qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells

We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell

Linear stability analysis of miscible two-fluid flow in a channel with velocity slip at the walls

The linear stability characteristics of pressure-driven miscible two-fluid flow with same density and varying viscosities in a channel with velocity slip at the wall are examined.Aprominent feature of the instability is that only a band ofwave numbers is unstable whatever the Reynolds number is, whereas shorter wavelengths and smaller wave numbers are observed to be stable. The stability characteristics are different from both the limiting cases of interface dominated flows and continuously stratified flows in a channel with velocity slip at the wall. The flow system is destabilizing when a more viscous fluid occupies the region closer to the wall with slip. For this configuration a new mode of instability, namely the overlap mode, appears for high mass diffusivity of the two fluids. This mode arises due to the overlap of critical layer of dominant instability with the mixed layer of varying viscosity. The critical layer contains a location in the flowdomain atwhich the base flowvelocity equals the phase speed of themost unstable disturbance. Such amode also occurs in the corresponding flow in a rigid channel, but absent in either of the above limiting cases of flow in a channel with slip. The flow is unstable at low Reynolds numbers for a wide range of wave numbers for low mass diffusivity, mimicking the interfacial instability of the immiscible flows. A configuration with less viscous fluid adjacent to the wall is more stable at moderate miscibility and this is also in contrast with the result for the limiting case of interface dominated flows in a channel with slip, where the above configuration ismore unstable. It is possible to achieve stabilization or destabilization of miscible two-fluid flow in a channel with wall slip by appropriately choosing the viscosity of the fluid layer adjacent to the wall. In addition, the velocity slip at the wall has a dual role in the stability of flow system and the trend is influenced by the location of the mixed layer, the location of more viscous fluid and the mass diffusivity of the two fluids. It is well known that creating a viscosity contrast in a particularway in a rigid channel delays the occurrence of turbulence in a rigid channel. The results of the present study show that the flow system can be either stabilized or destabilized by designing the walls of the channel as hydrophobic surfaces, modeled by velocity slip at the walls. The study provides another effective strategy to control the flow syste

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

The gene expression programs that define the identity of each cell are controlled by master transcription factors (TFs) that bind cell-type-specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here, we present evidence that signaling factors for the WNT, TGF-β, and JAK/STAT pathways use their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. We show that the WNT coactivator β-catenin interacts both with components of condensates and DNA-binding factors to selectively occupy super-enhancer-associated genes. We propose that the cell-type specificity of the response to signaling is mediated in part by the IDRs of the signaling factors, which cause these factors to partition into condensates established by the master TFs and Mediator at genes with prominent roles in cell identity