title: Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase.
abstract: During cellular reprogramming, only a small fraction of cells become induced pluripotent stem cells (iPSCs). Previous analyses of gene expression during reprogramming were based on populations of cells, impeding single-cell level identification of reprogramming events. We utilized two gene expression technologies to profile 48 genes in single cells at various stages during the reprogramming process. Analysis of early stages revealed considerable variation in gene expression between cells in contrast to late stages. Expression of Esrrb, Utf1, Lin28, and Dppa2 is a better predictor for cells to progress into iPSCs than expression of the previously suggested reprogramming markers Fbxo15, Fgf4, and Oct4. Stochastic gene expression early in reprogramming is followed by a late hierarchical phase with Sox2 being the upstream factor in a gene expression hierarchy. Finally, downstream factors derived from the late phase, which do not include Oct4, Sox2, Klf4, c-Myc, and Nanog, can activate the pluripotency circuitry.
authors.affiliation: The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Yosef
authors.initials: Y
authors.lastname: Buganim
authors.forename: Dina A
authors.initials: DA
authors.lastname: Faddah
authors.forename: Albert W
authors.initials: AW
authors.lastname: Cheng
authors.forename: Elena
authors.initials: E
authors.lastname: Itskovich
authors.forename: Styliani
authors.initials: S
authors.lastname: Markoulaki
authors.forename: Kibibi
authors.initials: K
authors.lastname: Ganz
authors.forename: Sandy L
authors.initials: SL
authors.lastname: Klemm
authors.forename: Alexander
authors.initials: A
authors.lastname: van Oudenaarden
authors.forename: Rudolf
authors.initials: R
authors.lastname: Jaenisch
mesh_terms: D000818:Animals; D002460:Cell Line; D065150:Cellular Reprogramming; D004622:Embryo, Mammalian / Q000166:cytology; D053595:Embryonic Stem Cells; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D005819:Genetic Markers; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D000090062:Kruppel-Like Factor 4; D051379:Mice; D046210:Microfluidic Analytical Techniques; D055748:SOXB1 Transcription Factors / Q000378:metabolism; D059010:Single-Cell Analysis; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D005819:Genetic Markers; C000715468:Klf4 protein, mouse; D000090062:Kruppel-Like Factor 4; D055748:SOXB1 Transcription Factors; C527783:Sox2 protein, mouse; D014157:Transcription Factors