模式动物果蝇的基因调控前沿技术

doi:10.16288/j.yczz.21-347

遗传 ›› 2022, Vol. 44 ›› Issue (1): 3-14.doi: 10.16288/j.yczz.21-347

模式动物果蝇的基因调控前沿技术

韩玉婷(), 许博文, 李羽童, 卢心怡, 董习之, 邱雨浩, 车沁耘, 朱芮葆, 郑丽, 李孝宸, 司绪, 倪建泉()

清华大学医学院,基因表达与调控实验室,北京 100084

收稿日期:2021-10-07 修回日期:2021-12-21 出版日期:2022-01-20 发布日期:2022-01-04
通讯作者: 倪建泉 E-mail:hanyt19@mails.tsinghua.edu.cn;nijq@mail.tsinghua.edu.cn
作者简介:韩玉婷,在读博士研究生,研究方向：基因调控技术。E-mail: hanyt19@mails.tsinghua.edu.cn, 倪建泉课题组以果蝇为模式动物,开发遗传工具,研究表观遗传蛋白与信号通路在干细胞稳态中发挥的作用。课题组开发了包括基于CRISPR的基因编辑技术、基因定点激活技术和新一代转基因干扰技术在内的一系列果蝇遗传学新技术,实现在个体水平上特异调控细胞组织器官基因的表达。利用这些技术,建立转基因果蝇资源库,并进行了发育与干细胞相关的研究,主要成果包括确立组蛋白H1对干细胞的直接和间接调控作用;发现HP1c直接参与Notch信号的抑制,调控消化道干细胞稳态;确定了3个组蛋白乙酰化酶在果蝇眼睛发育中的协同作用及机制。相关研究成果发表在PNAS、Nature Communications、EMBO Reports 等期刊上。现作为课题组长,参与科技部支撑计划和发育代谢重大研发计划等。
基金资助:
国家自然科学基金项目编号(20181300988);国家自然科学基金项目编号(20201300797);科技部国家重点研发计划资助编号(2016YFE0113700)

The cutting edge of gene regulation approaches in model organism Drosophila

Yuting Han(), Bowen Xu, Yutong Li, Xinyi Lu, Xizhi Dong, Yuhao Qiu, Qinyun Che, Ruibao Zhu, Li Zheng, Xiaochen Li, Xu Si, Jianquan Ni()

Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China

Received:2021-10-07 Revised:2021-12-21 Online:2022-01-20 Published:2022-01-04
Contact: Ni Jianquan E-mail:hanyt19@mails.tsinghua.edu.cn;nijq@mail.tsinghua.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China Nos(20181300988);Supported by the National Natural Science Foundation of China Nos(20201300797);the National Key Technology Research and Development Program of the Ministry of Science and Technology of the People’s Republic of China No(2016YFE0113700)

摘要/Abstract

摘要：

转基因调控技术在生命医学研究中扮演了重要的角色,是探究个体发育和致病机制的必备工具。常用的转基因调控技术包括基因突变、基因干扰和基因转录激活等。果蝇由于具有基因的保守性、遗传工具的多样性以及不受伦理限制等优势,成为生命科学研究中经典模式动物之一,并由此开发出了多种时间和组织特异性的基因调控工具。本文主要介绍了目前在果蝇中常用的基因调控技术,包括CRISPR/Cas9介导的基因突变系统、基于miRNA的新一代转基因干扰系统以及基于CRISPR/dCas9的转录激活(flySAM)系统,希望通过对这几种系统设计原理、操作过程、相关的技术工具及相关资源品系的介绍,提升人们对这些前沿的果蝇遗传学基因表达调控技术及构建的相关果蝇资源品系重要性认识,进而推动生命医学研究发展。

关键词: 果蝇, 基因调控, CRISPR/Cas9, 基因编辑, 转基因RNAi, CRISPRa

Abstract:

Transgenic gene regulatory techniques play a critical role in biomedical fields since they are essential for researchers to study the molecular mechanisms of development and diseases. The currently prevalent transgenic techniques include specific gene mutation, transgenic RNAi and targeting activation, etc. Specifically, various gene regulatory tools have been developed to temporarily and spatially modulate genes in Drosophila melanogaster, which is a typical model organism with evolutionally conserved genome and without ethical issues in scientific research. Here, we introduce several gene regulatory techniques commonly used in Drosophila, including the principle, procedure, toolbox and related transgenic resource of CRISPR/Cas9-triggered heritable gene mutation system, next-generation transgenic RNAi and CRISPR/dCas9-based transcriptional activation (flySAM) approach. We wish to take this opportunity to raise the awareness of the importance of transgenic gene regulatory techniques development and related resource construction and thus to promote biomedical research progression.

Key words: Drosophila, gene regulation, CRISPR/Cas9, gene editing, transgenic RNAi, CRISPRa

韩玉婷, 许博文, 李羽童, 卢心怡, 董习之, 邱雨浩, 车沁耘, 朱芮葆, 郑丽, 李孝宸, 司绪, 倪建泉. 模式动物果蝇的基因调控前沿技术[J]. 遗传, 2022, 44(1): 3-14.

Yuting Han, Bowen Xu, Yutong Li, Xinyi Lu, Xizhi Dong, Yuhao Qiu, Qinyun Che, Ruibao Zhu, Li Zheng, Xiaochen Li, Xu Si, Jianquan Ni. The cutting edge of gene regulation approaches in model organism Drosophila[J]. Hereditas(Beijing), 2022, 44(1): 3-14.

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参考文献 40

[1]	Esquerda-Canals G, Montoliu-Gaya L, Güell-Bosch J, Villegas S. Mouse models of Alzheimer's disease. J Alzheimers Dis, 2017, 57(4):1171-1183. doi: 10.3233/JAD-170045 pmid: 28304309
[2]	Jin HL, He R, Oyoshi M, Geha RS. Animal models of atopic dermatitis. J Invest Dermatol, 2009, 129(1):31-40. doi: 10.1038/jid.2008.106
[3]	High KA, Roncarolo MG. Gene therapy. N Engl J Med, 2019, 381(5):455-464. doi: 10.1056/NEJMra1706910
[4]	Nüsslein-Volhard C, Wieschaus E. Mutations affecting segment number and polarity in Drosophila. Nature, 1980, 287(5785):795-801. doi: 10.1038/287795a0
[5]	Hoffmann JA. The immune response ofDrosophila. Nature, 2003, 426(6962):33-38. doi: 10.1038/nature02021
[6]	Konopka RJ, Benzer S. Clock mutants ofDrosophila melanogaster. Proc Natl Acad Sci USA, 1971, 68(9):2112-2116. doi: 10.1073/pnas.68.9.2112
[7]	Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DYR, Seydoux G, Mohr SE, Zuber J, Perrimon N. Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet, 2017, 18(1):24-40. doi: 10.1038/nrg.2016.118
[8]	Xu RG, Wang X, Shen D, Sun J, Qiao HH, Wang F, Liu LP, Ni JQ. Perspectives on gene expression regulation techniques inDrosophila. J Genet Genomics, 2019, 46(4):213-220. doi: 10.1016/j.jgg.2019.03.006
[9]	Xu J, Ren XJ, Sun J, Wang X, Qiao HH, Xu B-W, Liu LP, Ni JQ. A toolkit of CRISPR-based genome editing systems inDrosophila. J Genet Genomics, 2015, 42(4):141-149. doi: 10.1016/j.jgg.2015.02.007
[10]	Mohr SE, Smith JA, Shamu CE, Neumüller RA, Perrimon N. RNAi screening comes of age: improved techniques and complementary approaches. Nat Rev Mol Cell Biol, 2014, 15(9):591-600.
[11]	Qiao HH, Wang F, Xu RG, Sun J, Zhu R, Mao D, Ren XJ, Wang X, Jia Y, Peng P, Shen D, Liu LP, Chang ZJ, Wang GR, Li S, Ji JY, Liu QF, Ni JQ. An efficient and multiple target transgenic RNAi technique with low toxicity inDrosophila. Nat Commun, 2018, 9(1):4160. doi: 10.1038/s41467-018-06537-y
[12]	Ni JQ, Zhou R, Czech B, Liu LP, Holderbaum L, Yang-Zhou D, Shim HS, Tao R, Handler D, Karpowicz P, Binari R, Booker M, Brennecke J, Perkins LA, Hannon GJ, Perrimon N. A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat Methods, 2011, 8(5):405-407.
[13]	Jia Y, Xu RG, Ren XJ, Ewen-Campen B, Rajakumar R, Zirin J, Yang-Zhou D, Zhu RB, Wang F, Mao D, Peng P, Qiao HH, Wang X, Liu LP, Xu BW, Ji JY, Liu QF, Sun J, Perrimon N, Ni JQ. Next-generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM. Proc Natl Acad Sci USA, 2018, 115(18):4719-4724. doi: 10.1073/pnas.1800677115
[14]	Anderson P. Mutagenesis. Methods Cell Biol, 1995, 48:31-58.
[15]	Ren XJ, Holsteens K, Li HY, Sun J, Zhang YF, Liu LP, Liu QF, Ni JQ. Genome editing in Drosophila melanogaster: from basic genome engineering to the multipurpose CRISPR-Cas9 system. Sci China Life Sci, 2017, 60(5):476-489. doi: 10.1007/s11427-017-9029-9
[16]	Bak RO, Gomez-Ospina N, Porteus MH. Gene editing on center stage. Trends Genet, 2018, 34(8):600-611. doi: 10.1016/j.tig.2018.05.004
[17]	Gaj T, Gersbach CA, Barbas III CF. ZFN, TALEN, CRISPR/Cas-based methods for genome engineering. Trends Biotechnol, 2013, 31(7):397-405. doi: 10.1016/j.tibtech.2013.04.004
[18]	Musunuru K. The hope and hype of CRISPR-Cas9 genome editing: a review. JAMA Cardiol, 2017, 2(8):914-919. doi: 10.1001/jamacardio.2017.1713 pmid: 28614576
[19]	Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell, 2014, 157(6):1262-1278. doi: 10.1016/j.cell.2014.05.010
[20]	Ren XJ, Sun J, Housden BE, Hu YH, Roesel C, Lin SL, Liu LP, Yang ZH, Mao D, Sun LZ, Wu QJ, Ji JY, Xi JZ, Mohr SE, Xu J, Perrimon N, Ni JQ. Optimized gene editing technology forDrosophila melanogaster using germ line-specific Cas9. Proc Natl Acad Sci USA, 2013, 110(47):19012-19017. doi: 10.1073/pnas.1318481110
[21]	Peng P, Wang X, Shen D, Sun J, Jia Y, Xu RG, Zhu LF, Ni JQ. CRISPR-Cas9 mediated genome editing inDrosophila. Bio Protoc, 2019, 9(2):e3141.
[22]	Ren XJ, Yang ZH, Xu J, Sun J, Mao DC, Hu YH, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB, Ni JQ. Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters inDrosophila. Cell Rep, 2014, 9(3):1151-1162. doi: 10.1016/j.celrep.2014.09.044
[23]	Port F, Chen H, Lee T, Bullock S. Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering inDrosophila. Proc Natl Acad Sci USA, 2014, 111(29):E2967-E2976. doi: 10.1073/pnas.1405500111
[24]	Xue ZY, Wu MH, Wen KJ, Ren MD, Long L, Zhang XD, Gao GJ. CRISPR/Cas9 mediates efficient conditional mutagenesis inDrosophila. G3 (Bethesda), 2014, 4(11):2167-73. doi: 10.1534/g3.114.014159
[25]	Liu QH, Paroo Z. Biochemical principles of small RNA pathways. Annu Rev Biochem, 2010, 79:295-319. doi: 10.1146/biochem.2010.79.issue-1
[26]	Williams L, Carles CC, Osmont KS, Fletcher JC. A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets theArabidopsis ARF2, ARF3, and ARF4 genes. Proc Natl Acad Sci USA, 2005, 102(27):9703-9708. doi: 10.1073/pnas.0504029102
[27]	Brand AH, Perrimon N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development, 1993, 118(2):401-415. pmid: 8223268
[28]	McGuire SE, Le PT, Osborn AJ, Matsumoto K, Davis RL. Spatiotemporal rescue of memory dysfunction inDrosophila. Science, 2003, 302(5651):1765-1768. pmid: 14657498
[29]	Lam G, Thummel CS. Inducible expression of double- stranded RNA directs specific genetic interference inDrosophila. Curr Biol, 2000, 10(16):957-963. pmid: 10985382
[30]	Kennerdell JR, Carthew RW. Heritable gene silencing in Drosophila using double-stranded RNA. Nat Biotechnol, 2000, 18(8):896-898. pmid: 10932163
[31]	Ni JQ, Markstein M, Binari R, Pfeiffer B, Liu LP, Villalta C, Booker M, Perkins L, Perrimon N. Vector and parameters for targeted transgenic RNA interference inDrosophila melanogaster. Nat Methods, 2008, 5(1):49-51. doi: 10.1038/nmeth1146
[32]	Wang F, Qiao HH, Xu RG, Sun J, Zhu RB, Mao DC, Ni JQ. pNP transgenic RNAi system manual in Drosophila. Bio Protoc, 2019, 9(3):e3158.
[33]	Pfeiffer BD, Jenett A, Hammonds AS, Ngo T-TB, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, Celniker SE, Rubin GM. Tools for neuroanatomy and neurogenetics inDrosophila. Proc Natl Acad Sci USA, 2008, 105(28):9715-9720. doi: 10.1073/pnas.0803697105
[34]	Rørth P. A modular misexpression screen in Drosophila detecting tissue-specific phenotypes. Proc Natl Acad Sci USA, 1996, 93(22):12418-12422. doi: 10.1073/pnas.93.22.12418
[35]	Wei P, Xue W, Zhao Y, Ning G, Wang JW. CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500Drosophila genes conserved in humans. Genome Res, 2020, 30(1):95-106. doi: 10.1101/gr.250811.119
[36]	Sapranauskas R, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. TheStreptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res, 2011, 39(21):9275-9282. doi: 10.1093/nar/gkr606 pmid: 21813460
[37]	Lin SL, Ewen-Campen B, Ni XC, Housden BE, Perrimon N. In vivo transcriptional activation using CRISPR/Cas9 in Drosophila. Genetics, 2015, 201(2):433-442. doi: 10.1534/genetics.115.181065
[38]	Ewen-Campen B, Yang-Zhou D, Fernandes VR, González DP, Liu LP, Tao R, Ren XJ, Sun J, Hu YH, Zirin J, Mohr SE, Ni JQ, Perrimon N. Optimized strategy for in vivo Cas9-activation in Drosophila. Proc Natl Acad Sci USA, 2017, 114(35):9409-9414. doi: 10.1073/pnas.1707635114
[39]	Jia Y, Shen D, Wang X, Sun J, Peng P, Xu RG, Xu BW, Ni JQ. FlySAM transgenic CRISPRa system manual. Bio Protoc, 2019, 9(2):e3147. doi: 10.21769/BioProtoc.3147 pmid: 33654892
[40]	Mao DC, Jia Y, Peng P, Shen D, Ren XJ, Zhu RB, Qiu YH, Han YT, Yu JC, Che QY, Li YT, Lu XY, Liu LP, Wang Z, Liu QF, Sun J, Ni JQ. Enhanced efficiency of flySAM by optimization of sgRNA parameters in Drosophila. G3 (Bethesda), 2020, 10(12):4483-4488. doi: 10.1534/g3.120.401614

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果蝇食物	混合玉米面（济南佳硕生物技术有限公司）、红糖（网山）、白砂糖（龙二）、酵母（安琪）、琼脂（科百奥）、乙醇（沪试）、丙酸（沪试）、抗生素（Amresco）
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果蝇管	绍兴上虞八达通信电器有限公司
注射缓冲液	0.1 mM磷酸钠缓冲液(pH 6.8)、5 mM KCl

模式动物果蝇的基因调控前沿技术

The cutting edge of gene regulation approaches in model organism Drosophila

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