HOXD基因簇内一系列CTCF位点反转揭示绝缘子功能

doi:10.16288/j.yczz.21-131

遗传 ›› 2021, Vol. 43 ›› Issue (8): 758-774.doi: 10.16288/j.yczz.21-131

HOXD基因簇内一系列CTCF位点反转揭示绝缘子功能

何象龙(), 李金环, 吴强

上海交通大学系统生物医学研究院比较生物医学研究中心,系统生物医学教育部重点实验室,上海 200240

收稿日期:2021-04-11 修回日期:2021-05-12 出版日期:2021-08-20 发布日期:2021-06-30
作者简介:何象龙,在读硕士研究生,专业方向：生物学。E-mail: esroom@163.com
基金资助:
国家自然科学基金项目编号(31800636);国家自然科学基金项目编号(31630039);国家自然科学基金项目编号(91940303);上海市科学技术委员会项目资助编号(19JC1412500)

Combinatorial CRISPR inversions of CTCF sites in HOXD cluster reveal complex insulator function

Xianglong He(), Jinhuan Li, Qiang Wu

Center for Comparative Biomedicine, Key laboratory of Systems Biomedicine (Ministry of Education), Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China

Received:2021-04-11 Revised:2021-05-12 Online:2021-08-20 Published:2021-06-30
Supported by:
Supported by the National Nature Science Foundation of China Nos(31800636);Supported by the National Nature Science Foundation of China Nos(31630039);Supported by the National Nature Science Foundation of China Nos(91940303);Science and Technology Commission of Shanghai Municipality program No(19JC1412500)

摘要/Abstract

摘要：

CTCF (CCCTC-binding factor)是一种重要的染色质架构蛋白,其与绝缘子的方向性结合在哺乳动物基因组三维空间结构形成和维持中起着至关重要的作用。正向-反向相对方向的CTCF结合位点(简称CTCF位点)可以在染色质黏连蛋白(cohesin)的协助下,形成染色质环,介导远距离DNA元件之间的相互作用;而在染色质拓扑结构域边界区域的CTCF位点呈现反向-正向相背方向分布,发挥绝缘子的功能。为进一步研究CTCF介导染色质环的形成与其绝缘功能之间的关系,本研究采用DNA片段编辑方法通过设计成对sgRNA (dual sgRNA)构建了一系列HOXD基因簇区域CTCF位点反转的单细胞克隆。定量高分辨率染色质构象捕获实验显示边界区域CTCF位点反转会改变原有的染色质环方向,通过环挤出模型(loop extrusion)形成新的染色质环,引起染色质拓扑结构域边界漂移至新形成的一对反向-正向CTCF位点处。此外,串联排列的CTCF位点可以通过阻碍反方向渗透的黏连蛋白继续滑动发挥绝缘子的功能。RNA-seq实验发现CTCF位点反转引起的局部基因组空间结构变化会进一步影响基因的表达。上述研究表明相邻两个染色质拓扑结构域边界区域的反向-正向CTCF位点可以通过与各自所在拓扑结构域内相向的CTCF位点形成染色质环,阻碍黏连蛋白滑动,该发现为进一步研究CTCF的绝缘功能和其对基因组拓扑结构的影响提供了参考。

关键词: CTCF, 染色质环, HOXD, 绝缘子, CTCF位点反转

Abstract:

CTCF (CCCTC-binding factor) is a zinc-finger protein which plays a vital role in the three-dimensional (3D) genome architecture. A pair of forward-reverse convergent CTCF binding sites (CBS elements) mediates long-distance DNA interactions to form chromatin loops with the assistance of the cohesin complex, while CBS elements at the chromatin domain boundaries show reverse-forward divergent patterns and function as insulators to discriminate against DNA interaction between chromatin domains. However, there are still many unresolved problems regarding CTCF-mediated insulation function. In order to study the connections between chromatin loops and the insulation function of CBS elements, we combinatorically inverted CBS elements at the HOXD locus by using CRISPR/Cas9 DNA-fragment editing methods in the HEK293T cell line and obtained five different kinds of single-cell CRISPR clones. By performing quantitative high-resolution chromosome conformation capture copy (QHR-4C) experiments, we found that boundary CBS inversions abolish original chromatin loops and establish new loops from the opposite direction, thus shifting the insulator boundary to the new divergent CTCF sites. Furthermore, tandem CBS elements block cohesin permeated from the opposite orientation to function as insulators. RNA-seq experiments showed that alterations of local three-dimensional genome architecture would further influence gene expression of the HOXD cluster. In conclusion, a pair of divergent CBS elements function as insulators by forming chromatin loops within chromatin domains to block cohesin sliding.

Key words: CTCF, chromatin loop, HOXD, insulator, CBS inversion

何象龙, 李金环, 吴强. HOXD基因簇内一系列CTCF位点反转揭示绝缘子功能[J]. 遗传, 2021, 43(8): 758-774.

Xianglong He, Jinhuan Li, Qiang Wu. Combinatorial CRISPR inversions of CTCF sites in HOXD cluster reveal complex insulator function[J]. Hereditas(Beijing), 2021, 43(8): 758-774.

图/表 7

表1

引物序列"

类型	引物名称	序列(5′→3′)
sgRNA	a-sgRNA1F	accgCGAAGAGTGCGGGAGAACGG
	a-sgRNA1R	aaacCCGTTCTCCCGCACTCTTCG
	b-sgRNA1F	accgGGCGCATCAGGAATGTAAG
	b-sgRNA1R	aaacCTTACATTCCTGATGCGCC
	b-sgRNA2F	accgTTCCAGAGATTATGAGCCAG
	b-sgRNA2R	aaacCTGGCTCATAATCTCTGGAA
	c-sgRNA2F	accgAGTAAAACTGGGTGTTGCC
	c-sgRNA2R	aaacGGCAACACCCAGTTTTACT
	e-sgRNA1F	accgAACTGTGCTCAAACGCTCTC
	e-sgRNA1R	aaacGAGAGCGTTTGAGCACAGTT
	e-sgRNA2F	accgGAGGCGCAAACAGCTGTTGT
	e-sgRNA2R	aaacACAACAGCTGTTTGCGCCTC
PCR	a-1F	TTCCAGCACCTCGGCTTTGTC
	a-1R	CCCACTTTCCACCTCTGTCCTG
	b-1F	GTCCGCCCGTGAGCTTCTGAA
	b-1R	GCGTTGGCAGGGCTGGACTC
	b-1F1	TTCCCTGACCCTCCAAGCAC
	b-1R1	CTCACAGCAGCCGAAACCG
	b-2F	GACACCTTGGTTCAGGCTCG
	b-2R	CAGAGGCTGCATCAAACCAC
	c-1F	TGATGCAGCCTCTGTGACCG
	c-1R	AGTTTTCCCGTGGCGTCTGA
	c-2F	GGACAACCCCTCACCTTGAA
	c-2R	TATGGTGCCCAAAGTCCCAC
	e-1F	TTCCCTGTCCCAGCTTGATTTC
	e-1R	TCAACAGTGAAGGGCGGTGC
	e-2F	CAAGCCACTCTCCCGCCACTA
	e-2R	TCGCTCTCGTCCTCTCTTGGG
bio-primer	upstream-a-bioprimer	5′biotin-GGACGAGGGACATAGAGAGTTC
	downstream-e-bioprimer	5′biotin- AGGAGCCCAGGCATAGAGAC
	CS38-bioprimer	5′biotin-CCGAATTAAATCCCCGTGAC
	Island5-bioprimer	5′biotin-AAACACAAATGCATCAACCTG
P5 primer	upstream-a-P5	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCTGTCTAGAGATTCAAGTATTTCCCA
P5 primer	downstream-e-P5	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTACGCGATACTCAAGGGAATACAAGCC
	CS38-P5	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTAGGTTACAGTGTCATTTTCCCTG
	Island5-P5	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTATGCATCTCATGAAGCTGGCATCT
P7 index	P7-index-1	CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-2	CAAGCAGAAGACGGCATACGAGATTCTCCGGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-3	CAAGCAGAAGACGGCATACGAGATAATGAGCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-4	CAAGCAGAAGACGGCATACGAGATGGAATCTCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-5	CAAGCAGAAGACGGCATACGAGATTTCTGAATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-6	CAAGCAGAAGACGGCATACGAGATACGAATTCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-7	CAAGCAGAAGACGGCATACGAGATAGCTTCAGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-8	CAAGCAGAAGACGGCATACGAGATGCGCATTAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-9	CAAGCAGAAGACGGCATACGAGATCATAGCCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-10	CAAGCAGAAGACGGCATACGAGATTTCGCGGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-11	CAAGCAGAAGACGGCATACGAGATGCGCGAGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-12	CAAGCAGAAGACGGCATACGAGATCTATCGCTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-13	CAAGCAGAAGACGGCATACGAGATAGAGTACTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-14	CAAGCAGAAGACGGCATACGAGATGCTCCGTAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-15	CAAGCAGAAGACGGCATACGAGATCATGAGAGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-16	CAAGCAGAAGACGGCATACGAGATTGAATCGCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-17	CAAGCAGAAGACGGCATACGAGATGTCTGACTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-18	CAAGCAGAAGACGGCATACGAGATCTGAATGCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-19	CAAGCAGAAGACGGCATACGAGATCGCTTCTGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-20	CAAGCAGAAGACGGCATACGAGATTCGCATGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-21	CAAGCAGAAGACGGCATACGAGATAATAGCAGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-22	CAAGCAGAAGACGGCATACGAGATGTCGCGTAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-23	CAAGCAGAAGACGGCATACGAGATACGCGATAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
P7 index	P7-index-24	CAAGCAGAAGACGGCATACGAGATTGATCGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-25	CAAGCAGAAGACGGCATACGAGATCCGCATGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-26	CAAGCAGAAGACGGCATACGAGATCCACAATCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-27	CAAGCAGAAGACGGCATACGAGATGATGTTCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-28	CAAGCAGAAGACGGCATACGAGATGAATACGTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-29	CAAGCAGAAGACGGCATACGAGATTAGATACCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
	P7-index-30	CAAGCAGAAGACGGCATACGAGATTATGGTCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
adapter	adapter-upper	GACGTGTGCTCTTCCGATCTGNNNNNN-3`NH2 C6
adapter	adapter-lower	5′P-CAGATCGGAAGAGCACACGTC-3`NH2 C6

表1

图1

图2

图3

图4

图6

图7

参考文献 62

[1]	Kumar Y, Sengupta D, Bickmore W. Recent advances in the spatial organization of the mammalian genome. J Biosci, 2020, 45:18. doi: 10.1007/s12038-019-9968-1
[2]	Wu Q, Liu PF, Wang LY. Many facades of CTCF unified by its coding for three-dimensional genome architecture. J Genet Genomics, 2020, 47(8):407-424. doi: 10.1016/j.jgg.2020.06.008
[3]	Ning CY, He MN, Tang QZ, Zhu Q, Li MZ, Li DY. Advances in mammalian three-dimensional genome by using Hi-C technology approach. Hereditas(Beijing), 2019, 41(3):215-233.
	宁椿游, 何梦楠, 唐茜子, 朱庆, 李明洲, 李地艳. 基于Hi-C技术哺乳动物三维基因组研究进展. 遗传, 2019, 41(3):215-233.
[4]	Marchal C, Sima J, Gilbert DM. Control of DNA replication timing in the 3D genome. Nat Rev Mol Cell Biol, 2019, 20(12):721-737. doi: 10.1038/s41580-019-0162-y
[5]	Guo Y, Xu Q, Canzio D, Shou J, Li JH, Gorkin DU, Jung I, Wu HY, Zhai YN, Tang YX, Lu YC, Wu YH, Jia ZL, Li W, Zhang MQ, Ren B, Krainer AR, Maniatis T, Wu Q. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell, 2015, 162(4):900-910. doi: 10.1016/j.cell.2015.07.038 pmid: 26276636
[6]	de Laat W, Duboule D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature, 2013, 502(7472):499-506. doi: 10.1038/nature12753
[7]	Sanders JT, Freeman TF, Xu Y, Golloshi R, Stallard MA, Hill AM, San Martin R, Balajee AS, McCord RP. Radiation-induced DNA damage and repair effects on 3D genome organization. Nat Commun, 2020, 11(1):6178. doi: 10.1038/s41467-020-20047-w pmid: 33268790
[8]	Arnould C, Rocher V, Finoux AL, Clouaire T, Li K, Zhou F, Caron P, Mangeot PE, Ricci EP, Mourad R, Haber JE, Noordermeer D, Legube G. Loop extrusion as a mechanism for formation of DNA damage repair foci. Nature, 2021, 590(7847):660-665. doi: 10.1038/s41586-021-03193-z
[9]	Cremer T, Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol, 2010, 2(3):a003889.
[10]	Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science, 2002, 295(5558):1306-1311. pmid: 11847345
[11]	Zhao ZH, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, Ohlsson R. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet, 2006, 38(11):1341-1347. doi: 10.1038/ng1891
[12]	Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 2009, 326(5950):289-293. doi: 10.1126/science.1181369 pmid: 19815776
[13]	Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EGY, Huang PYH, Welboren WJ, Han YY, Ooi HS, Ariyaratne PN, Vega VB, Luo YQ, Tan PY, Choy PY, Wansa KDSA, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li HX, Desai KV, Thomsen JS, Lee YK, Karuturi RKM, Herve T, Bourque G, Stunnenberg HG, Ruan XA, Cacheux- Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan YJ. An oestrogen-receptor-α-bound human chromatin interactome. Nature, 2009, 462(7269):58-64. doi: 10.1038/nature08497
[14]	Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Bluthgen N, Dekker J, Heard E. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature, 2012, 485(7398):381-385. doi: 10.1038/nature11049
[15]	Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 2012, 485(7398):376-380. doi: 10.1038/nature11082
[16]	Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 2014, 159(7):1665-1680. doi: 10.1016/j.cell.2014.11.021
[17]	Guo Y, Monahan K, Wu HY, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q. CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proc Natl Acad Sci USA, 2012, 109(51):21081-21086. doi: 10.1073/pnas.1219280110
[18]	Sanborn AL, Rao SSP, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci USA, 2015, 112(47):E6456-E6465. doi: 10.1073/pnas.1518552112
[19]	Andrey G, Montavon T, Mascrez B, Gonzalez F, Noordermeer D, Leleu M, Trono D, Spitz F, Duboule D. A switch between topological domains underliesHoxD genes collinearity in mouse limbs. Science, 2013, 340(6137):1234167. doi: 10.1126/science.1234167
[20]	Dixon JR, Gorkin DU, Ren B. Chromatin domains: The unit of chromosome organization. Mol Cell, 2016, 62(5):668-680. doi: 10.1016/j.molcel.2016.05.018
[21]	Weintraub AS, Li CH, Zamudio AV, Sigova AA, Hannett NM, Day DS, Abraham BJ, Cohen MA, Nabet B, Buckley DL, Guo YE, Hnisz D, Jaenisch R, Bradner JE, Gray NS, Young RA. YY1 is a structural regulator of enhancer- promoter loops. Cell, 2017, 171(7): 1573-1588.e28. doi: S0092-8674(17)31317-X pmid: 29224777
[22]	Guo Y, Wu Q. Inversion of CTCF binding sites by DNA fragment editing alters genome topology and enhancer/ promoter functions. Hereditas(Beijing), 2015, 37(10):1073-1074.
	郭亚, 吴强. 采用DNA片段编辑技术反转CTCF结合位点改变基因组拓扑结构和增强子与启动子功能. 遗传, 2015, 37(10):1073-1074.
[23]	Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC- motif in the 5'-flanking sequence of the chicken c-myc gene. Oncogene, 1990, 5(12):1743-1753. pmid: 2284094
[24]	Yin ML, Wang JY, Wang M, Li XM, Zhang M, Wu Q, Wang YL. Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites. Cell Res, 2017, 27(11):1365-1377. doi: 10.1038/cr.2017.131
[25]	Nanni L, Ceri S, Logie C. Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries. Genome Biol, 2020, 21(1):197. doi: 10.1186/s13059-020-02108-x pmid: 32782014
[26]	Ghirlando R, Felsenfeld G. CTCF: Making the right connections. Genes Dev, 2016, 30(8):881-891. doi: 10.1101/gad.277863.116
[27]	Phillips JE, Corces VG. CTCF: Master weaver of the genome. Cell, 2009, 137(7):1194-1211. doi: 10.1016/j.cell.2009.06.001
[28]	de Wit E, Vos ESM, Holwerda SJB, Valdes-Quezada C, Verstegen MJAM, Teunissen H, Splinter E, Wijchers PJ, Krijger PHL, de Laat W. CTCF binding polarity determines chromatin looping. Mol Cell, 2015, 60(4):676-684. doi: 10.1016/j.molcel.2015.09.023
[29]	Lu YJ, Shou J, Jia ZL, Wu YH, Li JH, Guo Y, Wu Q. Genetic evidence for asymmetric blocking of higher-order chromatin structure by CTCF/cohesin. Protein Cell, 2019, 10(12):914-920. doi: 10.1007/s13238-019-00656-y
[30]	Wu Q, Jia ZL. Wiring the brain by clustered protocadherin neural codes. Neurosci Bull, 2021, 37(1):117-131. doi: 10.1007/s12264-020-00578-4
[31]	Narendra V, Rocha PP, An DS, Raviram R, Skok JA, Mazzoni EO, Reinberg D. CTCF establishes discrete functional chromatin domains at theHox clusters during differentiation. Science, 2015, 347(6225):1017-1021. doi: 10.1126/science.1262088 pmid: 25722416
[32]	Ren G, Jin WF, Cui KR, Rodrigez J, Hu GQ, Zhang ZY, Larson DR, Zhao KJ. CTCF-mediated enhancer-promoter interaction is a critical regulator of cell-to-cell variation of gene expression. Mol Cell, 2017, 67(6): 1049-1058.e6. doi: 10.1016/j.molcel.2017.08.026
[33]	Gómez-Marín C, Tena JJ, Acemel RD, López-Mayorga M, Naranjo S, de la Calle-Mustienes E, Maeso I, Beccari L, Aneas I, Vielmas E, Bovolenta P, Nobrega MA, Carvajal J, Gómez-Skarmeta JL. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders. Proc Natl Acad Sci USA, 2015, 112(24):7542-7547. doi: 10.1073/pnas.1505463112
[34]	Jia ZL, Li JW, Ge X, Wu YH, Guo Y, Wu Q. Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection. Genome Biol, 2020, 21(1):75. doi: 10.1186/s13059-020-01984-7
[35]	Zhang D, Huang P, Sharma M, Keller CA, Giardine B, Zhang HY, Gilgenast TG, Phillips-Cremins JE, Hardison RC, Blobel GA. Alteration of genome folding via contact domain boundary insertion. Nat Genet, 2020, 52(10):1076-1087. doi: 10.1038/s41588-020-0680-8
[36]	Zhai YN, Xu Q, Guo Y, Wu Q. Characterization of a cluster of CTCF-binding sites in a protocadherin regulatory region. Hereditas(Beijing), 2016, 38(4):323-336.
	翟亚男, 许泉, 郭亚, 吴强. 原钙粘蛋白基因簇调控区域中成簇的CTCF结合位点分析. 遗传, 2016, 38(4):323-336.
[37]	Zhang XF, Zhang Y, Ba ZQ, Kyritsis N, Casellas R, Alt FW. Fundamental roles of chromatin loop extrusion in antibody class switching. Nature, 2019, 575(7782):385-389. doi: 10.1038/s41586-019-1723-0
[38]	Xu DF, Ma RS, Zhang JH, Liu ZJ, Wu B, Peng JH, Zhai YN, Gong QG, Shi YY, Wu JH, Wu Q, Zhang ZY, Ruan K. Dynamic nature of CTCF tandem 11 zinc fingers in multivalent recognition of DNA as revealed by NMR spectroscopy. J Phys Chem Lett, 2018, 9(14):4020-4028. doi: 10.1021/acs.jpclett.8b01440
[39]	Amândio AR, Lopez-Delisle L, Bolt CC, Mascrez B, Duboule D. A complex regulatory landscape involved in the development of mammalian external genitals. eLife, 2020, 9:e52962. doi: 10.7554/eLife.52962
[40]	Bianco S, Annunziatella C, Andrey G, Chiariello AM, Esposito A, Fiorillo L, Prisco A, Conte M, Campanile R, Nicodemi M. Modeling single-molecule conformations of the HoxD region in mouse embryonic stem and cortical neuronal cells. Cell Rep, 2019, 28(6): 1574-1583.e4. doi: 10.1016/j.celrep.2019.07.013
[41]	Fabre PJ, Leleu M, Mormann BH, Lopez-Delisle L, Noordermeer D, Beccari L, Duboule D. Large scale genomic reorganization of topological domains at theHoxD locus. Genome Biol, 2017, 18(1):149. doi: 10.1186/s13059-017-1278-z
[42]	Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. The dynamic architecture of Hox gene clusters. Science, 2011, 334(6053):222-225. doi: 10.1126/science.1207194 pmid: 21998387
[43]	Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E, de Laat W, Spitz F, Duboule D. A regulatory archipelago controls Hox genes transcription in digits. Cell, 2011, 147(5):1132-1145. doi: 10.1016/j.cell.2011.10.023 pmid: 22118467
[44]	Rodríguez-Carballo E, Lopez-Delisle L, Willemin A, Beccari L, Gitto S, Mascrez B, Duboule D. Chromatin topology and the timing of enhancer function at theHoxD locus. Proc Natl Acad Sci USA, 2020, 117(49):31231-31241. doi: 10.1073/pnas.2015083117
[45]	Li JH, Shou J, Guo Y, Tang YX, Wu YH, Jia ZL, Zhai YN, Chen ZF, Xu Q, Wu Q. Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9. J Mol Cell Biol, 2015, 7(4):284-298. doi: 10.1093/jmcb/mjv016
[46]	Li JH, Shou J, Wu Q. DNA fragment editing of genomes by CRISPR/Cas9. Hereditas(Beijing), 2015, 37(10):992-1002.
	李金环, 寿佳, 吴强. CRISPR/Cas9系统在基因组DNA片段编辑中的应用. 遗传, 2015, 37(10):992-1002.
[47]	Liu PF, Wu Q. Probing 3D genome by CRISPR/Cas9. Hereditas(Beijing), 2020, 42(1):18-31.
	刘沛峰, 吴强. CRISPR/Cas9基因编辑在三维基因组研究中的应用. 遗传, 2020, 42(1):18-31.
[48]	Shou J, Li JH, Liu YB, Wu Q. Precise and predictable CRISPR chromosomal rearrangements reveal principles of Cas9-mediated nucleotide insertion. Mol Cell, 2018, 71(4): 498-509.e4. doi: S1097-2765(18)30466-0 pmid: 30033371
[49]	Wang LY, Huang HY, Wu Q. The diversity of DNA fragment editing by CRISPR/Cas9 in highly homologous or repetitive sequences. Hereditas(Beijing), 2017, 39(4):313-325.
	汪乐洋, 黄海燕, 吴强. 利用CRISPR/Cas9对基因组中高度同源DNA片段编辑多样性的遗传学研究. 遗传, 2017, 39(4):313-325.
[50]	Cong L, Ran FA, Cox D, Lin SL, Barretto R, Habib N, Hsu PD, Wu XB, Jiang WY, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas9 systems. Science, 2013, 339(6121):819-823. doi: 10.1126/science.1231143 pmid: 23287718
[51]	Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol, 2021, 12(11):828-856. doi: 10.1093/jmcb/mjaa060
[52]	Wang N, Jia ZL, Wu Q. RFX5 regulates gene expression of thePcdhα cluster. Hereditas(Beijing), 2020, 42(8):760-774. doi: 10.16288/j.yczz.20-184 pmid: 32952112
	王娜, 甲芝莲, 吴强. RFX5调控原钙粘蛋白α基因簇的表达. 遗传, 2020, 42(8):760-774. doi: 10.16288/j.yczz.20-184 pmid: 32952112
[53]	Wu YH, Jia ZL, Ge X, Wu Q. Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers atPcdhα locus. Sci China Life Sci, 2020, 63(6):835-844. doi: 10.1007/s11427-019-1598-4
[54]	Zuin J, Dixon JR, van der Reijden MIJA, Ye Z, Kolovos P, Brouwer RWW, van de Corput MPC, van de Werken HJG, Knoch TA, van IJcken WFJ, Grosveld FG, Ren B, Wendt KS. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci USA, 2014, 111(3):996-1001. doi: 10.1073/pnas.1317788111
[55]	Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E. HiC-Pro: An optimized and flexible pipeline for Hi-C data processing. Genome Biol, 2015, 16:259. doi: 10.1186/s13059-015-0831-x
[56]	Kruse K, Hug CB, Hernández-Rodríguez B, Vaquerizas JM. TADtool: Visual parameter identification for TAD- calling algorithms. Bioinformatics, 2016, 32(20):3190-3192. pmid: 27318199
[57]	Bailey TL, Johnson J, Grant CE, Noble WS. The meme suite. Nucleic Acids Res, 2015, 43(W1):W39-W49. doi: 10.1093/nar/gkv416
[58]	Chen FZ, You LJ, Yang F, Wang LN, Guo XQ, Gao F, Hua C, Tan C, Fang L, Shan RQ, Zeng WJ, Wang B, Wang R, Xu X, Wei XF. CNGBdb: China National GeneBank DataBase. Hereditas(Beijing), 2020, 42(8):799-809.
	陈凤珍, 游丽金, 杨帆, 王丽娜, 郭学芹, 高飞, 华聪, 谈聪, 方林, 单日强, 曾文君, 王博, 王韧, 徐讯, 魏晓锋. CNGBdb: 国家基因库生命大数据平台. 遗传, 2020, 42(8):799-809.
[59]	Guo XQ, Chen FZ, Gao F, Li L, Liu K, You LJ, Hua C, Yang F, Liu WL, Peng CH, Wang LN, Yang XX, Zhou FY, Tong JW, Cai J, Li ZY, Wan B, Zhang L, Yang T, Zhang MW, Yang LL, Yang YW, Zeng WJ, Wang B, Wei XF, Xu X. CNSA: a data repository for archiving omics data. Database (Oxford), 2020, 2020: baaa055.
[60]	Shi X, Shou J, Mehryar MM, Li JW, Wang LY, Zhang M, Huang HY, Sun XF, Wu Q. Cas9 has no exonuclease activity resulting in staggered cleavage with overhangs and predictable di- and tri-nucleotide CRISPR insertions without template donor. Cell Discov, 2019, 5:53. doi: 10.1038/s41421-019-0120-z
[61]	Gligoris TG, Scheinost JC, Burmann F, Petela N, Chan KL, Uluocak P, Beckouët F, Gruber S, Nasmyth K, Löwe J. Closing the cohesin ring: structure and function of its Smc3-kleisin interface. Science, 2014, 346(6212):963-967. doi: 10.1126/science.1256917 pmid: 25414305
[62]	Nishiyama T. Cohesion and cohesin-dependent chromatin organization. Curr Opin Cell Biol, 2019, 58:8-14. doi: S0955-0674(18)30166-2 pmid: 30544080

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HOXD基因簇内一系列CTCF位点反转揭示绝缘子功能

Combinatorial CRISPR inversions of CTCF sites in HOXD cluster reveal complex insulator function

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