Effect of Dot1 inhibition on local Sir density and net chromatin-bound Sir: The density of Sir occupancy, determined from simulations, in telomeres (blue solid line) and fraction of Sir chromatin-bound (green dashed line) as a function of increasing Dot1 activity () starting from <i>dot1</i> upto wild-type values.

<p>The system is bistable for all values explored here, however, the nature of the bistability transitions from <i>intermediate-silenced-bistable</i> to <i>active-silenced-bistable</i> at . Note that for decreasing , the local density of Sir protein decreases though the net fraction of chromatin bound Sir protein, counter-intuitively, increases. This is because compact silenced region are lost owing to Dot1 inhibition.</p

Example section of the models phase diagram showing all the possible phases: The phase space is four dimensional.

<p>This section corresponds to fixing Sir2 deacetylase activity () and Sir cooperative binding rates and varying the Sas2 activity () and cooperative Dot1 activity (). Red diamonds represent region where <i>silenced</i> state is stable, green stars where <i>active</i> state is stable, magenta circles where <i>bivalent</i> state is stable, blue crosses where <i>intermediate</i> state is stable, and regions of overlap of symbols are bistable regions. The bistable solutions merge on line to a single solution.</p

Effect of Dot1 inhibition: Density profile of silenced mark (red line), active mark (green line) and acetylation mark (blue line) states where top panel shows ill-defined establishment of silencing for Dot1 inhibition (low ) compared to wild-type values in the bottom panel for which silencing domains are well-defined.

<p>Effect of Dot1 inhibition: Density profile of silenced mark (red line), active mark (green line) and acetylation mark (blue line) states where top panel shows ill-defined establishment of silencing for Dot1 inhibition (low ) compared to wild-type values in the bottom panel for which silencing domains are well-defined.</p

The schematics of the minimal model: On a particular nucleosome, denotes the silencing mark, is no-mark, is the acetylation mark, is the methylation mark and is the active mark.

<p>All straight arrows represent local transitions of nucleosomal marks with rates shown. The thin straight arrows are the (low) overall rate of loss of histone marks. The curved arrows are cooperative interactions, where a neighboring nucleosome, bearing a mark (corresponding to the arrow's origin) influences the local transition of the nucleosome to another mark (corresponding to the arrow's target).</p

Effect of Sir2 perturbations: Correlation length of silenced mark () state of the system along the zero-velocity-line in Fig. 4. Sir inhibition pushes the system to the bivalent-stable phase.

<p>The transition from active-silenced-bistable state (wild-type) to the bivalent-stable phase is approximately at . The correlation length is high, as expected, in the bistable region where silencing domains are established, however, the system continues to enjoy relatively strong correlation lengths in the bivalent-stable phase. The scale on the y-axis depends on the (unknown) biophysical parameters of the wild-type system, we are only reporting the trend.</p

Inhibition and overexpression of Dot1: Section of phase space for fixed Sas2 activity () and Sir2 activity () showing the effect of varying Dot1 activity () with Sir cooperative binding rate ().

<p>The self-adjusting Sir binding owing to titration effect maintains the system on the zero-velocity line (grey line). The bivalent state (magenta) is stable for high and —overexpression of Dot1 pushes the system into this phase. The wild-type bistability (silenced-active-bistable) region is the overlap of the green and red regions. Inhibition of Dot1 pushes the system to another bistable region with silenced and intermediate states stable—the overlap of the red and blue region.</p

Effect of inhibition and overexpression of Dot1 activity on Sir domains: Correlation length of silenced mark () of the system along the zero-velocity-line in Fig. 4.

<p>There are two transitions, one from <i>silenced-intermediate-bistable</i> to <i>silenced-active-bistable</i> at and another from <i>silenced-active-bistable</i> to <i>bivalent-monostable</i> at , see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003121#pcbi-1003121-g007" target="_blank">Fig. 7</a>. The correlation length is high, as expected, in the bistable region (wild-type) where silencing domains are well-established. However, the system continues to enjoys high correlation length in the bivalent phase reached by Dot1 overepxression—long-lived patches of Sir domains persist in this region. For severe Dot1 inhibition, the correlation length drops in the silenced-intermediate-bistable phase, demonstrating that in spite of this state being bistable, silencing domains are ill-established. The scale on the y-axis depends on the (unknown) biophysical parameters of the wild-type system, we are only reporting the trend.</p

Two different possible hysteresis loops for the silencing level as a function of Sir2 activity.

<p>(A) This curve represents the gene expression level as one varies the Sir2 activity and the resulting change in the silencing level. As the system enters the monostable region with high gene expression, one of the two silencing solutions disappears and only one solution remains. In some parameter regime, there is a discontinuity between the two solutions at the transition point. Unlike in conventional saddle-node bifurcation, the slope of the upper branch is not smooth at the point of bifurcation. This is a consequence of the constraint on the total abundance SIR proteins in the cell. See Dayarian and Sengupta for more details <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113516#pone.0113516-Dayarian1" target="_blank">[27]</a>. (B) In some other parameter regime, as the system enters the monostable region with high gene expression, the two solutions merge in a continuous manner and form the single monostable solution <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113516#pone.0113516-Dayarian1" target="_blank">[27]</a>.</p

Survival rate for various intermediate concentrations of anti-silencing drugs.

<p>(A) The experimental results shown for two populations, one, which had been initially exposed to a high drug concentration (blue), and the other one which had not been exposed to any drug (green). The survival rate between the two populations differs by a few orders of magnitude for lower intermediate concentrations, consistent with bistable behavior of the wild-type. In addition, the lines for the two populations ‘meet’ past a critical concentration of about 25 µM of splitomycin, indicating a transition to a monostable ‘on’ regime. (B) The result of simulations for a model of SIR silencing.</p

Schematic presentation of various scenarios for the SIR silencing system.

<p>(A) A highly cooperative binding scheme for the inhibitor drug to Sir2p can cause the activity of the later to change drastically as a result of small change in the drug concentration. (B) The state of each nucleosome is independent, but the transcriptional readout depends on the histone modification status of multiple (neighboring) nucleosomes. (C) Polymerization/Oozing/Railroad model: the feedback from the neighboring silenced regions leads to the spreading of silenced domain. (D) Silencing is a consequence of subnuclear localization of loci and the presence of a higher concentration of Sir proteins in the subnuclear region. (E) Thanks to DNA looping, the strong positive feedback can come from many nuleosomes being in close proximity.</p