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

Using ATAC-seq to identify the chromatin accessibility activated by type Ⅰ interferon in human monocytes

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。

Objective To detect the genome-wide pro filing of chromatin accessibility in human monocytes after stimulated with interferon α(IFNα). Methods Blood samples were collected from 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 signi ficant up-regulated regions, and 442 signi ficant down-regulated regions. Most of the accessible regions were located at promoters and the adjacent areas of the genes, followed by the 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 signi ficantly 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 signi ficant 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 expression.