technology
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genome engineering with programmable nucleases for animal model and cell model generation

technology

NovoHelix is at the interface of many scientific disciplines including applied genetics, embryology, epigenetic reprogramming, genome engineering, regenerative and reproductive medicine, and basic molecular biology. We are constantly evaluating new technologies to advance our genome engineering platform including the ability to multiplex with novel programmable endonucleases for custom model generation. In the schematics below, we broadly describe strategies for generating targeted mutations in animal or cellular models that are commonly requested by our clients.  Leveraging our expertise, we routinely create constitutive knockouts, conditional knockouts (cKO), knock-ins, deploy site-specific recombinases for conditional genetic circuits and design gene drives for super-Mendelian inheritance.  NovoHelix has a customizable pipeline for targeted modification of any genomic locus.
knockouts (KO)
conditional knockout (cKO)
knockin (KI)
site-specific recombination technologies (SSR)
gene drive systems/ active genetics
references
knockouts (KO)

To advance the study of gene function, NovoHelix offers a comprehensive loss-of-function gene platform to generate the desired animal model.  CRISPR-nuclease assisted gene inactivation services include disruption of the translational reading frame such as frameshift stops (indels) to create simple knockouts, exonic deletions, single or multi-gene deletions, double knockouts (DKO), deletion of linked genes, megabase deletions and whole chromosomal ablation (induced aneuploidy). For knockout of multiple genes simultaneously also known as multiplexed genome engineering, the Cas12a (Cpf1) nuclease processes a single CRISPR array containing several target sites and disrupts the reading frames of multiple genes (Zetsche et al 2017, Campa et al 2019¹,²). While this multiplexing technology is still in preliminary stages, NovoHelix has demonstrated expertise using cutting edge research tools to inactivate multiple genes and has entered the digital genome engineering era.

gene knockout created by frameshift mutation via CRISPR
CRISPR mediated exon deletion
CRISPR-mediated double knockout—deletion of linked genes
CRISPR-mediated multi-gene deletion up to a megabase
CRISPR-mediated chromosome deletion—induced aneuploidy
conditional knockout (cKO)

In comparison to direct knockouts, conditional knockouts (cKO) allow for temporal and spatial control of gene disruption. To generate a cKO, the target gene’s critical exons are often flanked with directional loxP sites termed ‘floxed’ which can be excised by Cre recombinase. Crossing a Cre-expression driver mouse to this floxed allele affords the investigator to conditionally excise the targeted gene only in cells which express the recombinase Cre. Conditional gene disruption is useful for modeling embryonic lethal genes, tissue-specific gene deletion or developmental-stage gene disruption.  Our service packages include options such as guaranteed founders or pricing per microinjection session, flexible repair templates such as conditional donor vectors or long single-stranded DNA (lssDNA), and the choice of RNA molecule formats for guide RNA (gRNA) evaluation using the latest design guidelines:  full-length guides, synthetic single guide RNAs (sgRNAs), chemically-modified crRNA + tracrRNA or sgRNAs, truncated sgRNAs, & hairpin-sgRNAs (hp-sgRNAs). The advantage of testing multiple high-specificity Cas endonuclease variants and RNA molecule formats allows NovoHelix to tune the activity of custom RNP complexes to produce the highest on-target activity in our surrogate cell-based gene editing assays while limiting potential off-target activity. 

CRISPR-mediated conditional allele generation—floxing a critical exon
knockin (KI)
The scarless targeted integration of functional DNA elements such as mutations, protein tags, fluorescent reporters and humanized genes into the genome for disease modeling as well as developmental and mechanistic studies is routinely achieved by RNA-guided nuclease technologies such as CRISPR-Cas. In addition to the ability to edit or delete DNA sequences within the genome, a repair process known as homology-directed repair (HDR) offers the ability to seamlessly insert DNA sequences.  In the presence of a double-stranded DNA break (DSB) created by the Cas endonuclease and an accompanying repair template (ssODN, lssDNA, donor vector) with sufficient homologous sequence, the cellular machinery may repair the DSB during the mitotic S-phase when homologous recombination proteins are active.  As a consequence, the repair template may become seamlessly integrated at the target site within the genome: this technology is known as a knockin (KI). 


Allow NovoHelix to leverage its expertise to build custom rodent models containing small knockins such as insertion of point mutations, altering amino acid codons, insertion of tags and barcodes, reporter genes (mKusabira-Orange, mCitrine, mVenus, mNeonGreen, GFP, mEmerald, mCherry, tdTomato, mScarlet, mCerulean, mTFP1, etc.) and whole gene replacement such as humanization. For large knockins, NovoHelix has routinely introduced large DNA constructs some upwards of 90-kb into traditional safe harbor sites Rosa26 and AAVS1 and has built a suite of flexible donor vectors such as Rosa26-lox-stop-lox (Rosa26-LSL). From the initial project concept, we can assist with a flexible design that includes building advanced genetic circuits for knockin to any genomic locus to advance your field.
CRISPR-mediated knock-in of a reporter gene
CRISPR-mediated knock-in of a humanized allele—gene replacement knock-in
CRISPR-mediated knock-in of a point mutation
seamless knock-in of small protein tags or multiple point mutations by programmable nucleases
site-specific recombination technologies (SSR)
The deployment of SSR’s, i.e. Cre/CreET2, flippase (Flp/Flpe/Flpo), Dre, VCre, Vika, Nigri, Panto  & φC31,  and usage of heterotypic recombinase sites such as lox66/lox2272, Frt3/Frt5/Frt14/15, rox/rox12 creates a wealth of flexible allele design modalities for conditional mutagenesis such as cassette exchange or tight regulation of reporter gene expression through cassette inversion. Contact us to assist you in the design and construction of conditional alleles so that we may provide expertise with the following design strategies:


  •   conditional by inversion (COIN) as described by Economides et al, 2013³
  •   flip-excision switches (FLEx) as described by Schnütgen et al, 2013    
  •   invertible intronic cassette (FLIP) as described by Andersson-Rolf et al, 2017⁵
  •   Recombination mediated cassette exchange (RMCE) described in Lee et al, 2019⁶

FLEx or 'flip-excision' switches or double-inverted orientation (DIO)

FLEx or 'flip-excision' switches or double inverted orientation (DIO)

recombination mediated cassette exchange (RMCE)

recombination mediated cassette exchange (RMCE)
gene drive systems/ active genetics

In natural or synthetic contexts, gene drives often rely on some genetic element or circuit that can selfishly copy itself from one chromosome to another chromosome typically during early development or in germ cells. This selfish copying process known as an 'active genetic' allele spreads within a population at a higher frequency than traditional Mendelian inheritance. As such, this super-Mendelian inheritance is known as the gene drive. While gene drive systems have deployed homing nucleases such as I-SceI as described by Windbichler et al 2011, more recently CRISPR-mediated gene drives have been shown as a proof-of-concept to work within the mouse female germline (Grunwald et al 2018). Building on these milestones, the gene drive technology has the potential to transform the use of rodent biomedical models by reducing the number of matings needed to generate mutant offspring of desired alleles. Because the mutant allele can spread through a population rapidly, deployment of any gene drive requires a contemporaneous biocontainment strategy to mitigate spread to nontarget populations. One solution to the wild spreading of an allele is to deploy a local daisy-chain gene drive as described by Esvelt and Church (Noble et al 2019). NovoHelix can assist the client to develop the gene drive and appropriate biocontainment strategy: please inquire with our scientific leadership team.

references
1: Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F. Multiplex gene editing by CRISPR-Cpf1 using a single  crRNA array. Nat Biotechnol. 2017 Jan;35(1):31-34. doi: 10.1038/nbt.3737. Epub 2016 Dec 5. Erratum in: Nat Biotechnol. 2017 Feb 8;35(2):178. PubMed PMID: 27918548; PubMed Central PMCID: PMC5225075.

2: Campa CC, Weisbach NR, Santinha AJ, Incarnato D, Platt RJ. Multiplexed genome  engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nat Methods. 2019 Sep;16(9):887-893. doi: 10.1038/s41592-019-0508-6. Epub 2019 Aug 12. PubMed PMID: 31406383.

3: Economides AN, Frendewey D, Yang P, Dominguez MG, Dore AT, Lobov IB, Persaud T, Rojas J, McClain J, Lengyel P, Droguett G, Chernomorsky R, Stevens S, Auerbach W, Dechiara TM, Pouyemirou W, Cruz JM Jr, Feeley K, Mellis IA, Yasenchack J, Hatsell SJ, Xie L, Latres E, Huang L, Zhang Y, Pefanis E, Skokos D, Deckelbaum RA, Croll SD, Davis S, Valenzuela DM, Gale NW, Murphy AJ, Yancopoulos GD. Conditionals by inversion provide a universal method for the generation of conditional alleles. Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):E3179-88. doi: 10.1073/pnas.1217812110. Epub 2013 Aug 5. PubMed PMID: 23918385; PubMed Central PMCID: PMC3752204.

4: Friede RL, Roessmann U. Chronic tonsillar herniation: an attempt at classifying chronic hernitations at the foramen magnum. Acta Neuropathol. 1976 Mar 30;34(3):219-35. PubMed PMID: 1266580.

5: Andersson-Rolf A, Mustata RC, Merenda A, Kim J, Perera S, Grego T, Andrews K,  Tremble K, Silva JC, Fink J, Skarnes WC, Koo BK. One-step generation of conditional and reversible gene knockouts. Nat Methods. 2017 Mar;14(3):287-289.  doi: 10.1038/nmeth.4156. Epub 2017 Jan 30. PubMed PMID: 28135257; PubMed Central  PMCID: PMC5777571.

7: Windbichler N, Menichelli M, Papathanos PA, Thyme SB, Li H, Ulge UY, Hovde BT, Baker D, Monnat RJ Jr, Burt A, Crisanti A. A synthetic homing endonuclease-based  gene drive system in the human malaria mosquito. Nature. 2011 May 12;473(7346):212-5. doi: 10.1038/nature09937. Epub 2011 Apr 20. PubMed PMID: 21508956; PubMed Central PMCID: PMC3093433.

8: Grunwald HA, Gantz VM, Poplawski G, Xu XS, Bier E, Cooper KL. Super-Mendelian inheritance mediated by CRISPR-Cas9 in the female mouse germline. Nature. 2019 Feb;566(7742):105-109. doi: 10.1038/s41586-019-0875-2. Epub 2019 Jan 23. PubMed PMID: 30675057; PubMed Central PMCID: PMC6367021.

9: Noble C, Min J, Olejarz J, Buchthal J, Chavez A, Smidler AL, DeBenedictis EA,  Church GM, Nowak MA, Esvelt KM. Daisy-chain gene drives for the alteration of local populations. Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8275-8282. doi: 10.1073/pnas.1716358116. Epub 2019 Apr 2. PubMed PMID: 30940750; PubMed Central PMCID: PMC6486765.