title: Tracing dynamic changes of DNA methylation at single-cell resolution.
abstract: Mammalian DNA methylation plays an essential role in development. To date, only snapshots of different mouse and human cell types have been generated, providing a static view on DNA methylation. To enable monitoring of methylation status as it changes over time, we establish a reporter of genomic methylation (RGM) that relies on a minimal imprinted gene promoter driving a fluorescent protein. We show that insertion of RGM proximal to promoter-associated CpG islands reports the gain or loss of DNA methylation. We further utilized RGM to report endogenous methylation dynamics of non-coding regulatory elements, such as the pluripotency-specific super enhancers of Sox2 and miR290. Loci-specific DNA methylation changes and their correlation with transcription were visualized during cell-state transition following differentiation of mouse embryonic stem cells and during reprogramming of somatic cells to pluripotency. RGM will allow the investigation of dynamic methylation changes during development and disease at single-cell resolution.
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Yonatan
authors.initials: Y
authors.lastname: Stelzer
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
authors.forename: Chikdu Shakti
authors.initials: CS
authors.lastname: Shivalila
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Frank
authors.initials: F
authors.lastname: Soldner
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Styliani
authors.initials: S
authors.lastname: Markoulaki
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address: jaenisch@wi.mit.edu.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Jaenisch
mesh_terms: D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000378:metabolism; D053595:Embryonic Stem Cells; D004742:Enhancer Elements, Genetic; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism; D011401:Promoter Regions, Genetic; D055748:SOXB1 Transcription Factors / Q000378:metabolism; D059010:Single-Cell Analysis
chemical_list: C547384:MIRN290 microRNA, mouse; D035683:MicroRNAs; D055748:SOXB1 Transcription Factors; C527783:Sox2 protein, mouse; D015254:DNA Modification Methylases