Latest revision as of 22:44, 26 October 2012

Project

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 TALEs^3,4,5. 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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-[[File:projectsymbol.png|center|180px]]
+[[File:projectsymbolT.png|center|180px|link=]]
 <br>
-== Project overview ==
+== Overview ==
-<div align="justify">Originally, TAL proteins are virulence factors of the plant-pathogen Xanthomonas spp. that are injected into plant cells via a type III secretion system in order to modulate transcription1. For this purpose, their c-terminal end contains a nuclear localisation signal (NLS) and an acidic activation domain. The central part of the TAL protein contains a number of almost similar repeats that mediate specific binding to target loci in the genome (see figure 10).
+<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.
-In 2009, two groups have simultaneously pointed out that each of these repeats specifically binds to one base of the target DNA via two amino acids (aa 12 and 13), named the repeat variable diresidues (RVD) 2. Moreover, it has been shown that DNA binding of these proteins is highly modular, i.e. the number or order of bases in the target DNA can be changed by adjusting the number or order of the repeats in the TAL protein, respectively.
+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>).
-It is still unclear, how the sequence of DNA binding modules and TALE activity correlate.  The minimal condition for TALE activity is a thymine at the 5’ end of the target sequence. Further target sequence requirements that allow for one TALEN pair binding site every 35 bp (published by the Voytas lab in 20113) have recently been questioned by Reyon et al.4 In summary, it is very likely that you can find a potential TALE binding site in any sequence you want to target.
+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>.
-This, obviously, is very promising for biotechnological and clinical applications. Thus, two major classes of TAL Effectors have been created by replacing the natural acidic activation domain either by other transcription factors (TALE-TFs)5 or by – in most cases – a monomer of the non-sequence specific nuclease FokI, resulting in TAL Effector Nucleases (TALENS)6.
+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.
-A pair of TALENs can be designed to bind adjacent DNA sequences in a way that the two monomers are able to form a functional FokI dimer that produces a double strand break (DBS) within the spacer between the TAL-Effectors (see figure 13). Subsequently, the cell repairs the DBS by either non-homologous end joining (NHEJ, which results in indels at the DSB site) or homologous recombination of exogenously added genetic material.
-TALENs and TALE-TF have successfully been applied for manipulation of a series of genes in different organisms such as yeast7, tobacco3, fruitflies8,worms9, zebrafish10, rats11 and various human cell types, including human stem cells12.
-TALE technology is a huge revolution in synthetic biology not only because of higher sequence fidelity or less cytotoxicity compared to other DNA binding proteins (first of all zinc fingers). The main advantage is that they can be produced rationally to bind other a DNA sequence of choice, whereas zinc fingers with the desired binding properties need to be selected from a library of fingers. Although open source platforms have been published for zinc fingers13, this technology is therefore generally very costly, time consuming and does not guarantee binding sites for every predefined sequence.  So relatively few laboratories could actually afford using the zinc finger technology.
-Consequently, deciphering the TAL code also resulted in a huge step towards democratizing targeted DNA manipulation14. Moreover, multiple protocols and open source kits have been published by the few most influential labs in the field over the past year, which further popularized TALEs1534.
-However, we believe that the last step of democratizing precise gene targeting has not been made yet – this hypothesis 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 new method, called Golden Gate cloning- based, automatable TAL Effector (GATE) assembly, and built the genetic parts (the GATE assembly toolkit) to actually assemble custom TALEs. Furthermore, we quantified the efficiency of our GATE assembly and tested our construct 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 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.
-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 [RFC 10] standard.
+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 lay a solid foundation for super-easy site specific genome modifications by future iGEM teams.That is why we dedicated a whole subsection of our project description to a step-by-step GATE assembly protocol.
+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 whole genome, we have done the last step towards democratizing gene targeting. Although to date, the GATE assembly kit is complete for little less than a week, we get requests from research groups in Freiburg almost every day , asking for copies of the kit.
+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 are therefore thinking about giving the kit to the open source plasmid repository Addgene so that it can have a positive impact on the research world around iGEM.
-We believe that we have laid a solid foundation for super-easy site specific genome modifications by future iGEM teams.
+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/Overview|0. Introduction]]==
+== [[Team:Freiburg/Project/Intro|Introduction]]==
-<div style="color: #1C649F; font-size: 14px;font-family: Gill Sans MT">
+<div style="font-size: 12px">
 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/Overview|1. Golden Gate Standard]]==
+== [[Team:Freiburg/Project/Golden|Golden Gate Standard]]==
-<div style="color: #1C649F; font-size: 14px;font-family: Gill Sans MT;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 [RFC 10].</div>
+<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>
-==[[Team:Freiburg/Project/Vektor|2. The TAL Vector]]==
+==[[Team:Freiburg/Project/Vektor|The TAL Vector]]==
-<div style="color: #1C649F; font-size: 14px;font-family: Gill Sans MT;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>
+<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|3. GATE Assembly Kit]]==
+== [[Team:Freiburg/Project/Overview|GATE Assembly Kit]]==
-<div style="color: #1C649F; font-size: 14px;font-family: Gill Sans MT;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>
+<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|4. Using the Toolkit]]==
+==[[Team:Freiburg/Project/Tal|Using the Toolkit]]==
-<div style="color: #1C649F; font-size: 14px;font-family: Gill Sans MT;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 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|4. The future TAL projects]]==
+==[[Team:Freiburg/Project/Robot|The Future of TAL]]==
-<div style="color: #1C649F; font-size: 14px;font-family: Gill Sans MT;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>
+<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>
 <br>
-==[[Team:Freiburg/Project/Experiments|5. Experiments and Results]]==
+==[[Team:Freiburg/Project/Experiments|Experiments and Results]]==
-<div style="color: #1C649F; font-size: 14px;font-family: Gill Sans MT;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>
+<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>
-==[[Team:Freiburg/Project/References]]==
-.	Scholze, H. & Boch, J. TAL effectors are remote controls for gene activation. Current Opinion in Microbiology 14, 47–53 (2011).<br>
-.	Moscou, M. J. & Bogdanove, A. J. A Simple Cipher Governs DNA Recognition by TAL Effectors. Science 326, 1501–1501 (2009).<br>
-.	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>
-.	Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. Nature Biotechnology 30, 460–465 (2012).<br>
-.	Zhang, F. et al. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nature biotechnology 29, 149–153 (2011).<br>
-.	Miller, J. C. et al. A TALE nuclease architecture for efficient genome editing. Nature Biotechnology 29, 143–148 (2010).<br>
-.	Boch, J. et al. Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors. Science 326, 1509–1512 (2009).<br>
-.	Liu, J. et al. Efficient and Specific Modifications of the Drosophila Genome by Means of an Easy TALEN Strategy. Journal of Genetics and Genomics 39, 209–215 (2012).<br>
-.	Wood, A. J. et al. Targeted Genome Editing Across Species Using ZFNs and TALENs. Science 333, 307–307 (2011).<br>
-.	Sander, J. D. et al. Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol 29, 697–698 (2011).<br>
-.	Tesson, L. et al. Knockout rats generated by embryo microinjection of TALENs. Nature Biotechnology 29, 695–696 (2011).<br>
-.	Hockemeyer, D. et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nature Biotechnology 29, 731–734 (2011).<br>
-.	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>
-.	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>
-.	Sanjana, N. E. et al. A transcription activator-like effector toolbox for genome engineering. Nature Protocols 7, 171–192 (2012).<br>
-<!--- The Mission, Experiments --->
-===Zinc Finger Historical Timeline===
-<html>
-<!-- BEGIN TIMELINE WHITEBOX HERE -->
-<div name="zfhistory">
-<div id="timeline">
-<ul id="dates">
+==References==
-<li><a href="#" class="dateobject">1985</a></li>
-<li><a href="#" class="dateobject">1991</a></li>
-<li><a href="#" class="dateobject">1995</a></li>
-<li><a href="#" class="dateobject">1996</a></li>
-<li><a href="#" class="dateobject">2000</a></li>
-<li><a href="#" class="dateobject">2004</a></li>
-<li><a href="#" class="dateobject">2008</a></li>
-<li><a href="#" class="dateobject">2009</a></li>
-<li><a href="#" class="dateobject">2011</a></li>
-<li><a href="#" class="dateobject iGEM11">iGEM '11</a></li>
-</ul>
-<ul id="issues">
+.	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>
+.	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>
+.	Sanjana, N. E. et al. A transcription activator-like effector toolbox for genome engineering. ''Nature Protocols'' 7, 171–192 (2012).<br>
+.	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>
+.	Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. ''Nature Biotechnology'' 30, 460–465 (2012).<br>
+<br><br>
+[[#top|Back to top]]
-<li id="#1985">
-<img src="https://static.igem.org/mediawiki/2011/c/cb/HARV1985Miller_etal.png" width="256" height="256" />
-<div class="issuedate">Discovery of the zinc finger protein</div>
+<!--- The Mission, Experiments --->
-<p>Jonathon Miller, A. D. McLachlan, and Sir Aaron Klug first identify the repeated binding motif in Transcription Factor IIIA and are the first to use the term ‘zinc finger.'</p>
-</li>
-</ul>
-<div id="grad_left"></div>
-<div id="grad_right"></div>
-<a href="#" id="next">+</a>
-<a href="#" id="prev">-</a>
-</div>
-</div>
-<!-- END TIMELINE WHITEBOX HERE -->
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