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What is CRISPR?


A new world of genetic engineering

This project aims to answer these questions.

Background

Whether it is a single cell or a complex multicellular organism, all information on structure and function is stored in the genetic material, that is, DNA. The complete genetic material of a cell or of an organism is called a genome.

The genetic material of prokaryotic cells is organised in a single circular DNA molecule.

Study the structure of a bacterial cell in the following 3D scene.

The DNA macromolecules found in the nuclei of Eukaryoric cells form chromosomes (together with proteins).

The number of chromosomes is characteristic of the species. Humans have 23 pairs of chromosomes in the body cells and 23 chromosomes in the gametes.

Open the following 3D scene to learn about the structure of DNA and how it forms chromosomes. If you want to learn more, study the chemical structure of DNA.

What are genes?

The genome, that is, the genetic material of an organism consists of genes. Many of the genes encode proteins, while others contain information necessary for the regulation and synthesis of proteins that play a role in the growth and functioning of cells and the body.

The offspring inherit their genes from their parents.

How many protein-coding genes can an organism have?

The number of these genes varies greatly between species.

Organism Number of genes
maize 40 000
water flea 31 000
mouse 22 200
human 21 200
nematode 19 700
fruit fly 14 000
yeast 6 600
intestinal bacterium 5 000
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Formulate statements using the information in the table.

Can genes be modified?

Genes can modify in a natural way.

Genetic material can change in a permanent way. In this case, the alteration of the DNA is permanent. This is called mutation.

If only a small segment of the gene, that is, only some nucleotides change, the mutation is a point mutation. Scientists assume that 100-200 point mutations can occur in a single person in a lifetime. Not all mutations have noticeable effects, that is, not all mutations are expressed in the phenotype of the individual and not all are inherited by the offspring.

Researchers can also cause alteration in genes and thereby perform genetic modification.

Besides mapping the genome of species, scientists can also change the genes expressed in individuals. The technologies are called genetic engineering, gene therapy, genetic modification, etc.

What does CRISPR mean?

CRISPR is an acronym:

Clustered Regularly Interspaced Short Palindromic Repeats

A palindrome is a type of word play. In the strict, original sense, a palindrome is a word or phrase that reads the same backward as forward, e.g. madam, Was it a car or a cat I saw?

The genome of organisms can contain short sequences that are palindromic, and certain enzymes can easily recognise them. For example, the restriction enzymes (DNA-cleaving enzymes) of bacteria can cleave DNA at specific recognition sites, called restriction sites, which are palindromic sequences of nucleotides. The EcoRI enzyme, for example, recognises the palindromic sequence GAATTC and cuts between the G and the A.

But what does CRISPR mean?
In 1987, repeated sequences were identified in the genetic material of E. coli bacteria, but the function of those was not yet known. Later similar sequences were found in the genome of other bacteria too. It turned out that these short sequences, containing 20–50 base pairs, originate from viruses.

In the early 2000s, it was proven that bacteria are able to defend themselves against bacteriophages (viruses that infect bacteria). They can create a 'memory' of viruses by cleaving small snippets of the virus DNA using enzymes then incorporating them into their own bacterial genome (CRISPR). These snippets can later be used to detect and destroy the viruses.

When the offspring encounter the same virus, bacterial cells can 'remember' the viral infection and become immune to the given virus, similarly to the immune system of multicellular organisms.

Open the following 3D scene to see an introduction to the CRISPR-system.

How is the CRISPR system used as a genetic modification method?

In 2012, three independent research teams simultaneously described techniques for using the antiviral defence mechanisms of bacteria for genome editing in plant, animal or even human cells.

Genome editing is a type of genetic engineering in which a specific DNA sequence is deleted, inserted or replaced in the genome of an organism.

The CRISPR/Cas9 system makes it possible to make targeted mutations at specific places in the cells, which is also why it is often referred to as 'DNA scissors'.
The three components of the original system are the following.

  1. a short RNA produced by the CRISPR and carrying information about the DNA to be cleft. It is necessary for targeting (crRNA)
  2. a longer RNA with a constant sequence of bases, necessary for cleaving, called CRISPR trans-activating RNA (tracrRNA);
  3. Cas9 is a nuclease enzyme that is capable of cleaving the DNA of the virus.

Researchers modify the targeting RNA (crRNA), to match (that is, to be complementary to) a selected DNA sequence – whether it is a defective gene or that of a certain property to be modified – so that it is suitable for targeting the Cas9 enzyme as a single, short-chain RNA and allow it to cleave any selected sequence from the DNA of any cell. This single, modified targeting RNA, created by joining a crRNA and a trRNA, is called a guide RNA (gRNA).

In addition, this system can target multiple genes at once, so it can be used to treat diseases that are caused by more than one gene. Modifications can be made within living cells too, not only in test tubes.

Gene knockout

The CRISPR/Cas9 complex can be artificially engineered in laboratory circumstances and can be introduced into cells. During the production of the complex, it is possible to determine the DNA segment it will recognize, therefore it can also be used for high-precision modifications of the genes of living organisms. After the recognition, the complex cuts the gene, thus it will not be translated into a protein. This genetic engineering method is called gene knockout.

Gene knockin

With the CRISPR/Cas9 complex, gene knockin is also possible. In this process, a DNA segment of a foreign gene must also be introduced into the cell together with the complex. Once the complex has cut the genetic material of the cell, the foreign DNA segment can bind to the cut ends and the new, foreign gene can be incorporated into the genome, or a new gene that carries a mutation can be substituted for the original one.

What can gene modifications be used for?

Fears

  1. One problem is that we cannot be sure that a mutation created in a population will not be released from that population and spread to another species. An additional risk is that the change results in the disappearance of a species, it will probably affect other populations.
  2. It can also be dangerous: for example, researchers introduced a mutation-inducing CRISPR into mice using an inhalable virus and thereby created a model of human lung cancer in them. Even a small flaw in the design of the targeting RNA can result in an accident and create an “inhalable lung cancer” that infects humans.
  3. The long-term consequences of genome editing are not yet known. In 2018, a pair of gene-edited twins (the girls are known as Lulu and Nana) were born in China. While the original aim of the genetic modification was to make the children resistant to HIV, as a 'side effect', their intelligence may have also been enhanced. However, the modification may have shortened their life expectancy, according to a study. Adequate time must be devoted to risk assessment.
  4. In numerous cases, it has been shown that cleavage of the Cas9 complex occurred not only at the planned site in the genome of CRISPR-modified cells, but also in other chromosomes. A newer and more precise Cas9 protein should be used to eliminate such side effects.

Expectations

The technology may also be useful in creating more resistant plants, as well as to prevent epidemics and genetic diseases. Another promising possibility of using genetic modification is the eradication of antibiotic-resistant bacteria by removing the bacterial gene responsible for antibiotic resistance. It could also be used as a method of control for invasive plant species.

Some encouraging results

  1. A team of researchers at Harvard University used CRISPR technology to insert mammoth DNA into the cells of a modern elephant with the aim of reconstucting the genome of mammoths, or to resurrect this extinct animal species (March 2015).
  2. Researchers at the Sun Yat-sen University in China modified the genome in human embryos. They used non-viable embryos and attempted to modify the gene responsible for β-thalassaemia. Their article, however, was rejected by both Nature and Science for ethical reasons. (April 2015)
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  1. Genetic modification was used to make certain porcine organs suitable for being transplanted into human patients. Genes responsible for triggering organ rejection after implanting certain organs into humans were knocked out from pig genome.
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  1. Researchers modified the genome of malaria mosquitoes (anopheles) and thereby made female mosquitoes sterile. This resulted in a drastic decrease in the number of insects in a mosquito population, contributing to malaria control.
  1. A team of researchers at the University of California modified T-cells that play a key role in the functioning of the immune system. By inserting new sequences, they repaired T-cell mutations.
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  1. A group of researchers at Duke University performed genetic modification in mouse muscle in order to treat Duchenne muscular dystrophy. (2016). The technique has since been applied successfully on dogs and human cells too.
  1. There are promising results in the research regarding the use of genetic engineering in the treatment of cancer. In the research carried out at the University of Pennsylvania, the modified immune cells of cancer patients are reinserted into the patients, hoping that these modified immune cells would destroy cancer cells. 18 patients participated in the research (April 2019)
  2. Chinese scientists transferred a gene linked to human brain development into rhesus macaques to find out whether it is possible to to decrease the evolutionary distance between apes and humans (march 2019)
  3. A team of researchers at the University of Georgia performed the first successful genome editing in reptiles and edited a gene that affects skin pigmentation. The experiment resulted in the birth of albino lizards. (April 2019)
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  1. In agriculture, the method can be used for making crops more resistant:
  1. Genome editing was used to enhance powdery mildew resistance in wheat.
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  1. Non-browning mushrooms were produced. (april 2017).
  1. Researchers created waxy corn hybrids in which the cornstarts consists of amylopectin only. This substance has a number of uses in the food industry, in papermaking and in animal nutrition (April 2017).
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  1. Researchers genetically modified oilseed rape for an increased oil yield. This may make biodiesel fuel production more efficient (August 2017)
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  1. Drought- and salt-tolerant soybeans were produced to help adaptation to the effects of climate change (October 2017).

Is it allowed to carry out genetic modifications on humans?

Using the CRISPS/Cas9 system, the genetic modifications made in a fertilised human egg cell would be present in all the body cells of the human being. That is, it can be used for human genome editing.

In December 2015, ethical questions related to the new technology were discussed in an international conference. The conference was organised by David Baltimore, Nobel-prize winning molecular biologist and held in Washington, in the US. An agreement was made that making permanent, hereditary changes in the human genome is irresponsible.

In 2016 February, the modification of the genes of a human embryo was authorised in the UK but the embryo was to be destroyed within 14 days.

Genetically edited twin babies (Lulu and Nana) were born in China in a research funded by a private foundation in China, ignoring both Chinese and international laws regarding human genetic engineering. The researchers modified a gene in their genome to make their T-cells immune to HIV. Later it was announced that the genetic modification may have shortened the children's life expectancy.

Genetic defect causing haemophilia in the cells of Haemophilia A patients was corrected (2019).

Some clinical trials have already been approved in people with a terminal or incurable illness. For example, a trial will be launched for treating Leber’s congenital amaurosis by injecting the components of the gene-editing system directly into the eye. Previous clinical trials have used the CRISPR technique to edit the genomes of cells that have been removed from the body and then injected back. Scientists, however, fear that genetic engineering could lead to an unexpected disease in the patients.

The topic of 'designer babies' poses an ethical problem. That is, this technology would allow parents to pick a sex, eye colour, facial shape of their babies as well as the babies' susceptibility to illnesses and infections and even their psychological characteristics. The limit between preventing fatal illnesses and custom-picking characteristics for our offspring is not clear.

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