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Title:	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
Authors:	鄺芷君 Kuong, Chi-Kuan
Contributors:	張家銘 Chang, Jia-Ming 鄺芷君 Kuong, Chi-Kuan
Keywords:	建築蛋白絕緣子 architectural proteins Hi-C insulator
Date:	2020
Issue Date:	2020-10-05 15:17:05 (UTC+8)
Abstract:	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.
Reference:	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.
Description:	碩士國立政治大學資訊科學系 107753045
Source URI:	http://thesis.lib.nccu.edu.tw/record/#G0107753045
Data Type:	thesis
DOI:	10.6814/NCCU202001731
Appears in Collections:	[Department of Computer Science ] Theses

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