title: Probing the dynamic organization of transcription compartments and gene loci within the nucleus of living cells.
abstract: The three-dimensional organization of nuclear compartments within living cells determines genome function and yet their underlying self-organizing principles are unclear. We visualize in real-time transcriptionally active compartments (TCs) by the transient enrichment of fluorescently-labeled uridine 5'-triphosphate molecules within living cells. These TCs partially colocalize with active RNA-Pol II in the cell nucleus. Fluorescence anisotropy maps of chromatin compaction evidences a more open chromatin structure at the TCs. Using live-cell timelapse imaging, heterogeneity in the dynamic behavior of TCs has been revealed which falls into three distinct classes: subdiffusive, super-diffusive, and normal diffusive behavior. In contrast, the mobility of a candidate gene locus, either in the repressed or activated state, undergoes a differential restricted motion that is coupled to TC movement. Further TC dynamics is directly affected by small molecule chromatin structure modulators and adenosine triphosphate depletion. This heterogeneous behavior in TC dynamics within living cells could provide an interesting paradigm to explore the spatiotemporal dimension to gene transcription control.
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
authors.forename: Deepak Kumar
authors.initials: DK
authors.lastname: Sinha
authors.forename: Bidisha
authors.initials: B
authors.lastname: Banerjee
authors.forename: Shovamayee
authors.initials: S
authors.lastname: Maharana
authors.forename: G V
authors.initials: GV
authors.lastname: Shivashankar
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000818:Animals; D002417:Cattle; D002467:Cell Nucleus / Q000235:genetics* / Q000378:metabolism*; D002470:Cell Survival; D002843:Chromatin / Q000378:metabolism; D004058:Diffusion; D005454:Fluorescence Polarization; D005456:Fluorescent Dyes / Q000378:metabolism; D005796:Genes / Q000235:genetics*; D006367:HeLa Cells; D006801:Humans; D013696:Temperature; D014158:Transcription, Genetic; D014544:Uridine Triphosphate / Q000378:metabolism
chemical_list: D002843:Chromatin; D005456:Fluorescent Dyes; D000255:Adenosine Triphosphate; D014544:Uridine Triphosphate