Optogenetic Random Mutagenesis Using Histone-miniSOG in C. elegans

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Summary

Genetically-encoded histone-miniSOG induces genome-wide heritable mutations in a blue light-dependent manner. This mutagenesis method is simple, fast, free of toxic chemicals, and well-suited for forward genetic screening and transgene integration.

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Noma, K., Jin, Y. Optogenetic Random Mutagenesis Using Histone-miniSOG in C. elegans. J. Vis. Exp. (117), e54810, doi:10.3791/54810 (2016).

Abstract

Forward genetic screening in model organisms is the workhorse to discover functionally important genes and pathways in many biological processes. In most mutagenesis-based screens, researchers have relied on the use of toxic chemicals, carcinogens, or irradiation, which requires designated equipment, safety setup, and/or disposal of hazardous materials. We have developed a simple approach to induce heritable mutations in C. elegans using germline-expressed histone-miniSOG, a light-inducible potent generator of reactive oxygen species. This mutagenesis method is free of toxic chemicals and requires minimal laboratory safety and waste management. The induced DNA modifications include single-nucleotide changes and small deletions, and complement those caused by classical chemical mutagenesis. This methodology can also be used to induce integration of extrachromosomal transgenes. Here, we provide the details of the LED setup and protocols for standard mutagenesis and transgene integration.

Introduction

Forward genetic screens have been widely used to generate genetic mutants disrupting various biological processes in model organisms such as Caenorhabditis elegans (C. elegans)1. Analyses of such mutants lead to the discovery of functionally important genes and their signaling pathways1,2. Traditionally, mutagenesis in C. elegans is achieved using mutagenic chemicals, radiation, or transposons2. Chemicals such as ethyl methanesulfonate (EMS) and N-ethyl-N-nitrosourea (ENU) are toxic to humans; gamma-ray or ultraviolet (UV) radiation mutagenesis requires special equipment; and transposon-active strains, such as mutator strains3, can cause unnecessary mutations during maintenance. We have developed a simple approach to induce heritable mutations using a genetically-encoded photosensitizer4.

Reactive Oxygen Species (ROS) can damage DNA5. The mini Singlet Oxygen Generator (miniSOG) is a green fluorescent protein of 106 amino acids that was engineered from the LOV (Light, Oxygen, and Voltage) domain of Arabidopsis phototropin 2 6. Upon exposure to blue light (~450 nm), miniSOG generates ROS including singlet oxygen with flavin mononucleotide as a cofactor6-8, which is present in all cells. We constructed a His-mSOG fusion protein by tagging miniSOG to the C-terminus of histone-72, a C. elegans variant of Histone 3. We generated a single-copy transgene9 to express His-mSOG in the germline of C. elegans. Under normal culture conditions in the dark, the His-mSOG transgenic worms have normal brood size and life span4. Upon exposure to blue LED light, the His-mSOG worms produce heritable mutations among their progeny4. The spectrum of induced mutations includes nucleotide changes, such as G:C to T:A and G:C to C:G, and small chromosome deletions4. This mutagenesis procedure is simple to perform, and requires minimal lab safety setup. Here, we describe the LED illumination setup and procedures for optogenetic mutagenesis.

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Protocol

1. Construction of the LED Illuminator

NOTE: The required LED equipment is summarized in the List of Materials. The entire LED setup is small and can be placed anywhere in the lab, although we recommend it be placed in a dark room to control light exposure of worms4.

  1. Connect the LED to a controller with cables (Figure 1A, D).
  2. Connect the controller to a digital function generator/amplifier with a BNC cable (Figure 1A, C, D).
  3. Fix the LED light 10 cm above the stage using a custom holder (Figure 1A).
    NOTE: We made the holder with metal parts.
  4. Cover the LED illumination setup partially, but avoid heat accumulation (Figure 1B), which makes worms sick.
    NOTE: We use a custom-made hard plastic cover with open top and bottom (Figure 1A). The cover is not required for the mutagenesis itself, but is used to limit unnecessary exposure of the blue light to the surroundings. We advise to not cover the LED setup entirely (Figure 1B) to prevent overheating the worms.
  5. Wear laser-protective glasses.
    NOTE: We wear laser-protective glasses because the light is very bright. Sunglasses may work as well.
  6. Switch the lever of the LED controller to 'Int.' for continuous illumination (Figure 1D) and set it at 65% of the maximum power (Figure 1C).
  7. Use a photometer to measure the blue light intensity on the stage where the worms are placed using manufacturer's protocol. The setup gives 2.0 mW/mm2 under continuous illumination.

2. Blue Light Treatment

NOTE: Use the strain CZ20310 juSi164[Pmex-5-HIS-72::miniSOG-3'UTR(tbb-2) + Cb-unc-119(+)] unc-119(ed3)III4. The strain is available at the Caenorhabditis Genetics Center (CGC, http://www.cgc.cbs.umn.edu/).

  1. Maintain the His-mSOG strain in the dark on standard nematode growth medium (NGM) plates with E. coli OP50 following a standard protocol10,11.
    NOTE: Under ambient light, juSi164-containing strains do not display a mutation rate above a spontaneous rate4. Routine strain passage using a dissecting scope with a halogen lamp generally does not cause mutations as well. Nonetheless, care should be taken to avoid unnecessary exposure to light, e.g., keeping the strains in a standard dark-inside incubator, or covering the strains with foil. It is advised to freeze aliquots of the strain after receiving it in case unnecessary mutations accumulate over time.
  2. Pick gravid young adult (approximately 12 h post-L4) animals with a worm pick11.
    NOTE: Younger animals show less mutagenic effect4, while older animals may have lower brood size.
  3. Cut a filter paper to fit a 60 mm plate with a 25 mm x 25 mm square hole and place onto an unseeded plate (Figure 1E).
    NOTE: A square punch can be used but the size of the punch does not have to be precise.
  4. Drop 100 µL of 100 mM CuCl2 on the filter paper evenly to restrict worms within the square hole on the plate.
  5. Pick desired number of gravid young adult hermaphrodites (see Step 3 for an example) and transfer to the center of the CuCl2 plate.
  6. Wear laser protective glasses.
  7. Switch ON the LED and the function generator.
  8. Switch the lever of the LED controller to 'Ext.' to control it by the function generator (Figure 1D).
  9. Set the controller at 65% of the maximum power and the function generator as sine wave, 4 Hz (Figure 1C).
  10. Place the CuCl2 plate from Step 2.5 without a lid on the stage under the LED (Figure 1A).
  11. Illuminate the animals with blue light for 30 min.
  12. Transfer healthy looking worms to a seeded plate as P0.
    NOTE: The desired number of P0 depends on the type of screen. See Step 3 for an example. The P0 worms may appear to be uncoordinated immediately after light treatment and will recover over time.
  13. Keep worms covered using foil in an incubator or in the dark; and follow the standard procedure to begin screening desired phenotypes among their progeny2,10.

3. Example of a Forward Genetic Screen

NOTE: This is an example of the clonal screen with 120 haploid genomes to check if the LED and strain are working. Figure 2 shows a schematic of the procedure.

  1. [Day1] After blue light treatment, pick five healthy looking worms onto a NGM plate with OP50 as P0, keep them in a 20 °C incubator, and let them lay eggs for 1 d ('Day1' plate).
  2. [Day2] Transfer P0 onto a new seeded plate ('Day2' plate).
  3. [Day3] Pick and kill P0 on the 'Day2' plate by burning them.
  4. [Day4] Pick 30 gravid young adult F1 from the 'Day1' plate and transfer them onto individual plates (30 F1 plates for 'Day1').
  5. [Day5] Repeat Step 3.4 for the 'Day2' plate (30 F1 plates for 'Day2').
  6. [Day7-9] Check the abnormal morphologies and/or behavior of F2 worms compared to the WT strain (Figure 3A) under a standard stereomicroscope when they become adults.
    NOTE: A heritable mutation displays about a quarter of worms with the same phenotype among F2 when it is recessive with high penetrance. However, some mutants may grow slowly and/or show partial penetrance. Therefore, it is possible that less than a quarter of the mutants can be found on a plate.
  7. Pick worms with visible phenotypes individually and check the heritability of the phenotype in the next generation.

4. Example of an Extrachromosomal Transgene Integration

  1. Inject the DNA of interest into CZ20310 juSi164[Pmex-5-HIS-72::miniSOG-3'UTR(tbb-2) + Cb-unc-119(+)] unc-119(ed3) and prepare transgenic worms with a low transmission rate (10-30%) following a standard injection protocol12,13.
    NOTE: Alternatively, established extrachromosomal arrays can be crossed into the juSi164 strains. To avoid genotyping for juSi164, juSi164 heterozygotes may be used as the P0 although efficiency might be decreased. The genotyping method for juSi164 is described in Section 5.
  2. [Day1] Treat ~20 transgenic animals as P0 with blue light as described in Step 2.
    NOTE: More P0 worms are necessary depending on the transmission rate. Transgenes can be identified by phenotypes or coinjection marker12,13.
  3. Pick 10 healthy looking P0 onto individual plates, keep them in a 20 °C incubator, and let them lay eggs for a few days (P0 plates)
  4. [Day4] Single out 20 transgenic F1 worms from each P0 plate onto individual plates and let them lay eggs. (20 F1 x 10 P0 plates= 200 F1 plates in total.)
  5. [Day7] Find F1 plates with >75% F2 having transgenes.
  6. Pick five transgenic animals from the >75% transmission rate F1 plates (F2 plates).
  7. [Day10] Keep F2 plates with 100% transmission rate as potential integrated lines.
  8. Outcross the potential integrated lines using a standard procedure10 to check the Mendelian segregation and to remove potential background mutations.

5. Genotyping

  1. Lyse 20 outcrossed F2 worms in lysis buffer using a standard protocol14.
  2. Perform PCR using the primers for MosSCI insertion9, juSi164, (Table 1) with an annealing temperature of 58 °C following a standard protocol14.
    NOTE: It is unnecessary to genotype unc-119(ed3) because unc-119(ed3) can be detected by uncoordinated behavior after removing the rescuing transgene (juSi164) in the following Steps 5.4 and 5.5.
  3. Run agarose gel electrophoresis15 and examine the band sizes (Table 1) to find the WT for juSi164.
  4. Examine if the F2 progeny has paralyzed worms due to the existence of unc-119(ed3).
  5. If uncoordinated worms are found on step 5.4, single several nonuncoordinated worms to obtain all nonuncoordinated worms in the next generation.

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Representative Results

We performed a forward genetic screen with CZ20310 juSi164 unc-119(ed3) using 30 min light exposure following the standard protocol described in Sections 2 and 3. Among 60 F1 plates corresponding to 120 mutagenized haploid genomes, we found 8 F1 plates with F2 worms displaying visible phenotypes such as body size defect (Figure 3B), uncoordinated movement (Figure 3C), and adult lethality (Figure 3D). We did not notice any difference in the number of mutants between 'Day1' and 'Day2' plates. All progeny of singled small F2 worms and uncoordinated F2 worms showed the corresponding phenotypes, suggesting that they are heritable mutants. The full observation is summarized in Table 2. On average, a clonal screen with 120 haploid genomes will result in about 10 F1 plates containing worms with visibly detectable phenotypes such as body shape and locomotion that easily spotted under a stereomicroscope. More quantitative analysis is necessary to determine the mutation rate precisely4. The expected number of visible mutants from this screen suggests that the strain and setup are working properly for optogenetic mutagenesis.

Figure 1
Figure 1: The LED Setup. (A) The whole system. The LED was mounted on a custom-made holder. Details are found in the List of Materials. (B) The cover is made of plastic. It does not cover the system completely to avoid heat accumulation. (C) Controller and function generator. (D) The back side of the system. (E) An unseeded plate with CuCl2-soaked filter paper for blue light treatment. Please click here to view a larger version of this figure.

Figure 2
Figure 2: Experimental Procedure for a Clonal Screen. After blue light treatment, P0 worms are transferred to a seeded plate and allowed to lay eggs. P0 worms are transferred to a new seeded plate 1 d after light treatment and killed 2 d after light treatment. F1 worms are singled from the P0 plates. Phenotypes of F2 worms are examined after they become adults. Please click here to view a larger version of this figure.

Figure 3
Figure 3: Example of Mutants. (A) Original strain for optogenetic mutagenesis: CZ20310 juSi164 unc-119(ed3). This strain has normal body shape, behavior, and brood size. Scale bar: 0.5 mm. (B - D) F2 progeny showing body size defect (B), uncoordinated (C), and lethal (D) phenotypes. Please click here to view a larger version of this figure.

Table 1
Table 1: Genotyping of juSi164 and unc-119(ed3).

Table 2
Table 2: Example of Phenotypes from a Clonal Screen.

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Discussion

Here, we describe a detailed procedure of optogenetic mutagenesis using His-mSOG expressed in the germline and provide an example of a small scale forward genetic screen. Compared to standard chemical mutagenesis, this optogenetic mutagenesis method has several advantages. Firstly, it is nontoxic, thereby keeping lab personnel away from toxic chemical mutagens such as EMS, ENU and trimethylpsoralen with ultraviolet light (TMP/UV). Secondly, the experimental procedure of mutagenesis can be used for a small number of the P0 animals and can be finished within one hour. Thirdly, the optogenetic mutagenesis produces a broad spectrum of mutations including nucleotide substitutions and chromosome deletions. Finally, the optogenetic mutagenesis can be used for integration of extrachromosomal transgenes.

The critical step in this mutagenesis protocol is to ensure that the LED setup works on His-mSOG containing strains at the expected efficiency. We recommend performing a pilot clonal screen, as described in Protocol Section 3, with about 100 haploid genomes. The mutagenesis is easily scalable from the small scale pilot screens to nonclonal screens by increasing the number of P0 for the light treatment. For large-scale nonclonal screens, we suggest synchronizing the worms to gravid young adults and transferring hundreds of them with M9 solution onto a CuCl2 plate for light treatment. The standard condition described in Steps 2 and 3 is estimated to have approximately 4.4 times lower efficiency than the widely used 50 mM EMS mutagenesis method4. The mutation rate may be improved by increasing the light exposure time and/or increasing the intensity of the light. However, these modifications can cause phototoxicity and lead to small brood size and sickness of light-treated worms. To increase the efficiency, it may be possible to use miniSOG derivatives with higher ROS yield such as miniSOG(Q103L) although it may increase the background mutagenesis effect without light treatment16,17. For the modification of the DNA construct, the Pmex-5-HIS-72::miniSOG-3'UTR(tbb-2) plasmid (pCZ886) is available commercially.

Under the conditions described here, integrated transgenes are generated at approximately one line per 200 F1 on average4 when using an extrachromosomal transgenic strain with a transmission rate of 10 - 30%. This efficiency may be increased by using extrachromosomal transgenic strains with high transmission rates as previously reported for a UV radiation method18.

His-mSOG-mediated optogenetic mutagenesis induces mutations in a wide range of genes. Also, the frequency of loci recovered from the rpm-1 suppressor screen using optogenetic mutagenesis is similar to those from the same screen using EMS4. However, it is possible that optogenetic mutagenesis using a histone gene may have a bias towards certain genes, due to unknown factors such as chromatin structure. To address this issue, it is necessary to analyze many optogenetically induced mutations by whole genome sequencing.

His-mSOG-mediated optogenetic mutagenesis causes a wide spectrum of mutations including single nucleotide substitutions and deletions ranging from 1 bp to a few hundred bp4. The spectrum of single nucleotide variants suggests that miniSOG-induced reactive oxygen species are the cause of the mutations4. It is also possible that miniSOG damages histone proteins and causes chromatin instability because miniSOG is used to inactivate proteins as well19. It may be possible to manipulate the type of mutations by using light of different intensities. Since optogenetic mutagenesis causes deletions, it is important to analyze deletions as well as single nucleotide changes in whole genome sequencing data for mapping20.

It was previously reported that an epifluorescent microscope is used for miniSOG-mediated cell ablation21,22. The light intensity of a standard epifluorescent compound microscope was measured to be ~0.5 mW/mm2 without a lens, which is about 4x lower than that used in the standard optogenetic mutagenesis protocol. Thus, it is highly advisable to empirically determine the efficiency when using an epi-fluorescent microscope as a light source. One advantage of the LED is the stability over thousands of hours. Previous studies have shown that miniSOG is more potent in ROS-mediated cell ablation under pulsed light22, although the precise mechanism remains to be determined. We used a digital function generator/amplifier to make pulsed light. Another option is to connect the light source to a computer using a USB-TTL interface (Figure 1A) to regulate the LED light by a program. The LED system described here can also be used for other purposes, such as optogenetic control of excitable cells using channelrhodopsin23, cell ablation using mitochondria- or cell-membrane-targeted miniSOG17,22, and Chromophore-Assisted Light Inactivation (CALI) of proteins19. Furthermore, this optogenetic mutagenesis has the potential to be applied to other organisms, such as bacteria, yeast, fly, and zebrafish, as well as mammalian cell lines.

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Disclosures

The authors have nothing to disclose.

Acknowledgments

The work is supported by HHMI. We thank our lab members for their help with testing the protocol and revising the manuscript.

Materials

Name Company Catalog Number Comments
Ultra High Power LED light source Prizmatix UHP-mic-LED-460 460 ± 5 nm
LED controller Prizmatix UHPLCC-01
Digital function generator/amplifier PASCO PI-9587C PI-9587C is no longer available. The replacement is PI-8127.
BNC cable male/male THORLABS CA3136
USB-TTL interface Prizmatix Optional
Photometer THORLABS PM50 and Model D10MM
Filter paper Whatman 1001-110
Stereomicroscope Leica MZ95
NGM plate Dissolve 5 g NaCl, 2.5 g Peptone, 20 g Agar, 10 µg/mL cholesterol in 1 L H2O. After autoclaving, add 1 mM CaCl2, 1 mM MgSO4, 25 mM KH2PO4(pH 6.0). 
Lysis solution 10 mM Tris(pH 8.8), 50 mM KCl, 0.1% Triton X-100, 2.5 mM MgCl2, 100 µg/mL Proteinase K

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References

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