Single-cell transcript analysis of human embryonic stem cells.
We demonstrate the qualitative and quantitative power of single-cell transcript analysis to characterize transcriptome dynamics in human embryonic stem cells (hESC's). Single-cell analysis can systematically determine unique cellular profiles for use in cell sorting and identification, show the potential to augment standing models of cellular differentiation, and elucidate the behavior of stem cells exiting pluripotency. Using single-cell analysis of H9 hESC's differentiating under three culture conditions, we revealed transient expression of mesendodermal markers in all three protocols, followed by increasingly stable expression of embryonic endoderm and extra-embryonic endoderm markers. Our single-cell profiles reveal mixed populations of cell types, with both transcriptional and temporal heterogeneity marking differentiation under all conditions. Interestingly, we also observe extensive and prolonged co-expression of markers regulating both pluripotency and lineage differentiation in all culture conditions, and we find that pluripotency marker transcripts remain detectable in the majority of cells for many days. Finally, we show that cells derived from undifferentiated hESC colonies display consistent gene expression profiles characterized by three cohorts of transcripts: uniform, absent and sporadically detected messages, and that a striking correlation exists between genes' membership in these cohorts and their hESC promoter chromatin state, with bivalent promoters dominating the sporadic transcripts.
Gibson
Jason D
JD
University of Connecticut, Department of Molecular and Cell Biology, Storrs, 06269-2131, USA. craig.nelson@uconn.edu
Jakuba
Caroline M
CM
Boucher
Nathalie
N
Holbrook
Kelly A
KA
Carter
Mark G
MG
Nelson
Craig E
CE
D028341:Activins / Q000494:pharmacology; D055415:Bone Morphogenetic Protein 4 / Q000494:pharmacology; D002454:Cell Differentiation / Q000235:genetics / Q000502:physiology; D002843:Chromatin / Q000235:genetics / Q000502:physiology; D053595:Embryonic Stem Cells / Q000166:cytology / Q000502:physiology*; D020869:Gene Expression Profiling; D006801:Humans; D012313:RNA / Q000737:chemistry / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
C525809:BMP4 protein, human; D055415:Bone Morphogenetic Protein 4; D002843:Chromatin; D028341:Activins; D012313:RNA