Journal: Nature

Article Title: Single Molecule Imaging of Transcription Dynamics in Somatic Stem Cells

doi: 10.1038/s41586-020-2432-4

Figure Lengend Snippet: a , Representative images of CMP in different states. Scale bar = 10μm. b , Gating scheme for assigning CMP to transcriptional states. See for details on the gating strategy. tSNE plot demonstrates the proximity of states to one another and to immunophenotypic GMP and MEP. Images and analyses derived from experimental datasets reported in and , Frequency distribution of transcriptional bursting for each gene in each transcriptional state. x-axis is the number of active alleles. d , (top) Schematic of “states” being the consequence of simple transcriptional noise of the LES state (right) versus truly separate transcriptional states (right) that require transition events (edges). (bottom) Time dependent behavior of simulated cells in a noise only (gray) or state transition system (red) shown as a bivariate plot of PU.1 copy number versus Gata1+Gata2 copy number. T indicates the amount of elapsed simulation time as a fraction of the final time. (e-f) , Gillespie simulations of state transitions, modulating half-life alone. If a transition to another state occurs by noise alone, the cell only changes the mRNA half-life of the mRNA defining that state. e , Endpoint states reached in the simulations (n=10,000) and f , 1000 representative simulation trajectories, color coded on the final endpoint state. Each panel is a different factor change in the mRNA half-life, with the left-most panel as the reference (i.e. the half-lives used in ), (second panel from left), 3X (second from right), and 4X (right-most).

Article Snippet: tSNE maps of primary KL cells were generated in MATLAB with the ‘tsne’ function using the mature and nascent mRNA values/cell for each gene as variables.

Techniques: Derivative Assay