title: The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
abstract: Defining the transcriptional dynamics of a temporal process such as cell differentiation is challenging owing to the high variability in gene expression between individual cells. Time-series gene expression analyses of bulk cells have difficulty distinguishing early and late phases of a transcriptional cascade or identifying rare subpopulations of cells, and single-cell proteomic methods rely on a priori knowledge of key distinguishing markers. Here we describe Monocle, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. Applied to the differentiation of primary human myoblasts, Monocle revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation. We validated some of these predicted regulators in a loss-of function screen. Monocle can in principle be used to recover single-cell gene expression kinetics from a wide array of cellular processes, including differentiation, proliferation and oncogenic transformation.
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA.
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA.|Harvard Stem Cell Institute, Harvard University, Cambridge, MA.
authors.forename: Davide
authors.initials: D
authors.lastname: Cacchiarelli
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA.
authors.forename: Jonna
authors.initials: J
authors.lastname: Grimsby
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA.
authors.forename: Prapti
authors.initials: P
authors.lastname: Pokharel
authors.affiliation: Fluidigm Corporation, South San Francisco, California, USA.
authors.forename: Shuqiang
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Morse
authors.affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA.
authors.forename: Niall J
authors.initials: NJ
authors.lastname: Lennon
authors.affiliation: Fluidigm Corporation, South San Francisco, California, USA.
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Livak
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA.|Harvard Stem Cell Institute, Harvard University, Cambridge, MA.
authors.forename: Tarjei S
authors.initials: TS
authors.lastname: Mikkelsen
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.|The Broad Institute of MIT and Harvard, Cambridge, Massachussetts, USA.
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
mesh_terms: D000465:Algorithms; D002454:Cell Differentiation / Q000235:genetics / Q000502:physiology; D002478:Cells, Cultured; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation / Q000235:genetics / Q000502:physiology; D023281:Genomics; D006801:Humans; D024510:Muscle Development / Q000235:genetics / Q000502:physiology; D032446:Myoblasts / Q000378:metabolism; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics / Q000502:physiology
chemical_list: D014157:Transcription Factors