MacroH2A1 is a histone variant that is enriched on the inactive X chromosome (Xi) in mammals and is postulated to play an important, but unknown, role in the repression of gene expression. Here we show that, although macroH2A1 marks repressed autosomal chromatin, it positively regulates transcription when located in the transcribed regions of a subset of its target genes. We used chromatin immunoprecipitation (ChIP) coupled with tiling microarrays (ChIP–chip) to determine the genomic localization of macroH2A1 in IMR90 human primary lung fibroblasts and MCF-7 breast cancer cells. The patterns of macroH2A1 deposition are largely similar across the autosomes of both cell lines. Our studies revealed a genomic localization pattern unique among histone variants; namely, the occupation by macroH2A1 of large chromatin domains (>500 kb in some cases) that contain repressive chromatin marks (e.g., histone H3 Lys 27 trimethylation). The boundaries of macroH2A1-containing domains tend to occur in promoter-proximal regions. Not all promoters, however, serve as macroH2A1 boundaries; many macroH2A1-containing chromatin domains invade the transcribed regions of genes whose products play key roles in development and cell–cell signaling. Surprisingly, the expression of a subset of these genes is positively regulated by macroH2A1. MacroH2A1 also plays a role in augmenting signal-regulated transcription, specifically for genes responsive to serum starvation. Collectively, our results document an unexpected role for macroH2A1 in the escape from heterochromatin-associated silencing and the enhancement of autosomal gene transcription.

We study the effect of electrolyte concentration on the shape of ion current pulses in resistive-pulse sensing. We show that electrokinetic passage of several hundred nanometers in diameter charged polystyrene particles through a micropore leads to formation of current increase when the particles exit the pore. The particle entrance, as reported before, causes formation of the current decrease, which is a measure of the particle size. Formation of the double peak, i.e., current decrease followed by a current increase, is especially pronounced if the resistive-pulse experiments are carried out in KCl concentrations below 200 mM. In order to explain the pulse shape, experiments were designed in which the particles passed through the pore only by either electroosmosis or electrophoresis. The presented experiments and modeling indicate that while both electroosmosis and electrophoresis affect the ion current pulse, formation of the positive peak is mainly determined by the latter effect and the charged state of the particle. The importance of the findings for resistive-pulse analysis is discussed.

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Single pores in the resistive-pulse technique are used as an analytics tool to detect, size, and characterize physical as well as chemical properties of individual objects such as molecules and particles. Each object passing through a pore causes a transient change of the transmembrane current called a resistive pulse. In high salt concentrations when the pore diameter is significantly larger than the screening Debye length, it is assumed that the particle size and surface charge can be determined independently from the same experiment. In this article we challenge this assumption and show that highly charged hard spheres can cause a significant increase of the resistive-pulse amplitude compared to neutral particles of a similar diameter. As a result, resistive pulses overestimate the size of charged particles by even 20%. The observation is explained by the effect of concentration polarization created across particles in a pore, revealed by numerical modeling of ionic concentrations, ion current, and local electric fields. It is notable that in resistive-pulse experiments with cylindrical pores, concentration polarization was previously shown to influence ionic concentrations only at pore entrances; consequently, additional and transient modulation of resistive pulses was observed when a particle entered or left the pore. Here we postulate that concentration polarization can occur across transported particles at any particle position along the pore axis and affect the magnitude of the entire resistive pulse. Consequently, the recorded resistive pulses of highly charged particles reflect not only the particles' volume but also the size of the depletion zone created in front of the moving particle. Moreover, the modeling identified that the effective surface charge density of particles depended not only on the density of functional groups on the particle but also on the capacitance of the Stern layer. The findings are of crucial importance for sizing particles and characterizing their surface charge properties.

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