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Team:UPO-Sevilla/Project/Epigenetic Flip Flop/Strategy
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<h1>Strategy</h1> | <h1>Strategy</h1> | ||
| - | <p>In order to create a <strong>bistable</strong> in <em>S. pombe</em> based on epigenetic regulation, we have mimic | + | <p>In order to create a <strong>bistable</strong> in <em>S. pombe</em> based on epigenetic regulation, we have mimic the architecture of natural genes, that are flanked by regulatory sequences, and we have designed a gene expression reporter system (promoter:GFP) which is flanked upstream and downstream by binding sites for engineering silencing proteins (SP). This reporter system will be <strong>integrated in <em>S. pombe</em> genome</strong>. The silencing proteins consist of fusion proteins or kymeras, composed by tetracycline repressor (tetR) and one silencing protein, or a domain of it. TetR will cause binding to tetR operator sites (tetO) and silencing proteins will be responsible for the recruitment of silencing proteins that will compact and inactivate the promoter. |
We expect that the <strong>recruitment and spreading of silencing proteins</strong> at flanking region of promoters will have a drastic effect on gene expression, due to the interference of promoter activity. When silencing proteins are expressed, compaction of DNA sequence will lead to gene repression, resulting in the OFF state. The ON state will be attained by repressing the expression of silencing proteins that will result in decompaction of nucleated structure, just like a <strong>zip</strong>. The result of this experimental design will be an epigenetic bistable.</p> | We expect that the <strong>recruitment and spreading of silencing proteins</strong> at flanking region of promoters will have a drastic effect on gene expression, due to the interference of promoter activity. When silencing proteins are expressed, compaction of DNA sequence will lead to gene repression, resulting in the OFF state. The ON state will be attained by repressing the expression of silencing proteins that will result in decompaction of nucleated structure, just like a <strong>zip</strong>. The result of this experimental design will be an epigenetic bistable.</p> | ||
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| - | <p><strong>ON state:</strong> To reach this state it is necessary the addition of | + | <p><strong>ON state:</strong> To reach this state it is necessary the addition of three different chemicals to the cell culture: <strong>thiamine, doxicycline and uracil</strong>. Thiamine is used to repress the promoter of silencing genes. Thiamine regulates expression of Pnmt1 promoter (<em>no message in thiamine promoter</em>, 41X). Doxicycline functions as a decompaction compound, because of it ability to dissolve the structure nucleated around operator sites of reporter module, allowing the expression of GFP. Uracil is the activator of inducible urg1 promoter, that regulates the expression of marker protein GFP. Addition of this thee chemical leads to <strong>inhibition of silencing proteins expression</strong>, <strong>decompaction</strong> of nucleated structure and finally <strong>synthesis of the marker protein</strong>, in a short interval of time, less than half an hour, due to chemicals and promoter activities (<a href="http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0061(199807)14:10<943::AID-YEA292>3.0.CO;2-Y/pdf" target="_blank" title="Bähler et al, 1998">Bähler et al, 1998</a>; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001428" target="_blank" title="Watt et al, 2008">Watt et al, 2008</a>).</p> |
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| - | <img width=" | + | <img width="700px" src="https://static.igem.org/mediawiki/2011/d/d8/UPOSevillaEpigeneticFlipFlop.png" alt="Epigenetic Switch" /> |
| - | " alt="Epigenetic Switch" /> | + | <p><strong>Figure 1.</strong> Representation of ON and OFF states in the epigenetic switch.</p> |
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| - | <p><strong>OFF state:</strong> To reach this state it is necessary the <strong> | + | <p><strong>OFF state:</strong> To reach this state it is necessary the <strong>drug wash out</strong> (doxicycline, thiamine and uracil). For that reason chemical must be removed from the medium by sequential washing in cell culture. After washing out these compounds it will begin the <strong>expression of silencing genes</strong> and the <strong>repression of GFP expression</strong>. Synthesized proteins get back to the nucleus and stochastically find tetR operator sites and form a nucleation point. Spreading of SP produce a total repression of reporter module. Due to promoter characteristics, around 10-12 hours are needed to reach this state (<a href="http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0061(199807)14:10<943::AID-YEA292>3.0.CO;2-Y/pdf" target="_blank" title="Bähler et al, 1998">Bähler et al, 1998</a>; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001428" target="_blank" title="Watt et al, 2008">Watt et al, 2008</a>).</p> |
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Latest revision as of 23:32, 28 October 2011
Strategy
In order to create a bistable in S. pombe based on epigenetic regulation, we have mimic the architecture of natural genes, that are flanked by regulatory sequences, and we have designed a gene expression reporter system (promoter:GFP) which is flanked upstream and downstream by binding sites for engineering silencing proteins (SP). This reporter system will be integrated in S. pombe genome. The silencing proteins consist of fusion proteins or kymeras, composed by tetracycline repressor (tetR) and one silencing protein, or a domain of it. TetR will cause binding to tetR operator sites (tetO) and silencing proteins will be responsible for the recruitment of silencing proteins that will compact and inactivate the promoter. We expect that the recruitment and spreading of silencing proteins at flanking region of promoters will have a drastic effect on gene expression, due to the interference of promoter activity. When silencing proteins are expressed, compaction of DNA sequence will lead to gene repression, resulting in the OFF state. The ON state will be attained by repressing the expression of silencing proteins that will result in decompaction of nucleated structure, just like a zip. The result of this experimental design will be an epigenetic bistable.
ON state: To reach this state it is necessary the addition of three different chemicals to the cell culture: thiamine, doxicycline and uracil. Thiamine is used to repress the promoter of silencing genes. Thiamine regulates expression of Pnmt1 promoter (no message in thiamine promoter, 41X). Doxicycline functions as a decompaction compound, because of it ability to dissolve the structure nucleated around operator sites of reporter module, allowing the expression of GFP. Uracil is the activator of inducible urg1 promoter, that regulates the expression of marker protein GFP. Addition of this thee chemical leads to inhibition of silencing proteins expression, decompaction of nucleated structure and finally synthesis of the marker protein, in a short interval of time, less than half an hour, due to chemicals and promoter activities (Bähler et al, 1998; Watt et al, 2008).
Figure 1. Representation of ON and OFF states in the epigenetic switch.
OFF state: To reach this state it is necessary the drug wash out (doxicycline, thiamine and uracil). For that reason chemical must be removed from the medium by sequential washing in cell culture. After washing out these compounds it will begin the expression of silencing genes and the repression of GFP expression. Synthesized proteins get back to the nucleus and stochastically find tetR operator sites and form a nucleation point. Spreading of SP produce a total repression of reporter module. Due to promoter characteristics, around 10-12 hours are needed to reach this state (Bähler et al, 1998; Watt et al, 2008).
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