Team:Freiburg/Project/crrna

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CrispR

Targeting

crRNA design tool

Enter Target Sequence

Choose Program

Which strand should be targeted?

non coding strand coding strand

This tool helps you to design a crRNA-insert for dCAS RNA plasmid: "uniCAS RNaimer" ( BBa_K1150034 ).
Using this tool you do not have to do this on your own. Just insert the desired target sequence and you get all different oligo possibilities and their positions. The oligos contain overhangs which fit to this plasmid's BbsI-overhangs and are ready to use.
The two different target possibilities are the coding and non-coding strand, depending on the desired target sequence.

a) For repression of gene transcription by targeting the coding sequence it´s crucial to target the non template (= coding) DNA strand.
Therefore the oligos must be designed as follows:

  1. Search at your desired target sequence for a CCN (reverse complement of the PAM sequence) at the coding strand.
  2. Extract the following (3') 30 nucleotides.
  3. Extract the reverse complement.
  4. Add AAAC at the 5' end and GT at the 3' end. This will be your fist oligo.
  5. Take the sequence from step 2 and add TAAAAC at the 5' end. This will be your second oligo.

b) For repression of gene transcription by targeting the non-coding sequence it´s crucial to target the template DNA strand.
Therefore the oligos must be designed as follows:

  1. Search at your desired target sequence for a NGG (the PAM sequence) at the non-coding strand.
  2. Extract the 30 nucleotides before (5') the PAM sequence.
  3. Extract the reverse complement.
  4. Add TAAAAC at the 5' end. This will be your second oligo.
  5. Take the sequence from step 2 and add AAAC at the 5' end and GT at the 3' end. This will be your first oligo.

(the oligos are designed analog to: Cong L, Ran FA, Cox D, Lin S, Barretto R,Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex (2013 Jan 3). Genome Engineering using CRISPR/Cas Systems. Science. DOI: 10.1126/science.1231143 )

Multiple targeting

Introduction

One of the biggest advantages of the CRISPR-Cas system compared to other transcription activators (e.g. Zn fingers, TALEs) is that only one protein is required for targeting several DNA sites: For a new target there has to be just another crRNA. We designed an RNA plasmid containing the tracrRNA, where the crRNA can be introduced easily by digesting with BbsI and inserting two previous annealed oligos. Two of these RNA plasmids (with different crRNAs) can be fused using the iGEM biobrick system. This way it is possible to get two or more crRNAs on one plasmid.

Fig. 1: RNA plasmid (BBa_K1150034)
Our RNA plasmid contains the tracrRNA and a site where the desired crRNA can be inserted. Both RNAs are driven by different human RNA polymerase III promoters. Assembly of multiple crRNAs can be easily done by digestion with enzymes of prefix and suffix and combining these parts according to iGEM standard assembly.

As it is important that the RNAs are not being marked for protein expression the RNA polymerase III is required for transcription. RNA polymerase III mainly synthesize small non-coding RNAs (e.g. tRNAs or rRNAs) whereas the commonly used polymerase II is responsible for transcription of mainly mRNAs [1,2] . We chose the human U6- and H1-promoter to drive the RNAs as they are exclusively recognized by polymerase III [2] .
With this RNA plasmid and another plasmid containing the Cas9-effector fusion protein it is possible to target several DNA sites at once by transfecting only two plasmids. This could mean the simultaneous regulation of different genes or a stricter controlling of one gen by bringing more effector domains to this gene.

Results

Activation of different genes

In order to test the simultaneously activation of several genes we assembled 3 plasmids containing different fluorescent proteins. Every protein is fused to a different signal for intracellular localization. Thus, we were able to distinguish better between the different fluorescent proteins, because there will be no interference of the emitted light.
Fig. 2: Plasmids encoding the fluorescent proteins
Each fluorescent protein is driven by a CMV minimal promoter, that can be switched on by binding of TetR-VP16 to the TetO sequence. Between TetO and CMVmin there is a target site for Cas9 binding, a different on each plasmid. The fluorescent were fused to signal sequences for subcellular localization, so mCherry will be in the nucleus, GFP in the Golgi apparatus and BFP at the membrane. T: terminator.
Fig. 3: Microscopy pictures of fluorescent proteins expressed in HeLa cells
Fluorescence pictures were taken of fixed HeLa cells transfected with Golgi-GFP and mCherry-NLS. Channels of GFP and mCherry were merged. All pictures have the same scale.
HEK cells were transfected with different combinations of these plasmids and Cas9-VP16 or TetR-VP16 (4 fold amount of effector DNA) After 2 days of expression the cells were analysed by flow cytometry. This way the fluorescence intensity of every cell could be determined (Fig. 4).
Fig. 4: Activation of expression of different fluorescent proteins
The fluorescence intensity of each cell was analysed by flow cytometry. The mean fluorescence intensity was calculated with the intensities of the cells which were brighter than untransfected cells. The bars represent the mean with standard deviation of these mean fluorescences of three different cell populations.
blue: only the plasmid containing the fluorescent proteins with minimal promoter were transfected; green: the minimal promoter driven fluorescent proteins were cotransfected with TetR-VP16; yellow: the minimal promoter driven fluorescent proteins were cotransfected with Cas9-VP16.
Unfortunately Cas9-VP16 was not able to increase the intensity of any fluorescent protein at all, even when transfected exclucively, whereas TetR-VP16 strongly activates the expression of fluorescent proteins. This may be due to the higher number of binding sites for TetR (16 in comparison with 1 for Cas9).

Stricter gen regulation by targeting different loci simultaneously

As we wanted to improve the efficiency of our gene regulation tool kit, we tried to target several loci upstream of the reporter gene's promoter at once. Thus, we ordered crRNAs that are complementary to sequences on the SEAP reporter plasmid with different distances to the promoter.

TABELLE: Targets on SEAP reporter plasmid

HEK cells were transfected with the SEAP reporter plasmid, Cas9-VP16 (iGEM standard), one or two RNA plasmids and a plasmid coding for Renilla luciferase for a internal standard (to eliminate variabilities of different cell numbers or expression levels). The total amount of RNA plasmids was always the same, so it can be exclude that an increase of SEAP expression is due to more available crRNA. When combining the Targets EMX1 and T2 there could be observed a higher SEAP activation than the sum of the single targets (Fig. 5).
Fig. 5: Effects of different target numbers
SEAP activity was divided through luminescence intensity of Renilla luciferase. The bars represent the mean of biological triplicates with standard deviation. All samples were transfected with CMV::Cas9-VP16 in pSB1C3 and with no (left), one (middle) or two RNA plasmids (right).

multiple RNA plasmid

Summary

So it is not possible to make a statement about the ability of activating multiple genes.

References

[1] Dieci G,et al. (1987). The expanding RNA polymerase III transcriptome.Trends Genet. 2007 Dec;23(12):614-22.
[2] Myslinski E, et al. (1987). An unusually compact external promoter for RNA polymerase III transcription of the human H1RNA gene.Nucleic Acids Res. 2001 Jun 15;29(12):2502-9.

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