RT Journal Article
SR Electronic
T1 Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 608695
DO 10.1101/608695
A1 Enoch Boasiako Antwi
A1 Ada Olins
A1 Vladimir B Teif
A1 Matthias Bieg
A1 Tobias Bauer
A1 Zuguang Gu
A1 Benedikt Brors
A1 Roland Eils
A1 Donald Olins
A1 Naveed Ishaque
YR 2019
UL http://biorxiv.org/content/early/2019/04/13/608695.abstract
AB Background Myeloid differentiation gives rise to a plethora of immune cells in the human body. This differentiation leaves strong signatures in the epigenome through each differentiated state of genetically identical cells. The leukemic HL-60/S4 promyelocytic cell can be easily differentiated from its undifferentiated promyelocyte state into neutrophil-and macrophage-like cell states, making it an excellent system for studying myeloid differentiation. In this study, we present the underlying genome and epigenome architecture of HL-60/S4 through its undifferentiated and differentiated cell states.Results We performed whole genome bisulphite sequencing of HL-60/S4 cells and their differentiated counterparts. With the support of karyotyping, we show that HL-60/S4 maintains a stable genome throughout differentiation. Analysis of differential CpG methylation reveals that most methylation changes occur in the macrophage-like state. Differential methylation of promoters was associated with immune related terms. Key immune genes, CEBPA, GFI1, MAFB and GATA1 showed differential expression and methylation. However, we observed strongest enrichment of methylation changes in enhancers and CTCF binding sites, implying that methylation plays a major role in large scale transcriptional reprogramming and chromatin reorganisation during differentiation. Correlation of differential expression and distal methylation with support from chromatin capture experiments allowed us to identify putative proximal and long-range enhancers for a number of immune cell differentiation genes, including CEBPA and CCNF. Integrating expression data, we present a model of HL-60/S4 differentiation in relation to the wider scope of myeloid differentiation.Conclusions For the first time, we elucidate the genome and CpG methylation landscape of HL-60/S4 during differentiation. We identify all differentially methylated regions and positions. We link these to immune function and to important factors in myeloid differentiation. We demonstrate that methylation plays a more significant role in modulating transcription via enhancer reprogramming, rather than by promoter regulation. We identify novel regulatory regions of key components in myeloid differentiation that are regulated by differential methylation. This study contributes another layer of “omics” characterisation of the HL-60/S4 cell line, making it an excellent model system for studying rapid in vitro cell differentiation.Summary statement Epigenomics plays a major role in cell identity and differentiation. We present the DNA methylation landscape of leukemic cells during in-vitro differentiation, to add another ‘omics layer to better understand the mechanisms behind differentiation.HL-60/S4human myeloid leukemic cell line HL-60/S4 (ATCC CRL-3306).UNundifferentiated HL-60/S4TPAtetradecanoyl phorbol acetate treated HL-60/S4CpGCytosine-phosphate-Guanine dinucleotideCpGICpG islandDMPdifferential methylated CpG positionDMRdifferentially methylated CpG regionMPPmultipotent progenitor cellsCMPcommon myeloid progenitor cellsGMPgranulocyte monocyte progenitor cellsMEPmegakaryocyte erythrocyte progenitor cellWGBSwhole genome bisulphite sequencingFISHfluorescent in-situ hybridisationM-FISHmultiplex FISHLINElong interspersed nuclear elementTSStranscription start siteCHIA-PETChromatin interaction analysis by paired end tag sequencingIM-PETintegrated method for predicted enhancer targets