[1]林达,洪萍,李国亮,等.DLO Hi-C染色体构象捕获技术[J].南京农业大学学报,2018,41(4):577-579.[doi:10.7685/jnau.201806031]
 LIN Da,HONG Ping,LI Guoliang,et al.Digestion-ligation-only Hi-C(DLO Hi-C)for chromosome conformation capture[J].Journal of Nanjing Agricultural University,2018,41(4):577-579.[doi:10.7685/jnau.201806031]
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DLO Hi-C染色体构象捕获技术()
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《南京农业大学学报》[ISSN:1000-2030/CN:32-1148/S]

卷:
41卷
期数:
2018年4期
页码:
577-579
栏目:
出版日期:
2018-07-09

文章信息/Info

Title:
Digestion-ligation-only Hi-C(DLO Hi-C)for chromosome conformation capture
作者:
林达1 洪萍2 李国亮2 曹罡1
1. 华中农业大学农业微生物学国家重点实验室, 湖北 武汉 430070;
2. 华中农业大学作物遗传改良国家重点实验室, 湖北 武汉 430070
Author(s):
LIN Da1 HONG Ping2 LI Guoliang2 CAO Gang1
1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
2. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
关键词:
三维基因组染色体构象捕获Hi-CDLO Hi-C(酶切酶连Hi-C)染色体易位
Keywords:
3D genomechromosome conformation captureHi-CDLO Hi-C(digestion-ligation-only Hi-C)chromosomal translocation
分类号:
Q756
DOI:
10.7685/jnau.201806031
摘要:
基因组三维结构在DNA复制、DNA损伤修复、基因转录调控中扮演着重要的角色。Hi-C是目前研究基因组三维结构的主要手段之一,但是存在背景噪音大、试验成本高、试验流程繁琐,缺乏对随机连接噪音的评价等缺陷,因而限制了三维基因组学的发展。为此,我们开发了一种简单经济的染色体构象捕获技术,即DLO Hi-C(digestion-ligation-only Hi-C)。该技术去掉了生物素标记的步骤,只需要2轮简单的酶切酶连反应即可构建高质量的DLO Hi-C测序文库。为了评价文库中的随机连接噪音的比例,我们在文库构建步骤中加入了噪音评价的步骤。研究结果显示,与当前的in situ Hi-C等方法比较,我们的DLO Hi-C试验时间短、试验成本低、测序成本低,有更多的有效交互数据。将DLO Hi-C应用于肿瘤细胞系,我们找到了已知和新的基因组结构变异。所以,我们希望DLO Hi-C技术将对研究染色体的三维构象、基因的转录调控及基因组的组装有重要的促进作用。
Abstract:
The 3D structure of the genome has an important role in DNA replication,DNA damage repair,and transcriptional regulation. However,high background noise,high cost,and a lack of straightforward noise evaluation in the Hi-C methods impede the advancement of 3D genomic research. Here we develop a simple digestion-ligation-only Hi-C(DLO Hi-C)technology to explore the 3D landscape of the genome. This method requires only two rounds of digestion and ligation,without the need for biotin labeling. Notably,random ligation could be quickly evaluated in an early quality-control step before sequencing. Our results show that DLO Hi-C experiment has a shorter time,lower experimental cost,lower sequencing cost,and more effective interaction data than current in situ Hi-C methods. Applying DLO Hi-C to tumor cell lines,we find known and new genomic translocations. This technology may facilitate investigation of genomic organization,gene regulation,and genome assembly.

参考文献/References:

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备注/Memo

备注/Memo:
收稿日期:2018-06-21。
基金项目:国家重点基础研究专项基金(2016YFA0102500);国家自然科学基金项目(31771402)
作者简介:林达,博士,主要进行新型染色体构象捕获技术的开发;洪萍,博士研究生,主要进行基因组三维结构分析软件的开发。
通信作者:李国亮,教授,博导,研究方向为三维基因组学、表观遗传学和生物信息学,E-mail:guoliang.li@mail.hzau.edu.cn;曹罡,教授,博导,研究方向为神经生物学与病原学交叉学科,E-mail:gcao@mail.hzau.edu.cn
更新日期/Last Update: 1900-01-01