Team:Hong Kong HKUST/riboregulator

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<p><b><u>Background</b></u>
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<p class="first_letter_enhanced">Regulatory RNAs are RNAs that regulate biological processes on genetic and metabolic levels, and their importance has been established through the discoveries including those of RNA interference (RNAi) and long noncoding RNAs (lncRNA). The elucidation of their mechanism has enabled their reverse engineering, transforming them into versatile tools in synthetic biology.
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<p class="first_letter_enhanced">Regulatory RNAs are RNAs that regulate biological processes on genetic and metabolic levels, and their importance has been established through the discoveries including those of RNA interference (RNAi) and long noncoding RNAs (lncRNA). The elucidation of their mechanism has enabled their reverse engineering, transforming them into versatile tools in synthetic biology.  
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Riboregulators belong to a class of regulatory RNAs that controls translation by pairs of cis-repressing (CR) and trans-activating (TA) RNAs. They have received attention from at least 7 teams during the early years of iGEM. For example, Farren Isaacs in 2005, iGEM 2006 UC Berkeley team and iGEM 2007 Caltech team contributed many CR and TA devices to the Registry. Though there are more than > 100 riboregulator BioBrick records, comprehensive characterization information is missing. This hinders the iGEM community to compare and contrast different riboregulators pairs and evaluate their performances. For example, if we want to use the CR and TA devices that Berkeley 2006 made, we would not know which one to use and whether the device would work, because documentations then were not put down in the Registry or wiki page and were therefore no longer accessible.
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Riboregulators belong to a class of regulatory RNAs that controls translation by pairing of cis-repressing (CR) and trans-activating (TA) RNAs. They have received attention from at least 7 teams during the early years of iGEM. For example, Farren Isaacs in 2005, iGEM 2006 UC Berkeley team and iGEM 2007 Caltech team contributed many CR and TA devices to the Registry. Though there are more than > 100 riboregulator BioBrick records, comprehensive characterization information is missing. This hinders the iGEM community to compare and contrast different riboregulator pairs and evaluate their performance. For example, if we want to use the CR and TA devices that Berkeley 2006 made, we would not know which one to use and whether the device would work, because documentations were not put down in the Registry or wiki page and were therefore no longer accessible.
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Given this situation, iGEM 2014 HKUST team decided to embark on "Project Riboregulator", and we aim to:
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In light of this situation, iGEM 2014 HKUST team decided to embark on "Project Riboregulator", and we aim to:  
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Update the choice of “Categories” when documenting “hard information” of a BioBrick, and; <br>Write up a guideline for other teams to tag their new regulatory RNAs so they will show up on the catalog page under the relevant sub-category.</li>
Update the choice of “Categories” when documenting “hard information” of a BioBrick, and; <br>Write up a guideline for other teams to tag their new regulatory RNAs so they will show up on the catalog page under the relevant sub-category.</li>
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Given its size, "Project Riboregulator" is expected to take more than just a summer to complete. Thus at the moment of wiki freeze, information available here is bound to be limited. However, the project will continue on well after the Giant Jamboree. Information will be continuously and regularly updated, and because of its nature, <u>"Project Riboregulator" is not part of our work for competing awards of any kind or in any year</u>, but rather, a tribute to the Part Registry and iGEM community alone.</p>
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Artificial cis-repressing and trans-activating riboregulator system was introduced to the iGEM community by Isaacs in 2005.
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Artificial cis-repressing and trans-activating riboregulator system was introduced to the iGEM community by Isaacs in 2005. The riboregulator system as a whole acts to regulate translation at the RNA level. One component of the system, crRNA, which contains a cis-repressing sequence at the 5' of the RBS, the RBS, and the gene of interest. <br><br>The cis-repressing sequence can form a loop form complementary base pairs with the RBS to prevent the recognition of RBS by ribosomes. The translation crRNA is also commonly described as a &quot;lock&quot; because it &quot;locks&quot; the RBS and prevent translation. The &quot;key&quot; to this system is the taRNA. taRNA can interact  
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The riboregulator system as a whole acts to regulate translation at the RNA level. One component of the system ,crRNA, which  
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(in <i>trans</i>) with the cis-repressing sequence to unlock the RBS and therefore activate translation (Figure 1.).
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contains a cis-repressing sequence at the 5&#39; of the RBS, RBS, and gene of interest. <br><br>The cis-repressing sequence can form a loop form  
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complementary base pairs with the RBS to prevent the recognition of RBS by ribosomes. The translation crRNA is also commonly  
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described as a &quot;lock&quot; because it &quot;locks&quot; the RBS and prevent translation. The &quot;key&quot; to this system is the taRNA. taRNA can interact  
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(in trans) with the cis-repressing sequence to unlock the RBS and therefore activate translation (Figure 1.).
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Latest revision as of 02:32, 18 October 2014



Project Riboregulator Abstract



Regulatory RNAs are RNAs that regulate biological processes on genetic and metabolic levels, and their importance has been established through the discoveries including those of RNA interference (RNAi) and long noncoding RNAs (lncRNA). The elucidation of their mechanism has enabled their reverse engineering, transforming them into versatile tools in synthetic biology.

Riboregulators belong to a class of regulatory RNAs that controls translation by pairing of cis-repressing (CR) and trans-activating (TA) RNAs. They have received attention from at least 7 teams during the early years of iGEM. For example, Farren Isaacs in 2005, iGEM 2006 UC Berkeley team and iGEM 2007 Caltech team contributed many CR and TA devices to the Registry. Though there are more than > 100 riboregulator BioBrick records, comprehensive characterization information is missing. This hinders the iGEM community to compare and contrast different riboregulator pairs and evaluate their performance. For example, if we want to use the CR and TA devices that Berkeley 2006 made, we would not know which one to use and whether the device would work, because documentations were not put down in the Registry or wiki page and were therefore no longer accessible.

In light of this situation, iGEM 2014 HKUST team decided to embark on "Project Riboregulator", and we aim to:

  1. Provide Characterization information on riboregulator BioBricks so that teams and labs will be confident in using these devices.
  2. Summarize available information of existing riboregulators into a Feature Page and promote their uses.
  3. Create a Catalog Page for all identifiable regulatory RNAs;
    Update the choice of “Categories” when documenting “hard information” of a BioBrick, and;
    Write up a guideline for other teams to tag their new regulatory RNAs so they will show up on the catalog page under the relevant sub-category.


Given its size, "Project Riboregulator" is expected to take more than just a summer to complete. Thus at the moment of wiki freeze, information available here is bound to be limited. However, the project will continue on well after the Giant Jamboree. Information will be continuously and regularly updated, and because of its nature, "Project Riboregulator" is not part of our work for competing awards of any kind or in any year, but rather, a tribute to the Part Registry and iGEM community alone.

CR and TA riboregulator system

Figure 1. Riboregulator Overview Diagram



Artificial cis-repressing and trans-activating riboregulator system was introduced to the iGEM community by Isaacs in 2005. The riboregulator system as a whole acts to regulate translation at the RNA level. One component of the system, crRNA, which contains a cis-repressing sequence at the 5' of the RBS, the RBS, and the gene of interest.

The cis-repressing sequence can form a loop form complementary base pairs with the RBS to prevent the recognition of RBS by ribosomes. The translation crRNA is also commonly described as a "lock" because it "locks" the RBS and prevent translation. The "key" to this system is the taRNA. taRNA can interact (in trans) with the cis-repressing sequence to unlock the RBS and therefore activate translation (Figure 1.).

The benefits of this system, as described in Isaacs et al.'s paper, are leakage minimization, fast response time, tunability, independent regulation of multiple genes etc.

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