Project description:Although the variation in chromatin architecture during adaptive immune responses has been thoroughly investigated, the 3D landscape of innate immunity is still unknown. Herein, chromatin regulation and heterogeneity among human primary monocytes were investigated. Peripheral blood was collected from two healthy persons and two patients with systemic lupus erythematosus (SLE), and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq analyses. Raw data from the THP1 cell line Hi-C library were used for comparison. For each sample, we constructed three Hi-C libraries and obtained approximately 3 billion paired-end reads in total. Resolution analysis showed that more than 80% of bins presented depths greater than 1000 at a 5 kb resolution. The constructed high-resolution chromatin interaction maps presented similar landscapes in the four individuals, which showed significant divergence from the THP1 cell line chromatin structure. The variability in chromatin interactions around HLA-D genes in the HLA complex region was notable within individuals. We further found that the CD16-encoding gene (FCGR3A) is located at a variable topologically associating domain (TAD) boundary and that chromatin loop dynamics might modulate CD16 expression. Our results indicate both the stability and variability of high-resolution chromatin interaction maps among human primary monocytes. This work sheds light on the potential mechanisms by which the complex interplay of epigenetics and spatial 3D architecture regulates chromatin in innate immunity.
Project description:Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary.
Project description:Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary.
Project description:Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary.
Project description:Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary.
