Using ATAC-seq to identify the chromatin accessibility activated by type I interferon in human monocytes
10.3969/j.issn.1674-8115.2019.05.003
- Author:
Ye OUYANG
1
Author Information
1. Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine
- Publication Type:Journal Article
- Keywords:
Assay for transposase-accessible chromatin using sequencing (ATAC-seq);
Chromatin accessibility;
Epigenetics;
Monocyte;
Type I interferon signaling pathway
- From:
Journal of Shanghai Jiaotong University(Medical Science)
2019;39(5):451-457
- CountryChina
- Language:Chinese
-
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 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 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, 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 significantly enhanced at the promoters and transcriptional start sites of effect or 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 typeinterferon stimulation and makes preparation for downstream gene expression.
