Latest revision as of 13:05, 2 October 2024

fgRNA processing casette

Incorporating Cas12a into our Cas staple design allows us to utilize the ability of processing its own pre-crRNA by recognizing the hairpin structures of the scaffolds. The cutting of the pre-crRNA into crRNA happens upstream of the scaffold, suggesting the Cas12a to be able to process a CRISPR-array of fgRNA, while maintaining functionality.

While synthetic biology has in the past focused on engineering the genomic sequence of organisms, the 3D spatial organization of DNA is well-known to be an important layer of information encoding in particular in eukaryotes, playing a crucial role in gene regulation and hence cell fate, disease development, evolution, and more. However, tools to precisely manipulate and control the genomic spatial architecture are limited, hampering the exploration of 3D genome engineering in synthetic biology. We - the iGEM Team Heidelberg 2024 - have developed PICasSO, a powerful molecular toolbox for rationally engineering genome 3D architectures in living cells, based on various DNA-binding proteins.

The PICasSO part collection offers a comprehensive, modular platform for precise manipulation and re-programming of DNA-DNA interactions using engineered "protein staples" in living cells. This enables researchers to recreate naturally occurring alterations of 3D genomic interactions, such as enhancer hijacking in cancer, or to design entirely new spatial architectures for artificial gene regulation and cell function control. Specifically, the fusion of two DNA binding proteins enables to artificially bring otherwise distant genomic loci into spatial proximity. To unlock the system's full potential, we introduce versatile chimeric CRISPR/Cas complexes, connected either at the protein or - in the case of CRISPR/Cas-based DNA binding moieties - the guide RNA level. These complexes are referred to as protein- or Cas staples, respectively. Beyond its versatility with regard to the staple constructs themselves, PICasSO includes robust assay systems to support the engineering, optimization, and testing of new staples in vitro and in vivo. Notably, the PICasSO toolbox was developed in a design-build-test-learn engineering cycle closely intertwining wet lab experiments and computational modeling and iterated several times, yielding a collection of well-functioning and -characterized parts.

At its heart, the PICasSO part collection consists of three categories.
(i) Our DNA-binding proteins include our finalized Cas staple experimentally validated using an artificial "enhancer hijacking" system as well as "half staples" that can be combined by scientists to compose entirely new Cas staples in the future. We also include our Simple staples comprised of particularly small, simple and robust DNA binding domains well-known to the synthetic biology community, which serve as controls for successful stapling and can be further engineered to create alternative, simpler, and more compact staples.
(ii) As functional elements, we list additional parts that enhance and expand the functionality of our Cas and Basic staples. These consist of staples dependent on cleavable peptide linkers targeted by cancer-specific proteases or inteins that allow condition-specific, dynamic stapling in vivo. We also include several engineered parts that enable the efficient delivery of PICasSO's constructs into target cells, including mammalian cells, with our new interkingdom conjugation system.
(iii) As the final category of our collection, we provide parts that underlie our custom readout systems. These include components of our established FRET-based proximity assay system, enabling users to confirm accurate stapling. Additionally, we offer a complementary, application-oriented testing system based on a luciferase reporter, which allows for straightforward experimental assessment of functional enhancer hijacking events in mammalian cells.

The following table gives a comprehensive overview of all parts in our PICasSO toolbox. The highlighted parts showed exceptional performance as described on our iGEM wiki and can serve as a reference. The other parts in the collection are versatile building blocks designed to provide future iGEMers with the flexibility to engineer their own custom Cas staples, enabling further optimization and innovation in the new field of 3D genome engineering.

Our part collection includes:

DNA-Binding Proteins: Modular building blocks for engineering of custom staples to mediate defined DNA-DNA interactions in vivo
BBa_K5237000	Fusion Guide RNA Entry Vector MbCas12a-SpCas9	Entry vector for simple fgRNA cloning via SapI
BBa_K5237001	Staple Subunit: dMbCas12a-Nucleoplasmin NLS	Staple subunit that can be combined with crRNA or fgRNA and dSpCas9 to form a functional staple
BBa_K5237002	Staple Subunit: SV40 NLS-dSpCas9-SV40 NLS	Staple subunit that can be combined with a sgRNA or fgRNA and dMbCas12a to form a functional staple
BBa_K5237003	Cas Staple: SV40 NLS-dMbCas12a-dSpCas9-Nucleoplasmin NLS	Functional Cas staple that can be combined with sgRNA and crRNA or fgRNA to bring two DNA strands into close proximity
BBa_K5237004	Staple Subunit: Oct1-DBD	Staple subunit that can be combined to form a functional staple, for example with TetR. Can also be combined with a fluorescent protein as part of the FRET proximity assay
BBa_K5237005	Staple Subunit: TetR	Staple subunit that can be combined to form a functional staple, for example with Oct1. Can also be combined with a fluorescent protein as part of the FRET proximity assay
BBa_K5237006	Simple Staple: TetR-Oct1	Functional staple that can be used to bring two DNA strands in close proximity
BBa_K5237007	Staple Subunit: GCN4	Staple subunit that can be combined to form a functional staple, for example with rGCN4
BBa_K5237008	Staple Subunit: rGCN4	Staple subunit that can be combined to form a functional staple, for example with rGCN4
BBa_K5237009	Mini Staple: bGCN4	Assembled staple with minimal size that can be further engineered
Functional Elements: Protease-cleavable peptide linkers and inteins are used to control and modify staples for further optimization for custom applications
BBa_K5237010	Cathepsin B-cleavable Linker: GFLG	Cathepsin B-cleavable peptide linker that can be used to combine two staple subunits to make responsive staples
BBa_K5237011	Cathepsin B Expression Cassette	Expression cassette for the overexpression of cathepsin B
BBa_K5237012	Caged NpuN Intein	A caged NpuN split intein fragment that undergoes protein trans-splicing after protease activation, which can be used to create functionalized staple subunits
BBa_K5237013	Caged NpuC Intein	A caged NpuC split intein fragment that undergoes protein trans-splicing after protease activation, which can be used to create functionalized staple subunits
BBa_K5237014	Fusion Guide RNA Processing Casette	Processing cassette to produce multiple fgRNAs from one transcript, that can be used for multiplexed 3D genome reprogramming
BBa_K5237015	Intimin anti-EGFR Nanobody	Interkingdom conjugation between bacteria and mammalian cells, as an alternative delivery tool for large constructs
BBa_K4643003	IncP Origin of Transfer	Origin of transfer that can be cloned into the plasmid vector and used for conjugation as a means of delivery
Readout Systems: FRET and enhancer recruitment readout systems to rapidly assess successful DNA stapling in bacterial and mammalian cells
BBa_K5237016	FRET-Donor: mNeonGreen-Oct1	FRET donor-fluorophore fused to Oct1-DBD that binds to the Oct1 binding cassette, which can be used to visualize DNA-DNA proximity
BBa_K5237017	FRET-Acceptor: TetR-mScarlet-I	Acceptor part for the FRET assay binding the TetR binding cassette, which can be used to visualize DNA-DNA proximity
BBa_K5237018	Oct1 Binding Casette	DNA sequence containing 12 Oct1 binding motifs, compatible with various assays such as the FRET proximity assay
BBa_K5237019	TetR Binding Cassette	DNA sequence containing 12 Oct1 binding motifs, can be used for different assays such as the FRET proximity assay
BBa_K5237020	Cathepsin B-Cleavable Trans-Activator: NLS-Gal4-GFLG-VP64	Readout system that responds to protease activity, which was used to test cathepsin B-cleavable linker
BBa_K5237021	NLS-Gal4-VP64	Trans-activating enhancer, that can be used to simulate enhancer hijacking
BBa_K5237022	mCherry Expression Cassette: UAS, minimal Promoter, mCherry	Readout system for enhancer binding, which was used to test cathepsin B-cleavable linker
BBa_K5237023	Oct1 - 5x UAS Binding Cassette	Oct1 and UAS binding cassette, that was used for the simulated enhancer hijacking assay
BBa_K5237024	TRE-minimal Promoter- Firefly Luciferase	Contains firefly luciferase controlled by a minimal promoter, which was used as a luminescence readout for simulated enhancer hijacking

1. Sequence Overview

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 276
Illegal XhoI site found at 305
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

2. Usage and Biology

2.1 The CRISPR/Cas System as a Gene Editing Tool

Figure 2: The CRISPR/Cas System A and B, schematic structure of Cas9 and Cas12a with their sgRNA/crRNA, sitting on a DNA strand with the PAM. The spacer sequence forms base pairings with the dsDNA. In case of Cas9, the spacer is located at the 5' prime end, for Cas12a at the 3' end of the gRNA. The scaffold of the gRNA forms a specific secondary structure enabling it to bind to the Cas protein. The cut sites by the cleaving domains, RuvC and HNH, are symbolized by the scissors.

In 2012, Jinek et al.. discovered the use of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas system to induce double-strand breaks in DNA. Since then, the system has been well-established as a tool for genome editing. The CRISPR/Cas system, which originates from the bacterial immune system, is constituted by a ribonucleoprotein complex. For class 1 CRISPR systems, the RNA is complexed by multiple Cas proteins, whereas class 2 systems consist of a singular protein and RNA. The class 2 type II system describes all ribonucleoprotein (RNP) complexes with Cas9 (Pacesa et al.., 2024). They include a CRISPR RNA (crRNA), which specifies the target with a 20 nucleotide (nt) spacer sequence, and a transactivating CRISPR RNA (tracrRNA), which induces the processing by the Cas protein (Jinek et al.., 2012) (Fig. 1A). Furthermore, a specific three nucleotide sequence (NGG) on the 3' end in the targeted DNA is needed for binding and cleavage. This is referred to as the protospacer adjacent motif (PAM) (Sternberg et al.., 2014). The most commonly used Cas9 protein is SpCas9 or SpyCas9, which originates from Streptococcus pyogenes (Pacesa et al.., 2024).

A significant enhancement of this system was the introduction of single guide RNAs (sgRNAs), which combine the functions of a tracrRNA and crRNA (Mali et al., 2013). Moreover, Cong (2013) established precise targeting of human endogenous loci by designing the 20 nt spacer sequence accordingly.

2.2 Differences Between Cas9 and Cas12a

Over the following years, further CRISPR/Cas systems have been discovered, including the Cpf1 system, which has been classified as Cas12a since then (Zetsche et al.., 2015). Cas12a forms a class 2 type V system with its RNA, that in comparison to the type II systems, only requires a crRNA for targeting and activation. Cas12a is capable of processing the precursor crRNA into crRNA independently, whereas Cas9 requires the RNase III enzyme and tracrRNA for this process (Paul and Montoya, 2020). This crRNA is often also referred to as a guide RNA (gRNA). However, the stem-loop, that is formed when binding the Cas protein is structurally distinct from the Cas9 gRNA and positioned on the 5' side of the crRNA (fig. 1B). Similarly, the PAM (TTTV) is also on the 5' side (Pacesa et al.., 2024). Cas9 possesses RuvC and HNH domains that are catalytically active, each of which cleaves one of the DNA strands at the same site, resulting in the formation of blunt end cuts (Nishimasu et al.., 2014). Cas12a possesses one RuvC-like domain that creates staggered cuts with overhangs that are about 5 nt long (Paul and Montoya, 2020).

2.3 Dead Cas Proteins and their Application

Figure 3: Pre-fgRNA Maturation by Cas12a Depicted are the stages of a pre-fgRNA being expressed from the genome, cut by Cas12a into fgRNA molecules forming an RNP with the Cas12a.

Specific mutations of these domains result in catalytic inactivity and therefore allow for the creation of nickases, that only cut one of the DNA strands, or completely inactive Cas proteins (Koonin et al.., 2023) (Kleinstiver et al.., 2019). These are referred to as dead Cas proteins or dCas9 and dCas12a. Kweon et al.. (2017) further expanded the ways in which the CRISPR/Cas system could be used by introducing the concept of fusion guide RNAs (fgRNAs). By fusing the 3' end of a Cas12a crRNA to the 5' end of a Cas9 gRNA, the newly created fgRNA could be used by both proteins independently for either multiplex genome editing or transcriptional regulation and genome editing in parallel, while allowing for Cas12a to process the pre-fgRNA into individual fgRNA molecules (Fig. 3). This allows for even greater multiplexing.

3. Assembly and Part Evolution

For the cloning, we employed the fgRNA entry vector (BBa_K5237000) resulting in a GGA using SapI with the insert being ordered as a DNA fragment.
Cloning via this strategy resulted in the designed and planned out construct being confirmed by Sanger sequencing (fig. 4)

Figure 4: Positive Cloning of the Desired Construct Confirmed by Sanger Sequencing. Two clones were picked and mini prepped after 16 h hours and sent to sequencing. Both clones had positive results and clean reads.

4. Results

Due to time constraints, we are not able to show data, nevertheless we are actively working on this assay.
The construct will be transfected into HEK293T cells together with a plasmid containing Cas12a and with a plasmid containing a fusion Cas (BBa_K5237003). The experiment will be carried out in technical replicates on a 6-well plate.
Lysis of the cells will occur 36 hours after transfection. Immediate RNA extraction will be performed with the miRNeasy Tissue/Cells Advanced Kit by QIAGEN to ensure the extraction of short RNA fragments below 200 nucleotides like the fgRNA.
When the extraction of the RNA was successful, reverse transcription into cDNA is started, followed by a qPCR. Each sample is screened with SYBR green labeled qPCR primers once for a housekeeper gene and for a sequence incorporated into the pre-fgRNA. Proper amplification between the chosen sites within the pre-fgRNA processing cassette can only take place when no processing has taken place into fgRNAs.

5. In Silico Characterization using DaVinci

We developed the in silico model DaVinci for rapid engineering and development of our PICasSO system. DaVinci acts as a digital twin to PICasSO, designed to understand the forces acting on our system, refine experimental parameters, and find optimal connections between protein staples and target DNA.
We calibrated DaVinci with literature and our own experimental affinity data obtained via EMSA assays and purified proteins. This enabled us to simulate enhancer hijacking in silico, providing valuable input for the design of further experiments. Additionally, we apply the same approach to our part collection.

DaVinci is divided into three phases: static structure prediction, all-atom dynamics simulation, and long-ranged dna dynamics simulation. Here, we applied the last step to our parts, characterizing structure and dynamics of the dna-binding interaction.

5.1. Enhancer Hijacking is successfully studied in silico

Figure 11: Cas stapled plasmids.

With the Cas staple, we aimed to simulate the principles of enhancer hijacking experiments we conducted in the lab. For these experiments, we modeled the two plasmids also used in the wet lab (BBa_K5237023 and BBa_K5237024). On top of the two plasmids, we modeled the Cas staple by applying a “DNA-DNA tethering force” throughout our simulation, selectively on the regions targeted by the fgRNA. This force was based on simulation data acquired in earlier phases of DaVinci. As there is no suitable model available that also simulates proteins, this proved to be the most effective modeling strategy.

Our simulation showed the expected behavior, holding the target sequences of the Cas staple (Fig. 12). Overall, these exciting results demonstrate that we can successfully model the core principles of enhancer hijacking with a total of 20 thousand simulated nucleotides in silico.

Figure 12: Fusion Cas staples hold stapled nucleotides in close proximity.

5.2. Cas staple forces do not distrub DNA strand integrity

Figure 13: Cas stapled plasmids.

Next, we aimed to stress test our system to determine the amount of force required to induce DNA double-strand breaks. To achieve this, we used an identical setup to the previous experiment but instead of experimentally determined forces, we used artificial forces of varying strength. It is important to know that our in silico model responds to forces that cause double-strand breaks by scattering the nucleotides across the simulation box. As the specified bonds cannot actually break within the simulation, the phosphate backbone bonds become severely distorted and exhibit erratic behavior in the simulation videos. From our extensive simulations, we concluded that the forces required to damage the DNA are approximately 320 times (Fig. 15) and 680 times greater (Fig. 16) than the forces exerted by the Cas staple, respectively.

This provides important evidence regarding the safety of our staple approach for 3D genome engineering: According to our model, DNA-DNA tethering with our Cas staples is not expected to have a negative effect on the DNA stability.

Figure 14: Applying a force that is 270 times greater
than the predicted force typically exerted by a Cas staple on DNA.

Figure 15: Applying a force that is 320 times greater
than the predicted force typically exerted by a Cas staple on DNA.

Figure 16: Applying a force that is 680 times greater
than the predicted force typically exerted by a Cas staple on DNA.

Figure 17: Applying a force that is more than 1000 times greater
than the predicted force typically exerted by a Cas staple on DNA.

5.3. DaVinci Helps to Design Multi-Staple Arrangements

Figure 18: Double Cas stapling within 40 nucleotide distance induces double-strand breaks.

Finally, we simulated the behavior of multiple staples at once. Therefore, we expanded our previously introduced experimental setup by a second Cas staple.
In a first approach, we targeted an additional region next to the original chosen one. This region is 40 nucleotides away from the first target region on the plasmid displayed in blue connecting it to the opposite site of the orange plasmid, therefore bringing both ends of the orange plasmid together (Fig. 18).
Our simulation predicted that with these staple points, DNA double-strand breaks would occur as clearly visible by the scattered nucleotides (Fig. 19).

Figure 19: Double Cas stapling within 40 nucleotide distance induces double-strand breaks.

Figure 20: Stable multiplexing with 2 Cas staples. On the blue plasmid, the Cas binding sequences are 980 nucleotides apart.

To simulate a setup where we expect no double-strand breaks, we increased the distance between the stapling sites on the blue plasmid (BBa_K5237023) from 40 to 980 nucleotides (Fig. 20).
With this increased distance between stapling sites, we observed a stabilized system. Most interestingly, the non-stapled regions showed maximum distances close to 500 nm, indicating that the two staples led to more compact plasmid structures.

In conclusion, we show that applying multiple staples on the same structures can lead to double-strand breaks if the staples are positioned closely to one another. However, increasing the separation of staples leads to a stable system without DNA damage. Thus, it is definitely possible to multiplex Cas staples, thereby increasing the compactness of DNA structures (Fig. 21). This shows the potential of creating complex regulatory networks by bringing genetic elements into spatial proximity with a multitude of Cas protein staples.

Figure 21: Increasing the distance between Cas staple targets to 980 nucleotides stabilizes multiplexing.

5. References

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and Charpentier, E. (2012). A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science 337, 816–821. https://doi.org/10.1126/science.1225829.

Kleinstiver, B. P., Sousa, A. A., Walton, R. T., Tak, Y. E., Hsu, J. Y., Clement, K., Welch, M. M., Horng, J. E., Malagon-Lopez, J., Scarfò, I., Maus, M. V., Pinello, L., Aryee, M. J., and Joung, J. K. (2019). Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nature Biotechnology 37, 276–282. https://doi.org/10.1038/s41587-018-0011-0.

Koonin, E. V., Gootenberg, J. S., and Abudayyeh, O. O. (2023). Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox. Biochemistry 62, 3465–3487. https://doi.org/10.1021/acs.biochem.3c00159.

Kweon, J., Jang, A.-H., Kim, D.-e., Yang, J. W., Yoon, M., Rim Shin, H., Kim, J.-S., and Kim, Y. (2017). Fusion guide RNAs for orthogonal gene manipulation with Cas9 and Cpf1. Nature Communications 8. https://doi.org/10.1038/s41467-017-01650-w.

Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., and Church, G. M. (2013). RNA-Guided Human Genome Engineering via Cas9. Science 339, 823–826. https://doi.org/10.1126/science.1232033.

Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., and Nureki, O. (2014). Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell 156, 935–949. https://doi.org/10.1016/j.cell.2014.02.001.

Pacesa, M., Pelea, O., and Jinek, M. (2024). Past, present, and future of CRISPR genome editing technologies. Cell 187, 1076–1100. https://doi.org/10.1016/j.cell.2024.01.042.

Paul, B., and Montoya, G. (2020). CRISPR-Cas12a: Functional overview and applications. Biomedical Journal 43, 8–17. https://doi.org/10.1016/j.bj.2019.10.005.

Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., and Doudna, J. A. (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62–67. https://doi.org/10.1038/nature13011.

Wu, T., Cao, Y., Liu, Q., Wu, X., Shang, Y., Piao, J., Li, Y., Dong, Y., Liu, D., Wang, H., Liu, J., & Ding, B. (2022). Genetically Encoded Double-Stranded DNA-Based Nanostructure Folded by a Covalently Bivalent CRISPR/dCas System. Journal of the American Chemical Society, 144(14), 6575-6582. https://doi.org/10.1021/jacs.2c01760.

Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., Koonin, E. V., and Zhang, F. (2015). Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell 163, 759–771. https://doi.org/10.1016/j.cell.2015.09.038.

Difference between revisions of "Part:BBa K5237014"