學術產出-學位論文
文章檢視/開啟
書目匯出
-
題名 透過 Cp190和CTCF的缺失HiC實驗了解建築蛋白在果蠅染色體三結構角色
Loss of Cp190 and CTCF defines a genomic map of architectural elements in Drosophila Genomics of Drosophila architectural elements作者 鄺芷君
Kuong, Chi-Kuan貢獻者 張家銘
Chang, Jia-Ming
鄺芷君
Kuong, Chi-Kuan關鍵詞 建築蛋白
絕緣子
architectural proteins
Hi-C
insulator日期 2020 上傳時間 5-十月-2020 15:17:05 (UTC+8) 摘要 在哺乳類動物中，TAD的邊界上富集了CTCF與cohesin的複合物。然而科學家發現在果蠅身上並未能找到CTCF/cohesin, 而富集在果蠅的TAD邊界上更多的是BEAF-32/CP190 或是 BEAF-32/Chromator。本文透過利用各種資料視覺化方法呈現建築蛋白以及與其結合位點間的相互作用與關係，從而推論昆蟲和哺乳動物是否通過不同的機制來構建TAD，結構蛋白對於昆蟲和哺乳動物基因組的折疊是否同樣重要。在這次研究中使用了Chip-Seq，Hi-C和RNA-Seq數據，並且開發了相應的算法以證明在果蠅身上的絕緣子蛋白結合機制中，CP190在招募其他絕緣子並形成絕緣複合體中擔任了關鍵角色。
CTCF enriched around Mammals’ TAD boundaries, colocalized with cohesin complex, is one of Chromatin architectural proteins. However, instead of the absence of CTCF/cohesin, BEAF-32/CP190 and BEAF-32/Chromator were found at Drosophila’s TAD boundaries. The architectural proteins and their binding sites were used to probe into the relationships between architectural proteins via various visualization data approaches. And extending a provocative question of whether architectural proteins are equally important for proper folding of the insect and vertebrate genomes. Here, we analyzed Chip-Seq, Hi-C, and RNA-Seq data and developed a couple of analysis tools to identify the insulator protein binding mechanism in Drosophila. Cp190 is shown as a critical player in recruiting other insulators and forming an insulation complex.參考文獻 Bonev, Boyan, Netta Mendelson Cohen, Quentin Szabo, Lauriane Fritsch, Giorgio L. Papadopoulos, Yaniv Lubling, Xiaole Xu, et al. 2017. “Multiscale 3D Genome Rewiring during Mouse Neural Development.” Cell 171 (3): 557–72.e24.Despang, Alexandra, Robert Schöpflin, Martin Franke, Salaheddine Ali, Ivana Jerković, Christina Paliou, Wing-Lee Chan, et al. 2019. “Functional Dissection of the Sox9–Kcnj2 Locus Identifies Nonessential and Instructive Roles of TAD Architecture.” Nature Genetics. https://doi.org/10.1038/s41588-019-0466-z.Dolgin, Elie. 2017. “DNA’s Secret Weapon against Knots and Tangles.” Nature News 544 (7650): 284.Gel, Bernat, Anna Díez-Villanueva, Eduard Serra, Marcus Buschbeck, Miguel A. Peinado, and Roberto Malinverni. 2015. “regioneR: An R/Bioconductor Package for the Association Analysis of Genomic Regions Based on Permutation Tests.” Bioinformatics. https://doi.org/10.1093/bioinformatics/btv562.Gómez-Díaz, Elena, and Victor G. Corces. 2014. “Architectural Proteins: Regulators of 3D Genome Organization in Cell Fate.” Trends in Cell Biology 24 (11): 703–11.Harmston, Nathan, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, and Boris Lenhard. 2015. “GenomicInteractions: An R/Bioconductor Package for Manipulating and Investigating Chromatin Interaction Data.” BMC Genomics 16 (November): 963.Imakaev, Maxim, Geoffrey Fudenberg, Rachel Patton McCord, Natalia Naumova, Anton Goloborodko, Bryan R. Lajoie, Job Dekker, and Leonid A. Mirny. 2012. “Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization.” Nature Methods. https://doi.org/10.1038/nmeth.2148.jmchanglab. n.d. “Jmchanglab/hicmaptools.” GitHub. Accessed July 27, 2020. https://github.com/jmchanglab/hicmaptools.Kahn, Tatyana G., Eshagh Dorafshan, Dorothea Schultheis, Aman Zare, Per Stenberg, Ingolf Reim, Vincenzo Pirrotta, and Yuri B. Schwartz. 2016. “Interdependence of PRC1 and PRC2 for Recruitment to Polycomb Response Elements.” Nucleic Acids Research 44 (21): 10132–49.Knight, P. A., and D. Ruiz. 2013. “A Fast Algorithm for Matrix Balancing.” IMA Journal of Numerical Analysis. https://doi.org/10.1093/imanum/drs019.Kumar, Rajendra, Haitham Sobhy, Per Stenberg, and Ludvig Lizana. 2017. “Genome Contact Map Explorer: A Platform for the Comparison, Interactive Visualization and Analysis of Genome Contact Maps.” Nucleic Acids Research 45 (17): e152.Lieberman-Aiden, Erez, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, et al. 2009. “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome.” Science 326 (5950): 289–93.Nagano, Takashi, Yaniv Lubling, Csilla Várnai, Carmel Dudley, Wing Leung, Yael Baran, Netta Mendelson Cohen, Steven Wingett, Peter Fraser, and Amos Tanay. 2017. “Cell-Cycle Dynamics of Chromosomal Organization at Single-Cell Resolution.” Nature. https://doi.org/10.1038/nature23001.Nègre, Nicolas, Christopher D. Brown, Parantu K. Shah, Pouya Kheradpour, Carolyn A. Morrison, Jorja G. Henikoff, Xin Feng, et al. 2010. “A Comprehensive Map of Insulator Elements for the Drosophila Genome.” PLoS Genetics 6 (1): e1000814.Olivares-Chauvet, Pedro, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Noa Oded Elkayam, Yaniv Lubling, Gintaras Deikus, Robert P. Sebra, and Amos Tanay. 2016. “Capturing Pairwise and Multi-Way Chromosomal Conformations Using Chromosomal Walks.” Nature. https://doi.org/10.1038/nature20158.Rao, Suhas S. P., Miriam H. Huntley, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, et al. 2014. “A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping.” Cell 159 (7): 1665–80.Rowley, M. Jordan, M. Jordan Rowley, and Victor G. Corces. 2018. “Organizational Principles of 3D Genome Architecture.” Nature Reviews Genetics. https://doi.org/10.1038/s41576-018-0060-8.Schwartz, Y. B., D. Linder-Basso, P. V. Kharchenko, M. Y. Tolstorukov, M. Kim, H-B Li, A. A. Gorchakov, et al. 2012. “Nature and Function of Insulator Protein Binding Sites in the Drosophila Genome.” Genome Research. https://doi.org/10.1101/gr.138156.112.Sexton, Tom, Frédéric Bantignies, and Giacomo Cavalli. 2009. “Genomic Interactions: Chromatin Loops and Gene Meeting Points in Transcriptional Regulation.” Seminars in Cell & Developmental Biology 20 (7): 849–55.Sexton, Tom, Eitan Yaffe, Ephraim Kenigsberg, Frédéric Bantignies, Benjamin Leblanc, Michael Hoichman, Hugues Parrinello, Amos Tanay, and Giacomo Cavalli. 2012. “Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome.” Cell. https://doi.org/10.1016/j.cell.2012.01.010.Simonis, Marieke, Petra Klous, Erik Splinter, Yuri Moshkin, Rob Willemsen, Elzo de Wit, Bas van Steensel, and Wouter de Laat. 2006. “Nuclear Organization of Active and Inactive Chromatin Domains Uncovered by Chromosome Conformation Capture–on-Chip (4C).” Nature Genetics. https://doi.org/10.1038/ng1896.Stansfield, John C., Kellen G. Cresswell, and Mikhail G. Dozmorov. 2019. “multiHiCcompare: Joint Normalization and Comparative Analysis of Complex Hi-C Experiments.” Bioinformatics 35 (17): 2916–23.Wang, Qi, Qiu Sun, Daniel M. Czajkowsky, and Zhifeng Shao. n.d. “Sub-Kb Resolution Hi-C in D. Melanogaster Reveals Conserved Characteristics of TADs between Insect and Mammalian Cells.” https://doi.org/10.1101/164467.Yaffe, Eitan, and Amos Tanay. 2011. “Probabilistic Modeling of Hi-C Contact Maps Eliminates Systematic Biases to Characterize Global Chromosomal Architecture.” Nature Genetics. https://doi.org/10.1038/ng.947.Yan, Li, Haoyu Wang, Hui Xu, Rui Zheng, and Zhengyu Shen. 2020. “Epidermal Stimulating Factors-Gelatin/polycaprolactone Coaxial Electrospun Nanofiber: Ideal Nanoscale Material for Dermal Substitute.” Journal of Biomaterials Science. Polymer Edition, September, 1–16. 描述 碩士
國立政治大學
資訊科學系
107753045資料來源 http://thesis.lib.nccu.edu.tw/record/#G0107753045 資料類型 thesis dc.contributor.advisor 張家銘 zh_TW dc.contributor.advisor Chang, Jia-Ming en_US dc.contributor.author (作者) 鄺芷君 zh_TW dc.contributor.author (作者) Kuong, Chi-Kuan en_US dc.creator (作者) 鄺芷君 zh_TW dc.creator (作者) Kuong, Chi-Kuan en_US dc.date (日期) 2020 en_US dc.date.accessioned 5-十月-2020 15:17:05 (UTC+8) - dc.date.available 5-十月-2020 15:17:05 (UTC+8) - dc.date.issued (上傳時間) 5-十月-2020 15:17:05 (UTC+8) - dc.identifier (其他 識別碼) G0107753045 en_US dc.identifier.uri (URI) http://nccur.lib.nccu.edu.tw/handle/140.119/132070 - dc.description (描述) 碩士 zh_TW dc.description (描述) 國立政治大學 zh_TW dc.description (描述) 資訊科學系 zh_TW dc.description (描述) 107753045 zh_TW dc.description.abstract (摘要) 在哺乳類動物中，TAD的邊界上富集了CTCF與cohesin的複合物。然而科學家發現在果蠅身上並未能找到CTCF/cohesin, 而富集在果蠅的TAD邊界上更多的是BEAF-32/CP190 或是 BEAF-32/Chromator。本文透過利用各種資料視覺化方法呈現建築蛋白以及與其結合位點間的相互作用與關係，從而推論昆蟲和哺乳動物是否通過不同的機制來構建TAD，結構蛋白對於昆蟲和哺乳動物基因組的折疊是否同樣重要。在這次研究中使用了Chip-Seq，Hi-C和RNA-Seq數據，並且開發了相應的算法以證明在果蠅身上的絕緣子蛋白結合機制中，CP190在招募其他絕緣子並形成絕緣複合體中擔任了關鍵角色。 zh_TW dc.description.abstract (摘要) CTCF enriched around Mammals’ TAD boundaries, colocalized with cohesin complex, is one of Chromatin architectural proteins. However, instead of the absence of CTCF/cohesin, BEAF-32/CP190 and BEAF-32/Chromator were found at Drosophila’s TAD boundaries. The architectural proteins and their binding sites were used to probe into the relationships between architectural proteins via various visualization data approaches. And extending a provocative question of whether architectural proteins are equally important for proper folding of the insect and vertebrate genomes. Here, we analyzed Chip-Seq, Hi-C, and RNA-Seq data and developed a couple of analysis tools to identify the insulator protein binding mechanism in Drosophila. Cp190 is shown as a critical player in recruiting other insulators and forming an insulation complex. en_US dc.description.tableofcontents 1. Introduction 11.1. High-throughput Chromatin Conformation Capture (Hi-C) 11.2. Topologically associating domains (TAD) 21.3. The loop-extrusion model in mammals 21.4. Insulator proteins in Drosophila 32. Dataset and Experiments 52.1. Chip-seq 52.2. Hi-C 52.3. RNA-seq 53. Analysis 63.1. Chip-seq Data Processing 63.1.1. Wild Type 63.1.2. True Insulator Sites 63.2. Hi-C Data Processing 63.2.1. Mapping 63.2.2. Validated Contact Pair 73.2.3. The clustering of Hi-C data 73.2.4. Normalization 83.3. Single insulator site analysis 93.3.1. Virtual 4C 93.3.2. Cis-decay curve 103.3.3. Scaling Factor 123.3.4. Insulation Curve 133.4. Pairwise contact intensity of two insulator sites 153.5. TAD 163.5.1. Define TAD boundary 163.5.2. TAD Overlap 163.6. RNA-Seq processing 174. Results 184.1. Comprehensive insulator classes 184.2. High-quality Hi-C Map 194.3. True insulator site 234.3.1. multiHiCcompare make Hi-C experiments compatible 234.3.2. Insulation Curve of MCIFS increasing in CP190-KO and CTCF-KO data 274.3.3. Select True Insulator Sites 314.3.4. Pairwise Contact Intensity 334.4. Highly correlated RNA-Seq data 354.5. Interactive analysis tools 364.6. Availability of data and materials 385. Discussion and Conclusion 39References 40 zh_TW dc.source.uri (資料來源) http://thesis.lib.nccu.edu.tw/record/#G0107753045 en_US dc.subject (關鍵詞) 建築蛋白 zh_TW dc.subject (關鍵詞) 絕緣子 zh_TW dc.subject (關鍵詞) architectural proteins en_US dc.subject (關鍵詞) Hi-C en_US dc.subject (關鍵詞) insulator en_US dc.title (題名) 透過 Cp190和CTCF的缺失HiC實驗了解建築蛋白在果蠅染色體三結構角色 zh_TW dc.title (題名) Loss of Cp190 and CTCF defines a genomic map of architectural elements in Drosophila Genomics of Drosophila architectural elements en_US dc.type (資料類型) thesis en_US dc.relation.reference (參考文獻) Bonev, Boyan, Netta Mendelson Cohen, Quentin Szabo, Lauriane Fritsch, Giorgio L. Papadopoulos, Yaniv Lubling, Xiaole Xu, et al. 2017. “Multiscale 3D Genome Rewiring during Mouse Neural Development.” Cell 171 (3): 557–72.e24.Despang, Alexandra, Robert Schöpflin, Martin Franke, Salaheddine Ali, Ivana Jerković, Christina Paliou, Wing-Lee Chan, et al. 2019. “Functional Dissection of the Sox9–Kcnj2 Locus Identifies Nonessential and Instructive Roles of TAD Architecture.” Nature Genetics. https://doi.org/10.1038/s41588-019-0466-z.Dolgin, Elie. 2017. “DNA’s Secret Weapon against Knots and Tangles.” Nature News 544 (7650): 284.Gel, Bernat, Anna Díez-Villanueva, Eduard Serra, Marcus Buschbeck, Miguel A. Peinado, and Roberto Malinverni. 2015. “regioneR: An R/Bioconductor Package for the Association Analysis of Genomic Regions Based on Permutation Tests.” Bioinformatics. https://doi.org/10.1093/bioinformatics/btv562.Gómez-Díaz, Elena, and Victor G. Corces. 2014. “Architectural Proteins: Regulators of 3D Genome Organization in Cell Fate.” Trends in Cell Biology 24 (11): 703–11.Harmston, Nathan, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, and Boris Lenhard. 2015. “GenomicInteractions: An R/Bioconductor Package for Manipulating and Investigating Chromatin Interaction Data.” BMC Genomics 16 (November): 963.Imakaev, Maxim, Geoffrey Fudenberg, Rachel Patton McCord, Natalia Naumova, Anton Goloborodko, Bryan R. Lajoie, Job Dekker, and Leonid A. Mirny. 2012. “Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization.” Nature Methods. https://doi.org/10.1038/nmeth.2148.jmchanglab. n.d. “Jmchanglab/hicmaptools.” GitHub. Accessed July 27, 2020. https://github.com/jmchanglab/hicmaptools.Kahn, Tatyana G., Eshagh Dorafshan, Dorothea Schultheis, Aman Zare, Per Stenberg, Ingolf Reim, Vincenzo Pirrotta, and Yuri B. Schwartz. 2016. “Interdependence of PRC1 and PRC2 for Recruitment to Polycomb Response Elements.” Nucleic Acids Research 44 (21): 10132–49.Knight, P. A., and D. Ruiz. 2013. “A Fast Algorithm for Matrix Balancing.” IMA Journal of Numerical Analysis. https://doi.org/10.1093/imanum/drs019.Kumar, Rajendra, Haitham Sobhy, Per Stenberg, and Ludvig Lizana. 2017. “Genome Contact Map Explorer: A Platform for the Comparison, Interactive Visualization and Analysis of Genome Contact Maps.” Nucleic Acids Research 45 (17): e152.Lieberman-Aiden, Erez, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, et al. 2009. “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome.” Science 326 (5950): 289–93.Nagano, Takashi, Yaniv Lubling, Csilla Várnai, Carmel Dudley, Wing Leung, Yael Baran, Netta Mendelson Cohen, Steven Wingett, Peter Fraser, and Amos Tanay. 2017. “Cell-Cycle Dynamics of Chromosomal Organization at Single-Cell Resolution.” Nature. https://doi.org/10.1038/nature23001.Nègre, Nicolas, Christopher D. Brown, Parantu K. Shah, Pouya Kheradpour, Carolyn A. Morrison, Jorja G. Henikoff, Xin Feng, et al. 2010. “A Comprehensive Map of Insulator Elements for the Drosophila Genome.” PLoS Genetics 6 (1): e1000814.Olivares-Chauvet, Pedro, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Noa Oded Elkayam, Yaniv Lubling, Gintaras Deikus, Robert P. Sebra, and Amos Tanay. 2016. “Capturing Pairwise and Multi-Way Chromosomal Conformations Using Chromosomal Walks.” Nature. https://doi.org/10.1038/nature20158.Rao, Suhas S. P., Miriam H. Huntley, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, et al. 2014. “A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping.” Cell 159 (7): 1665–80.Rowley, M. Jordan, M. Jordan Rowley, and Victor G. Corces. 2018. “Organizational Principles of 3D Genome Architecture.” Nature Reviews Genetics. https://doi.org/10.1038/s41576-018-0060-8.Schwartz, Y. B., D. Linder-Basso, P. V. Kharchenko, M. Y. Tolstorukov, M. Kim, H-B Li, A. A. Gorchakov, et al. 2012. “Nature and Function of Insulator Protein Binding Sites in the Drosophila Genome.” Genome Research. https://doi.org/10.1101/gr.138156.112.Sexton, Tom, Frédéric Bantignies, and Giacomo Cavalli. 2009. “Genomic Interactions: Chromatin Loops and Gene Meeting Points in Transcriptional Regulation.” Seminars in Cell & Developmental Biology 20 (7): 849–55.Sexton, Tom, Eitan Yaffe, Ephraim Kenigsberg, Frédéric Bantignies, Benjamin Leblanc, Michael Hoichman, Hugues Parrinello, Amos Tanay, and Giacomo Cavalli. 2012. “Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome.” Cell. https://doi.org/10.1016/j.cell.2012.01.010.Simonis, Marieke, Petra Klous, Erik Splinter, Yuri Moshkin, Rob Willemsen, Elzo de Wit, Bas van Steensel, and Wouter de Laat. 2006. “Nuclear Organization of Active and Inactive Chromatin Domains Uncovered by Chromosome Conformation Capture–on-Chip (4C).” Nature Genetics. https://doi.org/10.1038/ng1896.Stansfield, John C., Kellen G. Cresswell, and Mikhail G. Dozmorov. 2019. “multiHiCcompare: Joint Normalization and Comparative Analysis of Complex Hi-C Experiments.” Bioinformatics 35 (17): 2916–23.Wang, Qi, Qiu Sun, Daniel M. Czajkowsky, and Zhifeng Shao. n.d. “Sub-Kb Resolution Hi-C in D. Melanogaster Reveals Conserved Characteristics of TADs between Insect and Mammalian Cells.” https://doi.org/10.1101/164467.Yaffe, Eitan, and Amos Tanay. 2011. “Probabilistic Modeling of Hi-C Contact Maps Eliminates Systematic Biases to Characterize Global Chromosomal Architecture.” Nature Genetics. https://doi.org/10.1038/ng.947.Yan, Li, Haoyu Wang, Hui Xu, Rui Zheng, and Zhengyu Shen. 2020. “Epidermal Stimulating Factors-Gelatin/polycaprolactone Coaxial Electrospun Nanofiber: Ideal Nanoscale Material for Dermal Substitute.” Journal of Biomaterials Science. Polymer Edition, September, 1–16. zh_TW dc.identifier.doi (DOI) 10.6814/NCCU202001731 en_US
