sex-ratio (SR) meiotic drives, favoring the transmission of X over Y chromosome, lead to strong female-biased progeny of affected males. SR meiotic drives have been reported in several independent lineages. Yet, the molecular mechanism remains largely unclear. In Drosophila simulans, it has been known that many genes are involved in the Paris SR system, but only HP1D2, a member of the Heterochromatin Protein 1 (HP1) gene family, was identified. HP1D2 possesses a deletion of chromo shadow domain in SR strains and is expressed at lower level in SR relative to wild-type standard (ST) strains. To examine the correlation between the HP1D2 genotype and the SR phenotype, genotyping was performed. The observation of variation of HP1D2 in both ST and SR strains indicates that the genotypes alone cannot predict SR phenotypes. To systematically identify other SR-related genes, the transcriptomic differences of testicular expression between three ST and three SR strains were compared. Among these genes, they are highly enriched in genes associated with multicellular organism reproduction and immune response. The RT-qPCR analysis was then performed to validate 34 genes from the SR candidate genes. Although five genes, namely CG16772, CG15209, Ser7, CG34265, and CG43348, were consistently up-regulated in three SR strains, other differentially expressed genes differed among these strains. The underlying mechanisms and genetic bases of SR strains may be different. Based on the current results, although it is still difficult to distinguish major mechanisms, the killer-target drive or the poison-antidote drive, the killer-target drive is more consistent with the current results. If the target on Y chromosome can be identified, it is possible to elucidate the underlying mechanism of the Paris SR system. | en |
dc.description.provenance | Made available in DSpace on 2021-05-19T17:44:00Z (GMT). No. of bitstreams: 1 ntu-107-R05b48002-1.pdf: 971950 bytes, checksum: bc6d41cf98ce386f6afd3029e97283ab (MD5) Previous issue date: 2018 | en |
dc.description.tableofcontents | Acknowledgements (Chinese) i
Abstract (Chinese) iii Abstract v List of Figures viii List of Tables x Introduction 1 Materials and Methods 11 Results 22 Discussion 46 References 56 Appendix 69 | |
dc.language.iso | en | |
dc.title | 擬黃果蠅性別比減數分裂驅動之轉錄體學分析 | zh_TW |
dc.title | Transcriptomic Analyses of Sex-ratio Meiotic Drive in Drosophila simulans | en |
dc.type | Thesis | |
dc.date.schoolyear | 106-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 方淑(Shu Fang),蔡怡陞(Isheng Jason Tsai),呂俊毅(Jun-Yi Leu),莊樹諄(Trees-Juen Chuang) | |
dc.subject.keyword | 性別比,減數分裂驅動,轉錄體,擬黃果蠅,HP1D2, | zh_TW |
dc.subject.keyword | sex ratio,meiotic drive,transcriptome,Drosophila simulans,HP1D2, | en |
dc.relation.page | 75 | |
dc.identifier.doi | 10.6342/NTU201803419 | |
dc.rights.note | 同意授權(全球公開) | |
dc.date.accepted | 2018-08-16 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 基因體與系統生物學學位學程 | zh_TW |
dc.date.embargo-lift | 2023-08-18 | - |
顯示於系所單位: | 基因體與系統生物學學位學程 |
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