Name: silencing the spark: crispr/cas9 genome editing in weakly electric fish
Uploaded: 2019-10-27T14:00:00
Description: Watch this Scientific Journal Video about Silencing the Spark: CRISPR/Cas9 Genome Editing in Weakly Electric Fish at JoVE.com

The authors acknowledge the heroic efforts of Monica Lucas, Katherine Shaw, Ryan Taylor, Jared Thompson, Nicole Robichaud, and Hope Healey for help with fish husbandry, data collection, and early protocol development. We would also like to thank the three reviewers for their suggestions to the manuscript. We believe the final product to be of better quality after addressing their comments. This work was funded by support from the National Science Foundation #1644965 and #1455405 to JRG, and the Natural Sciences and Engineering Research Council DG grant to VLS.

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of Michigan State University.
1. Selecting sgRNA Targets
NOTE: A protocol is provided for manual design of sgRNAs in step 1.1. This was utilized for scn4aa target selection. An additional protocol is provided to facilitate this process (step 1.2) using the EFISHGENOMICS web portal. It is advised that users select protocol 1.2, which featur...

The phenotypic richness of weakly electric fish, together with a recent proliferation of genomics resources, motivates a strong need for functional genomic tools in the weakly electric fish model. This system is particularly attractive because of the convergent evolution of numerous phenotypic traits in parallel lineages of fish, which are easily kept in the laboratory.
The protocol described here demonstrates the efficacy of the CRISPR/Cas9 technique in lineages of weakly electric fish that e...

Electroreception and electrogenesis have changed in the evolutionary history of vertebrates. Two lineages of teleost fish, osteoglossiformes and siluriformes, evolved electroreception in parallel, and five lineages of teleosts (gymnotiformes, mormyrids, and the genera Astroscopus, Malapterurus, and Synodontis) evolved electrogenesis in parallel. There is a striking degree of convergence in these independently derived phenotypes, which share a common genetic architecture1,2,3.
This is perhaps best exemplified by the numerous convergent features of gymnotiforms and mormyrids, two species-rich teleost clades, which produce and detect weak electric fields and are called weakly electric fish. In the 50 years since the discovery that weakly electric fish use electricity to sense their surroundings and communicate4, a growing community of scientists has gained tremendous insights into evolution of development1,5,6, systems and circuits neuroscience7,8,9,10, cellular physiology11,12, ecology and energetics13,14,15,16,17, behavior18,19, and macroevolution3,20,21.
More recently, there has been a proliferation of genomic, transcriptomic, and proteomic resources for electric fish1,22,23,24,25,26,27,28. Use of these resources has already produced important insights regarding the connection between genotype and phenotype in these species1,2,3,28,29,30. A major obstacle to integrating genomics data with phenotypic data of weakly electric fish is a present lack of functional genomics tools31.
One such tool is the recently developed Clustered Regularly Interspaced Short Palindromic Repeats paired with Cas9 endonuclease (CRISPR/Cas9, CRISPR) technique. CRISPR/Cas9 is a genome editing tool that has entered widespread use in both model32,33,34 and non-model organisms35,36,37 alike. CRISPR/Cas9 technology has progressed to a point where a laboratory capable of basic molecular biology can easily generate gene-specific probes called short guide RNAs (sgRNAs), at a low cost using a non-cloning method38. CRISPR has advantages over other knockout/knockdown strategies, such as morpholinos39,40, transcription activator-like effector nucleases&#160;(TALENs), and zinc finger nucleases (ZFNs), which are costly and time-consuming to generate for every target gene.
The CRISPR/Cas9 system functions to create gene knockouts by targeting a specific region of the genome, directed by the sgRNA sequence, and causing a double-stranded break. The double-stranded break is detected by the cell and triggers endogenous DNA repair mechanisms preferentially using the non-homologous end joining (NHEJ) pathway. This pathway is highly error-prone: during the repair process, the DNA molecule will often incorporate insertions or deletions (indels) at the double-stranded break site. These indels can result in a loss of function due to either (1) shifts in the open reading frame, (2) insertion of a premature stop codon, or (3) shifts in the critical primary structure of the gene product. In this protocol, we utilize CRISPR/Cas9 editing to target point mutations in target genes using the NHEJ in weakly electric fish species. While simpler and more efficient than other techniques, this method of mutagenesis is expected to result in a range of phenotypic severities in F0, which is attributed to genetic mosaicism41,42,43,44.
Selection of Organisms 
For the purposes of facilitating future studies on the comparative genomics of weakly electric fish, a representative species for both gymnotiforms and mormyrids for protocol development needed to be selected. Following discussions during the 2016 Electric Fish meeting in Montevideo, Uruguay, there was community consensus to utilize species that already could be bred in the laboratory and that had genomic resources available. The gymnotiform Brachyhypopomus gauderio and the mormyrid Brienomyrus brachyistius were selected as species that fit these criteria. In both species, natural cues to induce and maintain breeding conditions are easy to mimic in captivity. B. gauderio, a gymnotiform species from South America, has the advantage of low husbandry requirements: fish can be kept at relatively high density in relatively small (4 L) tanks. B. gauderio also has fast generational turnover under captive conditions. Under laboratory conditions, B. gauderio can develop from egg to adult in about 4 months.
B. brachyistius, a species of mormyrid fish from West-Central Africa, breeds readily in captivity. B. brachyistius is readily available through the aquarium trade, has been widely used in many studies, and now has a number of genomic resources available. Their life cycle spans 1&#8722;3 years, depending on laboratory conditions. Husbandry requirements are somewhat more intensive for this species, requiring moderately sized tanks (50&#8722;100 L) due to their aggression during breeding.
Laboratories studying other species of electric fish should be able to easily adapt this protocol as long as the species can be bred, and single cell embryos can be collected and reared into adulthood. Housing, larval husbandry, and in vitro fertilization (IVF) rates will likely change with other species; however, this protocol can be used as a starting point for breeding attempts in other weakly electric fish.
An Ideal Gene Target for Proof of Concept: scn4aa 
Weakly electric mormyrid and gymnotiform fish generate electric fields (electrogenesis) by discharging a specialized organ, called the electric organ. Electric organ discharges (EODs) result from the simultaneous production of action potentials in the electric organ cells called electrocytes. EODs are detected by an array of electroreceptors in the skin to create high-resolution electrical images of the fish&#8217;s surroundings45. Weakly electric fish are also capable of detecting features of their conspecifics&#8217; EOD waveforms18 as well as their discharge rates46, allowing EODs to function additionally as a social communication signal analogous to birdsong or frog vocalizations47.
A main component of action potential generation in the electrocytes of both mormyrid and gymnotiform weakly electric fish is the voltage-gated sodium channel NaV1.42. Non-electric teleosts express two paralogous gene copies, scn4aa and scn4ab, coding for the voltage-gated sodium channel NaV1.430. In both gymnotiform and mormyrid weakly electric fish lineages, scn4aa has evolved rapidly and undergone numerous amino acid substitutions that affect its kinetic properties48. Most importantly, scn4aa has become compartmentalized in both lineages to the electric organ2,3. The relatively restricted expression of scn4aa to the electric organ, as well as its key role in the generation of EODs, makes it an ideal target for CRISPR/Cas9 knockout experiments, as it has minimal deleterious pleiotropic effects. Because weakly electric fish begin discharging their larval electric organs 6&#8722;8 days post fertilization (DPF), targeting of scn4aa is ideally suited for rapid phenotyping following embryo microinjection.

<table>
	<tbody>
		<tr>
			<td>20 mg/mL RNA grade Glycogen</td>
			<td>Thermo Scientific</td>
			<td>R0551</td>
			<td></td>
		</tr>
		<tr>
			<td>50 bp DNA ladder</td>
			<td>NEB</td>
			<td>N3236L</td>
			<td></td>
		</tr>
		<tr>
			<td>borosilicate glass capillary with filament</td>
			<td>Sutter Instrument</td>
			<td>BF100-58-10</td>
			<td>(O.D. 1.0mm, I.D. 0.58 mm, 10 cm length)</td>
		</tr>
		<tr>
			<td>Cas9 protein with NLS; 1 mg/mL</td>
			<td>PNA Biology</td>
			<td>CP01</td>
			<td></td>
		</tr>
		<tr>
			<td>Dneasy Blood &#38; Tissue Kit</td>
			<td>Qiagen</td>
			<td>69506</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf FemptoJet 4i Microinjector</td>
			<td>Fisher Scientific</td>
			<td>E5252000021</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf Microloader Pipette Tips</td>
			<td>Fisher Scientific</td>
			<td>10289651</td>
			<td></td>
		</tr>
		<tr>
			<td>Hamilton syringe</td>
			<td>Fisher Scientific</td>
			<td>14-824-654</td>
			<td>referred to as &#34;precision glass syringe&#34; in the protocol</td>
		</tr>
		<tr>
			<td>Kimwipe</td>
			<td>Fisher Scientific</td>
			<td>06-666</td>
			<td>referred to as &#34;delicate task wipe&#34; in the protocol</td>
		</tr>
		<tr>
			<td>MEGAscript T7 Transcription Kit</td>
			<td>Invitrogen</td>
			<td>AM1334</td>
			<td></td>
		</tr>
		<tr>
			<td>NEBuffer 3</td>
			<td>NEB</td>
			<td>B7003S</td>
			<td>used for in vitro cleavage assay</td>
		</tr>
		<tr>
			<td>OneTaq DNA kit</td>
			<td>NEB</td>
			<td>M0480L</td>
			<td></td>
		</tr>
		<tr>
			<td>Ovaprim</td>
			<td>Syndel USA</td>
			<td>https://www.syndel.com/ovaprim-ovammmlu010.html</td>
			<td>referred to as &#34;spawning agent&#34; in the protocol</td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Fisher Scientific</td>
			<td>S37440</td>
			<td>referred to as &#34;thermoplastic&#34; in the protocol</td>
		</tr>
		<tr>
			<td>Pipette puller</td>
			<td>WPI</td>
			<td>SU-P97</td>
			<td>sutter brand</td>
		</tr>
		<tr>
			<td>QIAquick PCR Purification Kit</td>
			<td>Qiagen</td>
			<td>28106</td>
			<td></td>
		</tr>
		<tr>
			<td>Reusable needle- requires customization</td>
			<td>Fisher Scientific</td>
			<td>7803-02</td>
			<td>Customize to 0.7 inches long; point style 4 and angle 25</td>
		</tr>
		<tr>
			<td>T4 DNA polymerase</td>
			<td>NEB</td>
			<td>M0203L</td>
			<td>Use with the 10X NEB buffer that is included</td>
		</tr>
		<tr>
			<td>Teflon coated tools</td>
			<td>bonefolder.com</td>
			<td>T-SPATULA4PIECE</td>
			<td>referred to as &#34;polytetrafluoroethene&#34; in the protocol</td>
		</tr>
	</tbody>
</table>

silencing the spark: crispr/cas9 genome editing in weakly electric fish

Electroreception and electrogenesis have changed in the evolutionary history of vertebrates. There is a striking degree of convergence in these independently derived phenotypes, which share a common genetic architecture. This is perhaps best exemplified by the numerous convergent features of gymnotiforms and mormyrids, two species-rich teleost clades that produce and detect weak electric fields and are called weakly electric fish. In the 50 years since the discovery that weakly electric fish use electricity to sense their surroundings and communicate, a growing community of scientists has gained tremendous insights into evolution of development, systems and circuits neuroscience, cellular physiology, ecology, evolutionary biology, and behavior. More recently, there has been a proliferation of genomic resources for electric fish. Use of these resources has already facilitated important insights with regards to the connection between genotype and phenotype in these species. A major obstacle to integrating genomics data with phenotypic data of weakly electric fish is a present lack of functional genomics tools. We report here a full protocol for performing CRISPR/Cas9 mutagenesis that utilizes endogenous DNA repair mechanisms in weakly electric fish. We demonstrate that this protocol is equally effective in both the mormyrid species Brienomyrus brachyistius and the gymnotiform Brachyhypopomus gauderio by using CRISPR/Cas9 to target indels and point mutations in the first exon of the sodium channel gene scn4aa. Using this protocol, embryos from both species were obtained and genotyped to confirm that the predicted mutations in the first exon of the sodium channel scn4aa were present. The knock-out success phenotype was confirmed with recordings showing reduced electric organ discharge amplitudes when compared to uninjected size-matched controls.

The sgRNA target sites were identified within exon 1 of scn4aa in both B. gauderio and B. brachyistius as described in Section 1. The sgRNAs were generated as described in Section 2. Following successful sgRNA selection and synthesis (Figure 1), in vitro cleavage was tested (Figure 2). The sgRNAs demonstrating in vitro cutting were then selected for single cell microinjections.
Adult fish were conditioned fo...

Watch this Scientific Journal Video about Silencing the Spark: CRISPR/Cas9 Genome Editing in Weakly Electric Fish at JoVE.com

Silencing the Spark: CRISPR/Cas9 Genome Editing in Weakly Electric Fish

Here, a protocol is presented to produce and rear CRISPR/Cas9 genome knockout electric fish. Outlined in detail are the required molecular biology, breeding, and husbandry requirements for both a gymnotiform and a mormyrid, and injection techniques to produce Cas9-induced indel F0 larvae.

Electroreception and electrogenesis have changed in the evolutionary history of vertebrates. There is a striking degree of convergence in these ...

CRISPR/Cas9 gene editing in weakly electric fish, particularly in a comparative context, will enable researchers to test hypotheses about how specific genes and genetic variance contribute to phenotypic variation. CRISPR/Cas9 is an efficient method for generating mutant F-zero embryos. This protocol allows researchers to conduct CRISPR-Cas9 manipulations in two convergently evolved species of weakly electric fish.The key to using this approach with some modifications in other electric fish or other fish species is the availability of transcriptomic or genomic resources to make sgRNAs. Performing the microinjections and visualizing the cells in a 3D location within a 2D plane can be difficult. Obtain a small zebrafish colony for eggs to practice general microinjection techniques.Demonstrating the procedure with Savvas Constantinou will be Jared Thompson, a technician from my laboratory. After housing the fish species of interest under the appropriate breeding conditions, identify female fish that appear gravid. In B.gauderio, the female will have swollen gonads just caudal to the vent.In B.brachyistius females will have swollen bellies and appear deep-bodied. After anesthesia administration, add spawning agent to four times the volume of DPBS in a PCR tube with thorough mixing. The solution will become cloudy.Use a pipette to measure out the calculated dose and dispense the diluted agent unto a piece of thermoplastic before drawing the solution into a precision glass syringe equipped with a 28-gauge 19 to 25-milliliter length beveled needle. Inject the solution into the dorsal trunk muscle at a smooth rate and let the needle sit for two to four seconds before removal. Then, immediately place fish into fresh system water for recovery.For B.gauderio sperm collection, after 24 hours, select a large male fish and as quickly as possible after sedation, dry the fish thoroughly, especially around the head and Vent. Place the dried fish ventral side up, anterior to the left in appropriate holder, covered in an MS222 soaked damp paper towel with the head as parallel with the table as possible. Immediately apply pressure in the caudal to rostral direction with light squeezing immediately over the gonads toward the vent and using a micropipetter with a tip, carefully collect the sperm as it is squeezed from the male in 50-microliter increments.Add aliquot of sperm directly onto 500-microliter volumes of sperm extender solution on ice. Immediately after the collection, place fish into slime coat protection product-treated fresh system water. For B.gauderio egg collection, after drying an a anesthetized B.gauderio female fish, immediately place the fish on its side with the head facing the nondominant hand and apply pressure in the caudal to rostral direction with light squeezing medially over the gonads toward the vent.Using a polytetrafluoroethylene tool, carefully collect the eggs as they are squeezed from the cloaca and quickly place the eggs in a small covered Petri dish. If working alone after squeezing, touch the egg mass to the base of the small Petri dish as they are expelled from the female. Immediately after collecting the eggs, place the fish in slime coat protection product-treated fresh system water.For B.gauderio in vitro fertilization, add 100 microliters of the well mixed sperm SES solution directly over the egg mass, followed by one milliliter of fresh system water. Mix the gametes suspension thoroughly for 30 to 60 seconds before adding an additional one to two milliliters of 0.22-micrometer pore filtered system water to the cells. Label the dish with the in vitro fertilization time and place the dish into a 29-degree Celsius incubator, setting a 50-minute timer to check the progress of the development.During the fertilization period, use a microloader pipette tip to backload two microliters of the injection solution of interest into a microinjection needle and expel the liquid as close to the tip as possible. When a single cell has formed at the animal pole of at least one cell, transfer the dish under a dissecting microscope and use a pair of fine forceps to break the needle tip at a beveled angle toward where the taper of the needle begins to demonstrate rigidity. The bore of the needle should remain as small as possible while maintaining a rigid taper.Identify the developing zygotes under the microscope and use a plastic transfer pipette with a cut tip to place 10 to 20 eggs in as little water as possible onto the edge of the glass microscope slide set in the inverted top of the Petri dish. Using a delicate task wipe, gently press the slide to remove the excess water to allow the eggs to adhere firmly to the edge of the slide. Water will be wicked under the slide and pull eggs against the edge.There should be just enough water to keep the eggs moist while maintaining little standing moisture to avoid egg movement during injection. Align the eggs against the slide vertically, perpendicular to the approaching needle, and use a micromanipulator to position the needle against the chorion. Then, holding the needle at a roughly 45-degree angle, insert the tip first into the chorion and then, into the single cell, injecting through the yolk if possible.Remove any broken eggs during the injection with fine forceps. When all of the eggs has been injected, use a squirt bottle of 0.22-micrometer pore filtered system water to gently flush the eggs from the injection stage into a new 100-millimeter diameter Petri dish. Following a successful short guide RNAs selection and synthesis, in vitro cleavage can be tested for selection for single cell microinjections.After PCR clean up and cloning, in this representative experiment, CRISPR-Cas9 induced mutations were identified in individual B.gauderio and B.brachyistius clones with strong electric organ discharge amplitude reduction, whereas uninjected controls displayed only referenced genotypes. Visualization of the electric organ discharge amplitude between confirmed CRISPR mutants and agent size matched uninjected controls demonstrated that both SCN-4 AA mutant B.brachyistius and B.gauderio embryos had significantly lower electric organ discharge amplitudes than controls. When performing the micro injections, move as quickly and deliberately as possible to maximize the number of single-cell injected embryos that survive.Do not waste time with difficult eggs. Once successful mutants have been identified, traditional breeding methods can create stable mutant lines, which eliminate CRSPR associated mosaicism concerns. This protocol will allow researchers to conduct comparative genomic studies with functional validation in two convergently evolved species of weakly electric fish.

Research

JoVE Journal

Biology

Agrobacterium-Mediated Virus-Induced Gene Silencing Assay In Cotton

Cotton (Gossypium hirsutum) is one of the most important crops worldwide. Considerable efforts have been made on molecular breeding of new varieties.  The ...

Genome Editing with CompoZr Custom Zinc Finger Nucleases (ZFNs)

Genome Editing with CompoZr Custom Zinc Finger Nucleases ZFNs

Genome editing is a powerful technique that can be used to elucidate gene function and the genetic basis of disease. Traditional gene editing methods such ...

Digital Inline Holographic Microscopy (DIHM) of Weakly-scattering Subjects

Digital Inline Holographic Microscopy DIHM of Weakly-scattering Subjects

Weakly-scattering objects, such as small colloidal particles and most biological cells, are frequently encountered in microscopy. Indeed, a range of ...

Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9

The prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 system may be re-purposed for site-specific ...

Genome Editing in Astyanax mexicanus Using Transcription Activator-like Effector Nucleases (TALENs)

Genome Editing in Astyanax mexicanus Using Transcription Activator-like Effector Nucleases TALENs

Identifying alleles of genes underlying evolutionary change is essential to understanding how and why evolution occurs.  Towards this end, much recent ...

Preparing and Injecting Embryos of Culex Mosquitoes to Generate Null Mutations using CRISPR/Cas9

Preparing and Injecting Embryos of Culex Mosquitoes to Generate Null Mutations using CRISPR/Cas9

Culex mosquitoes are the major vectors of several diseases that negatively impact human and animal health including West Nile virus and diseases caused by ...

Genome Engineering of Primary Human B Cells Using CRISPR/Cas9

B cells are lymphocytes derived from hematopoietic stem cells and are a key component of the humoral arm of the adaptive immune system. They make ...

Pupal and Adult Injections for RNAi and CRISPR Gene Editing in Nasonia vitripennis

Pupal and Adult Injections for RNAi and CRISPR Gene Editing in Nasonia vitripennis

The jewel wasp, Nasonia vitripennis, has become an efficient model system to study epigenetics of haplo-diploid sex determination, B-chromosome biology, ...

TGF-&#946;-mediated Endothelial to Mesenchymal Transition (EndMT) and the Functional Assessment of EndMT Effectors using CRISPR/Cas9 Gene Editing

TGF-&#946;-mediated Endothelial to Mesenchymal Transition EndMT and the Functional Assessment of EndMT Effectors using CRISPR/Cas9 Gene Editing

In response to specific external cues and the activation of certain transcription factors, endothelial cells can differentiate into a mesenchymal-like ...

Construction of Homozygous Mutants of Migratory Locust Using CRISPR/Cas9 Technology

The migratory locust, Locusta migratoria, is not only one of the worldwide plague locusts that caused huge economic losses to human beings but also an ...