上海交通大学学报（医学版）

上海交通大学学报（医学版） ›› 2019, Vol. 39 ›› Issue (5): 451-.doi: 10.3969/j.issn.1674-8115.2019.05.003

• 论著·基础研究 • 上一篇    下一篇

利用 ATAC -seq技术研究Ⅰ型干扰素通路活化后人单核细胞的染色质开放性改变

欧阳也 1，秦玉婷 1，姚超 2，沈南 1, 2   

  1. 1. 上海交通大学医学院附属仁济医院，上海市风湿病学研究所，上海 200125；2. 中国科学院上海营养与健康研究院，上海 200031
  • 出版日期:2019-05-28 发布日期:2019-07-26
  • 通讯作者: 沈南，电子信箱：nanshensibs@gmail.com。
  • 作者简介:欧阳也（1992—），男，硕士；电子信箱： yeouyang@sjtu.edu.cn。
  • 基金资助:
    国家自然科学基金（81601440, 31630021）

Using ATAC-seq to identify the chromatin accessibility activatedtype Ⅰ interferon in human monocytes

OUYANG Ye1, QIN Yu-ting1, YAO Chao2, SHEN Nan1, 2   

  1. 1. Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; 2. Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
  • Online:2019-05-28 Published:2019-07-26
  • Supported by:
    National Natural Science Foundation of China, 81601440, 31630021

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摘要： 目的 ·检测人单核细胞经干扰素 α（interferon α，IFNα）刺激后在全基因组水平上的染色质开放性变化。方法 ·收集健康人外周血单核细胞，运用基于转座酶和高通量测序的染色质分析（assay for transposase-accessible chromatin using sequencing，ATAC-seq）技术检测染色质开放性。使用生物信息学工具进行富集分析和可视化分析。结果 ·经过 IFNα处理后，染色质开放性发生显著增加的区域有 430个，显著降低的区域有 442个；大部分开放结构位于基因的启动子和临近区域，其次是基因间区域以及基因的内含子区域。富集分析显示，染色质开放性明显增加的区域所关联的基因涉及的生物学过程大多是与干扰素相关的信号通路和抗病毒反应。可视化相应的染色质区域，效应性干扰素诱导表达基因（ interferon-stimulated gene，ISG）的启动子及转录起始位点区域在 IFNα刺激之后 ATAC-seq信号强度明显增强；而调节性 ISG在 IFNα刺激前即已具备一定程度的开放性，刺激之后开放性有所增强。开放性增强区域含有干扰素刺激反应元件以及干扰素调控因子等重要转录因子的识别基序。结论 · Ⅰ型干扰素刺激后，人单核细胞的染色质开放性发生了特征性改变，为下游的相关基因表达做出准备。

关键词: Ⅰ型干扰素信号通路, 单核细胞, 转座酶和高通量测序的染色质分析, 染色质开放性, 表观遗传学

Abstract:

Objective · To detect the genome-wide profiling of chromatin accessibility in human monocytes after stimulated with interferon α (IFNα). Methods · Blood samples were collected a healthy donor. Assay for transposase-accessible chromatin using sequencing (ATAC-seq) technique was performed to detect the chromatin accessibility. Bioinformatic tools were used for enrichment analysis and visual analysis. Results · With the treatment of IFNα, there were 430 significant up-regulated regions, and 442 significant down-regulated regions. Most of the accessible regions were located at promoters and the adjacent areas of the genes, followedthe intergenic areas and introns. The enrichment analysis showed that the genes related with up-regulated regions were enriched to interferon relevant pathways or anti-virus reactions. To visualize the corresponding chromatin regions, it showed that the intensity of ATAC-seq signal was significantly enhanced at the promoters and transcriptional start sites of effector interferon-stimulated genes (ISGs) after IFNα stimulation; while for the regulatory ISGs, there was a certain degree of accessibility before stimulation, and the signal intensity was mildly improved. The motif analysis showed significant enrichment of interferon-stimulated response element and interferon regulatory factor in up-regulated regions. Conclusion · Chromatin accessibility of human monocytes has characteristic changes after type Ⅰ interferon stimulation and makes preparation for downstream gene .

Key words: type Ⅰ interferon signaling pathway, monocyte, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin accessibility, epigenetics

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