Team:Freiburg/Project

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= Project [[Image:Freigemsmallbarbetter.png|250px]] =
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= Project =
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<br>
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[[File:projectsymbolT.png|center|180px|link=]]
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<br>
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== Overview ==
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<div align="justify">TALE technology currently revolutionizes synthetic biology, not only because of higher sequence fidelity or less cytotoxicity compared to other DNA binding proteins (e.g. zinc fingers). The main advantage is that they can be produced rationally to bind a DNA sequence of choice, whereas zinc fingers with the desired binding properties need to be selected from a library of fingers.
 +
That is why TAL technology is generally much less costly, time consuming and does guarantee binding sites for every predefined sequence (although open source platforms have also been published for zinc fingers<sup>1</sup>).
 +
Consequently, deciphering the TAL code also resulted in an enormous step towards democratizing targeted DNA manipulation<sup>2</sup>. Moreover, multiple protocols and open source kits have been published by the most influential labs in the field over the past year, which further popularized TALEs<sup>3,4,5</sup>.
 +
However, we believe that the last step of democratizing precise gene targeting has not been made yet – this is corroborated by the fact that the biotech companies Cellectis bioresearch and Invitrogen have launched quite expensive new TAL effector product lines during the last few months.
 +
In order to bring TAL technology within reach for everyone, in particular for future iGEM students, we identified the two main bottlenecks of conventional TALE assembly, namely that it is very time consuming and requires substantial training in molecular biology.
 +
In the next steps, we invented a method, that we refer to as Golden Gate cloning- based, automatable TAL Effector (GATE) assembly, and built the genetic parts (the GATE assembly toolkit) to actually assemble custom TALEs at record speed. Furthermore, we quantified the efficiency of our GATE assembly and tested our constructs in a Human Embryonic Kidney (HEK) cell line. We are proud to say that with our GATE assembly kit, future iGEM students will be able to easily assemble custom 12.5 repeat TALEs faster than anyone else in the world.
 +
While working on the GATE assembly kit, we learned a lot about Golden Gate cloning and came up with a strategy to introduce this powerful cloning technology to the iGEM registry as the Golden Gate standard without compromising existing standards.
 +
Our major goal was to empower future iGEM students to use and further develop TALE technology. That is why we dedicated a whole subsection of our project description to a step-by-step GATE assembly protocol (including a video tutorial).
 +
We believe that by enabling virtually anyone to specifically manipulate any locus even in the context of a complex genome, we have done the last step towards democratizing gene targeting. Although to date, the GATE assembly kit is complete for only a few weeks, we regularly receive requests from research groups all over Europe, asking for copies of the kit. Moreover, we got approached by the open source plasmid repository [http://www.addgene.org/ Addgene] that wants to distribute our toolkit. We are currently preparing to send our kit to them so the GATE kit will be available to everyone soon! That way, we have a significant impact also on the research world around iGEM.
 +
 
 +
We believe that we have laid a solid foundation for super-easy site specific genome modifications for future iGEM teams.
 +
<br><br>
 +
 
 +
== [[Team:Freiburg/Project/Intro|Introduction]]==
 +
<div style="font-size: 12px">
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You don't know what TAL effectors actually are? We reviewed the recent literature for you, to give you a quick overview of this exciting new field of research.</div>
 +
<br>
 +
== [[Team:Freiburg/Project/Golden|Golden Gate Standard]]==
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 +
<div style=" font-size: 12px;align=justify"> Assembling multiple gene constructs in frame without leaving scars is not possible with existing iGEM standards. We therefore introduce the new Golden-Gate Standard that is fully compatible with RFC10.</div>
 +
<br>
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==[[Team:Freiburg/Project/Vektor|The TAL Vector]]==
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== Overall project ==
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<div style=" font-size: 12px;align=justify">Targeting a sequence and not doing something to it, is like throwing mechanics at your car. Your car will not get any better only the mechanics will get mad. Because we know this, we bring the tools you need to actually work with DNA.To make it even more easy these tools are deliverd already inside the final TAL backbone, just add the sequence and you're ready.</div>
 +
<br>
 +
== [[Team:Freiburg/Project/Overview|GATE Assembly Kit]]==
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Since April 2012, we are working in the field of so called TAL effectors in our lab. TAL effectors are molecular machines that are fused to DNA binding proteins in order to restrict their acticvity to specific loci in a genome. In particular, we develop a strategy to cheaply create novel TAL effectors in an extremely short period of time. This new method will enable us to test numerous novel effectors in human cells and to assess their therapeutic potential for genetic diseases, epigenetic alterations and cancer.
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<div style=" font-size: 12px;align=justify"> We have invented a super-fast, super-easy and super-cheap Method for custom TAL effector construction. Learn about the theory behind the TAL effector toolkit, how we created it and why we choose this design.</div>
 +
<br>
 +
==[[Team:Freiburg/Project/Tal|Using the Toolkit]]==
 +
<div style=" font-size: 12px; align=justify">Our overall goal is to empower future iGEM teams to use the most exciting new technology synthetic biology has to offer. We therefore not only invented the GATE assembly platform but wrote a step by step manual for super-easy custom TALE construction
 +
</div>
 +
<br>
 +
==[[Team:Freiburg/Project/Robot|The Future of TAL]]==
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<html>
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<div style=" font-size: 12px;align=justify">Until now, almost three years after deciphering the TALE code, only two types of TAL Effectors have been developed: TALENs and TAL-TFs. We herein propose additional classes of TAL effectors.</div>
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<iframe width="560" height="315" style="margin-left:100px; margin-top:20px ;margin-bottom:0;"src="http://player.vimeo.com/video/49902809" width="400" height="300" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>
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<br>
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</html>
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==[[Team:Freiburg/Project/Experiments|Experiments and Results]]==
 +
<div style=" font-size: 12px; align=justify">We not only rigorously tested if our in vitro TALE gene assembly method works but also if our TALE constructs actually work in a human cell line. Check out test design and results.</div>
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== Promote Synthetic Biology ==
 
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For us working on iGEM is not only staying in a laboratory and trying to create the best bio brick ever it’s also a great opportunity to promote synthetic biology.
 
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In that context we teach students the basic ideas of SynBio in order to direct and enhance their motivation to study life science.
 
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Within the visit we go into dialog with the students to clear things up concerning the ethnical dangers and economic chances of this big arising research area.
 
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The presentation of our project as well as the introduction to iGem in general is our third aim for the school visits.
 
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==References==
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So maybe we met some future iGem winners.
 
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1. Maeder, M. L. et al. Rapid ‘Open-Source’ Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification. ''Molecular Cell'' 31, 294–301 (2008).<br>
 +
2. Clark, K. J., Voytas, D. F. & Ekker, S. C. A TALE of two nucleases: gene targeting for the masses? ''Zebrafish'' 8, 147–149 (2011).<br>
 +
3. Sanjana, N. E. et al. A transcription activator-like effector toolbox for genome engineering. ''Nature Protocols'' 7, 171–192 (2012).<br>
 +
4. Cermak, T. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. ''Nucleic Acids Res'' 39, e82 (2011).<br>
 +
5. Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. ''Nature Biotechnology'' 30, 460–465 (2012).<br>
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Lastly we want to thank all classes, those we visited and those we are going to visit, because it’s inspiring when next generation researches meet enthusiastic students.
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<br><br>
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Latest revision as of 22:44, 26 October 2012





Project


ProjectsymbolT.png


Overview

TALE technology currently revolutionizes synthetic biology, not only because of higher sequence fidelity or less cytotoxicity compared to other DNA binding proteins (e.g. zinc fingers). The main advantage is that they can be produced rationally to bind a DNA sequence of choice, whereas zinc fingers with the desired binding properties need to be selected from a library of fingers.

That is why TAL technology is generally much less costly, time consuming and does guarantee binding sites for every predefined sequence (although open source platforms have also been published for zinc fingers1). Consequently, deciphering the TAL code also resulted in an enormous step towards democratizing targeted DNA manipulation2. Moreover, multiple protocols and open source kits have been published by the most influential labs in the field over the past year, which further popularized TALEs3,4,5. However, we believe that the last step of democratizing precise gene targeting has not been made yet – this is corroborated by the fact that the biotech companies Cellectis bioresearch and Invitrogen have launched quite expensive new TAL effector product lines during the last few months. In order to bring TAL technology within reach for everyone, in particular for future iGEM students, we identified the two main bottlenecks of conventional TALE assembly, namely that it is very time consuming and requires substantial training in molecular biology. In the next steps, we invented a method, that we refer to as Golden Gate cloning- based, automatable TAL Effector (GATE) assembly, and built the genetic parts (the GATE assembly toolkit) to actually assemble custom TALEs at record speed. Furthermore, we quantified the efficiency of our GATE assembly and tested our constructs in a Human Embryonic Kidney (HEK) cell line. We are proud to say that with our GATE assembly kit, future iGEM students will be able to easily assemble custom 12.5 repeat TALEs faster than anyone else in the world. While working on the GATE assembly kit, we learned a lot about Golden Gate cloning and came up with a strategy to introduce this powerful cloning technology to the iGEM registry as the Golden Gate standard without compromising existing standards. Our major goal was to empower future iGEM students to use and further develop TALE technology. That is why we dedicated a whole subsection of our project description to a step-by-step GATE assembly protocol (including a video tutorial). We believe that by enabling virtually anyone to specifically manipulate any locus even in the context of a complex genome, we have done the last step towards democratizing gene targeting. Although to date, the GATE assembly kit is complete for only a few weeks, we regularly receive requests from research groups all over Europe, asking for copies of the kit. Moreover, we got approached by the open source plasmid repository [http://www.addgene.org/ Addgene] that wants to distribute our toolkit. We are currently preparing to send our kit to them so the GATE kit will be available to everyone soon! That way, we have a significant impact also on the research world around iGEM.

We believe that we have laid a solid foundation for super-easy site specific genome modifications for future iGEM teams.

Introduction

You don't know what TAL effectors actually are? We reviewed the recent literature for you, to give you a quick overview of this exciting new field of research.


Golden Gate Standard

Assembling multiple gene constructs in frame without leaving scars is not possible with existing iGEM standards. We therefore introduce the new Golden-Gate Standard that is fully compatible with RFC10.


The TAL Vector

Targeting a sequence and not doing something to it, is like throwing mechanics at your car. Your car will not get any better only the mechanics will get mad. Because we know this, we bring the tools you need to actually work with DNA.To make it even more easy these tools are deliverd already inside the final TAL backbone, just add the sequence and you're ready.


GATE Assembly Kit

We have invented a super-fast, super-easy and super-cheap Method for custom TAL effector construction. Learn about the theory behind the TAL effector toolkit, how we created it and why we choose this design.


Using the Toolkit

Our overall goal is to empower future iGEM teams to use the most exciting new technology synthetic biology has to offer. We therefore not only invented the GATE assembly platform but wrote a step by step manual for super-easy custom TALE construction


The Future of TAL

Until now, almost three years after deciphering the TALE code, only two types of TAL Effectors have been developed: TALENs and TAL-TFs. We herein propose additional classes of TAL effectors.


Experiments and Results

We not only rigorously tested if our in vitro TALE gene assembly method works but also if our TALE constructs actually work in a human cell line. Check out test design and results.




References

1. Maeder, M. L. et al. Rapid ‘Open-Source’ Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification. Molecular Cell 31, 294–301 (2008).
2. Clark, K. J., Voytas, D. F. & Ekker, S. C. A TALE of two nucleases: gene targeting for the masses? Zebrafish 8, 147–149 (2011).
3. Sanjana, N. E. et al. A transcription activator-like effector toolbox for genome engineering. Nature Protocols 7, 171–192 (2012).
4. Cermak, T. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39, e82 (2011).
5. Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. Nature Biotechnology 30, 460–465 (2012).



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