原钙粘蛋白基因簇调控区域中成簇的CTCF结合位点分析

doi:10.16288/j.yczz.16-037

遗传 ›› 2016, Vol. 38 ›› Issue (4): 323-336.doi: 10.16288/j.yczz.16-037

原钙粘蛋白基因簇调控区域中成簇的CTCF结合位点分析

翟亚男, 许泉, 郭亚, 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:2016-01-21 修回日期:2016-03-01 出版日期:2016-04-20 发布日期:2016-04-20
通讯作者: 吴强,博士,教授,博士生导师,研究方向：基因表达调控及神经发育。E-mail: qwu123@gmail.com
作者简介:翟亚男,硕士研究生,专业方向：遗传学。E-mail: zhaichn@gmail.com
基金资助:
国家自然科学基金项目(编号：91519302)资助[Supported by the National Natural Science Foundation of China (No; 91519302)]

Characterization of a cluster of CTCF-binding sites in a protocadherin regulatory region

Yanan Zhai, Quan Xu, Ya Guo, Qiang Wu

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

Received:2016-01-21 Revised:2016-03-01 Online:2016-04-20 Published:2016-04-20

摘要/Abstract

摘要： 哺乳动物中原钙粘蛋白(Protocadherin, Pcdh)基因簇包含50多个串联排列的基因,这些基因形成3个紧密相连的基因簇(Pcdhα、Pcdhβ和Pcdhγ),所编码的原钙粘蛋白质群在神经元多样性(Neuronal diversity)和单细胞特异性(Single cell identity)以及神经突触信号转导中发挥重要作用。前期的工作已证实转录因子CTCF(CCCTC-binding factor)与CTCF结合位点(CTCF-binding site, CBS)的方向性结合能够决定增强子和启动子环化的方向以及其远距离交互作用的特异性,并进一步在Pcdh基因座(Locus)形成两个(Pcdhα和Pcdhγ)染色质拓扑结构域(CTCF/cohesin- mediated chromatin domain, CCD),而且染色质拓扑结构域对于控制基因表达调控至关重要。本文通过生物信息学方法对比人类和小鼠序列,发现Pcdhβγ染色质拓扑结构域调控区域中的DNase I超敏位点(DNase I hypersensitive sites, HSs)较为保守。染色质免疫沉淀及大规模测序实验(Chromatin immunoprecipitation and massive parallel sequencing, ChIP-Seq)揭示CBS位点在Pcdhβγ调控区域中成簇分布并且具有相同的方向。凝胶电泳迁移实验(Electrophoresis mobility shift assay, EMSA)确定Pcdhβγ调控区域内具体的42 bp CBS位点并且发现一个CTCF峰包含两个CBS位点。在全基因组范围内,运用计算生物学方法分析CTCF和增强子、启动子等调控元件的关系,发现CBS位点在调控元件附近有较多分布,推测CTCF通过介导增强子和启动子的特异性交互作用,在细胞核三维基因组内形成活性转录枢纽调控基因精准表达。

关键词: 原钙粘蛋白基因簇, 转录因子CTCF, CTCF结合位点, 染色质拓扑结构域CCD, 基因表达调控

Abstract: The mammalian clustered protocadherin (Pcdh) locus contains more than 50 highly-similar genes arrayed in tandem. These Pcdh genes are organized into three closely-linked clusters (Pcdhα, Pcdhβ, and Pcdhγ). The encoded PCDH proteins play critical roles in neuronal diversity, single cell identity, and synaptic connectivity. Recent studies revealed that directional CTCF (CCCTC-binding factor) binding to CBS (CTCF-binding site) determines the specific interaction between enhancers and promoters, and the three Pcdh clusters form two CCDs (CTCF/cohesin- mediated chromatin domain) which is important for gene regulation. Here, we characterized a regulatory region, which contains several HSs (DNase I hypersensitive sites), downstream of the Pcdhβγ clusters. Specifically, CTCF ChIP-Seq (Chromatin immunoprecipitation-sequencing) experiments revealed several peaks in the Pcdhβγ regulatory regions. In addition, we performed comprehensive EMSA (Electrophoresis mobility shift assay) experiments and identified exact 42-bp CBS sites for each CTCF peak. Interestingly, we found that single CTCF peaks can contain two CBS sites. Finally, genome-wide computational analyses revealed many CBS sites close to chromatin marks of regulatory elements, such as enhancers and promoters. We propose that CTCF may mediate specific interactions between enhancers and promoters to form active transcription hub for gene expression.

Key words: protocadherin, transcription factor CTCF, CTCF-binding site, CTCF/cohesin-mediated chromatin domain, regulation of gene expression

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[J]. 遗传, 2016, 38(4): 323-336.

Yanan Zhai, Quan Xu, Ya Guo, Qiang Wu. Characterization of a cluster of CTCF-binding sites in a protocadherin regulatory region[J]. HEREDITAS(Beijing), 2016, 38(4): 323-336.

参考文献

[1] Li W, Wu Q. Protocadherin and the diversity of neurons. Sci Technol Vision , 2013, (27): 14. 李伟, 吴强. 原钙粘蛋白分子与神经元的多样性. 科技视界, 2013, (27): 14.
[2] Chen WV, Alvarez FJ, Lefebvre JL, Friedman B, Nwakeze C, Geiman E, Smith C, Thu CA, Tapia JC, Tasic B, Sanes JR, Maniatis T. Functional significance of isoform diversification in the protocadherin gamma gene cluster. Neuron , 2012, 75(3): 402-409.
[3] Garrett AM, Schreiner D, Lobas MA, Weiner JA. γ-protocadherins control cortical dendrite arborization by regulating the activity of a FAK/PKC/MARCKS signaling pathway. Neuron , 2012, 74(2): 269-276.
[4] Hirayama T, Tarusawa E, Yoshimura Y, Galjart N, Yagi T. CTCF is required for neural development and stochastic expression of clustered Pcdh genes in neurons. Cell Rep , 2012, 2(2): 345-357.
[5] Lefebvre JL, Kostadinov D, Chen WV, Maniatis T, Sanes JR. Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. Nature , 2012, 488(7412): 517- 521.
[6] Suo L, Lu HN, Ying GX, Capecchi MR, Wu Q. Protocadherin clusters and cell adhesion kinase regulate dendrite complexity through Rho GTPase. J Mol Cell Biol , 2012, 4(6): 362-376.
[7] Wu Q. Comparative genomics and diversifying selection of the clustered vertebrate protocadherin genes. Genetics , 2005, 169(4): 2179-2188.
[8] Wu Q, Maniatis T. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Cell , 1999, 97(6): 779-790.
[9] Wu Q, Maniatis T. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. Proc Natl Acad Sci USA , 2000, 97(7): 3124-3129.
[10] Wu Q, Zhang T, Cheng JF, Kim Y, Grimwood J, Schmutz J, Dickson M, Noonan JP, Zhang MQ, Myers RM, Maniatis T. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Res , 2001, 11(3): 389-404.
[11] Zou C, Huang W, Ying G, Wu Q. Sequence analysis and expression mapping of the rat clustered protocadherin gene repertoires. Neuroscience , 2007, 144(2): 579-603.
[12] Tasic B, Nabholz CE, Baldwin KK, Kim Y, Rueckert EH, Ribich SA, Cramer P, Wu Q, Axel R, Maniatis T. Promoter choice determines splice site selection in protocadherin α and γ pre-mRNA splicing. Mol Cell , 2002, 10(1): 21-33.
[13] Wang XZ, Weiner JA, Levi S, Craig AM, Bradley A, Sanes JR. Gamma-protocadherins are required for survival of spinal interneurons. Neuron , 2002, 36(5): 843-854.
[14] Esumi S, Kakazu N, Taguchi Y, Hirayama T, Sasaki A, Hirabayashi T, Koide T, Kitsukawa T, Hamada S, Yagi T. Monoallelic yet combinatorial expression of variable exons of the protocadherin-alpha gene cluster in single neurons. Nat Genet , 2005, 37(2): 171-176.
[15] 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 alpha promoter choice. Proc Natl Acad Sci USA , 2012, 109(51): 21081-21086.
[16] Schreiner D, Weiner JA. Combinatorial homophilic interaction between gamma-protocadherin multimers greatly expands the molecular diversity of cell adhesion. Proc Natl Acad Sci USA , 2010, 107(33): 14893-14898.
[17] Thu CA, Chen WV, Rubinstein R, Chevee M, Wolcott HN, Felsovalyi KO, Tapia JC, Shapiro L, Honig B, Maniatis T. Single-cell identity generated by combinatorial homophilic interactions between α, β, and γ protocadherins. Cell , 2014, 158(5): 1045-1059.
[18] Ribich S, Tasic B, Maniatis T. Identification of long-range regulatory elements in the protocadherin-α gene cluster. Proc Natl Acad Sci USA , 2006, 103(52): 19719-19724.
[19] Wu HY, Guo Y, Li W, Wu Q. Cloning and functional analysis of the regulatory elements in the human protocadherin gene cluster. Life Sci Res , 2014, 18(2): 95-99. 吴海洋, 郭亚, 李伟, 吴强. 人类原钙粘蛋白基因簇调控元件的克隆及对其启动子活性的影响. 生命科学研究, 2014, 18(2): 95-99.
[20] Yokota S, Hirayama T, Hirano K, Kaneko R,

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

原钙粘蛋白基因簇调控区域中成簇的CTCF结合位点分析

Characterization of a cluster of CTCF-binding sites in a protocadherin regulatory region

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	王舜泽, 江丰, 朱东丽, 杨铁林, 郭燕. Hi-C技术在三维基因组学和疾病致病机理研究中的应用[J]. 遗传, 2023, 45(4): 279-294.
[2]	周聪, 周强伟, 成盛, 李国亮. CTCF在介导三维基因组形成及调控基因表达中的研究进展[J]. 遗传, 2021, 43(9): 816-821.
[3]	徐海冬, 宁博林, 牟芳, 李辉, 王宁. 选择性多聚腺苷酸化的生物学效应及其调控机制研究进展[J]. 遗传, 2021, 43(1): 4-15.
[4]	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[J]. 遗传, 2019, 41(3): 215-233.
[5]	施剑,李艳明,方向东. 长链非编码RNA通过细胞核高级结构调控真核基因表达及其临床意义[J]. 遗传, 2017, 39(3): 189-199.
[6]	路畅, 黄银花. 动物长链非编码RNA研究进展[J]. 遗传, 2017, 39(11): 1054-1065.
[7]	黄小庆,李丹丹,吴娟. 植物长链非编码RNA研究进展[J]. 遗传, 2015, 37(4): 344-359.
[8]	施子晗, 李泽琴, 张根发. 植物组蛋白赖氨酸化修饰参与基因表达调控的机理[J]. 遗传, 2014, 36(3): 208-219.
[9]	张韬杨足君. 植物基因组DNase I超敏感位点的研究进展[J]. 遗传, 2013, 35(7): 867-874.
[10]	夏天，肖丙秀，郭俊明. 长链非编码RNA的作用机制及其研究方法[J]. 遗传, 2013, 35(3): 269-280.
[11]	秦丹徐存拴. 非编码DNA序列的功能及其鉴定[J]. 遗传, 2013, 35(11): 1253-1264.
[12]	李泽琴，李静晓，张根发. 植物抗坏血酸过氧化物酶的表达调控以及对非生物胁迫的耐受作用[J]. 遗传, 2013, 35(1): 45-54.
[13]	罗茂，张志明，高健，曾兴，潘光堂. miR319在植物器官发育中的调控作用[J]. 遗传, 2011, 33(11): 1203-1211.
[14]	孟雅楠，孟丽军，宋亚娟，刘美玲，张秀军. 小RNA分子与精子发生调控[J]. 遗传, 2011, 33(1): 9-16.
[15]	程龙，黄翠芬，叶棋浓. 乳腺癌中雌激素受体α表达水平调节的分子机制[J]. 遗传, 2010, 32(3): 191-197.