What Is CRISPR? A Powerful Tool For Editing Genomes

Genomes encode a series of messages and instructions within their DNA sequences, and genome editing involves changing those sequences, thereby changing the messages they contain. This can be done by inserting a cut or break in the DNA and tricking a cell’s natural DNA repair mechanisms into introducing the targeted changes. CRISPR-Cas9 provides a means to do so.

What Is CRISPR?

CRISPR is a powerful tool for editing genomes, meaning it allows researchers to easily alter DNA sequences and modify gene function. It has many potential applications, including correcting genetic defects, treating and preventing the spread of diseases, and improving the growth and resilience of crops. However, despite its promise, the technology also raises ethical concerns.

In popular usage, “CRISPR” (pronounced “crisper”) is shorthand for “CRISPR-Cas9.” CRISPRs are specialized stretches of DNA, and the protein Cas9 — where Cas stands for “CRISPR-associated” — is an enzyme that acts like a pair of molecular scissors, capable of cutting strands of DNA.

CRISPR technology was adapted from the natural defense mechanisms of bacteria and archaea, a domain of relatively simple single-celled microorganisms. These organisms use CRISPR-derived RNA, a molecular cousin to DNA, and various Cas proteins to foil attacks by viruses. To foil attacks, the organisms chop up the DNA of viruses and then stow bits of that DNA in their own genome, to be used as a weapon against the foreign invaders should those viruses attack again.

When the components of CRISPR are transferred into other, more complex, organisms, those components can then manipulate genes, a process called “gene editing.” No one really knew what this process looked like until 2017, when a team of researchers led by Mikihiro Shibata of Kanazawa University in Japan and Hiroshi Nishimasu of the University of Tokyo showed, for the very first time, what it looks like when a CRISPR is in action, Live Science previously reported.

Key Components Of CRISPR

CRISPRs: The term “CRISPR” stands for “clusters of regularly interspaced short palindromic repeats” and describes a region of DNA made up of short, repeated sequences with so-called “spacers” sandwiched between each repeat.

When we talk about repeats in the genetic code, we’re talking about the ordering of rungs within the spiral ladder of a DNA molecule. Each rung contains two chemical bases bound together: A base called adenine (A) links up to another called thymine (T), and the base guanine (G) pairs with cytosine (C).

In a CRISPR region, these bases appear in the same order several times, and in these repeated segments, they form what’s known as “palindromic” sequences, according to the Max Planck Institute. A palindrome, like the word “racecar,” reads the same forward as it does backward; similarly, in a palindromic sequence, bases on one side of the DNA ladder match those on the opposing side when you read them in opposite directions.

For example, a super simple palindromic sequence might look like this:

  • Side 1 – GATC
  • Side 2 – CTAG

Short palindromic repeats appear throughout CRISPR regions of DNA, with each repeat bookended by “spacers.” Bacteria swipe such spacers from viruses that have attacked them, meaning they incorporate a bit of viral DNA into their own genome. These spacers serve as a bank of memories, which enables the bacteria to recognize the viruses if they should ever attack again. You can also think of spacers like “Wanted” posters, providing a snapshot of the bad guys so they can be easily spotted and brought to justice.

Rodolphe Barrangou and a team of researchers at Danisco, a food ingredients company, first demonstrated this process experimentally. In a 2007 paper published in the journal Science, the researchers used Streptococcus thermophilus bacteria, which are commonly found in yogurt and other dairy cultures, as their model, according to the Joint Genome Institute, part of the U.S. Department of Energy. They observed that after a viral attack, the bacteria incorporated new spacers into their CRISPR regions. Moreover, the DNA sequence of these spacers was identical to parts of the virus genome.

The team also manipulated the spacers by removing them and inserting new viral DNA sequences in their place. In this way, the researchers were able to alter the bacteria’s resistance to an attack by a specific virus, confirming CRISPRs’ role in regulating bacterial immunity.

CRISPR RNA (crRNA): CRISPR regions of DNA act as a kind of bank of viral memories; but for that stored information to be useful elsewhere in the cell, it must be copied, or “transcribed,” into a different genetic molecule called RNA. Unlike DNA sequences, which remain lodged inside the DNA molecule, this CRISPR RNA (crRNA) can roam about the cell and team up with proteins — namely the molecular scissors that snip viruses to bits.

RNA also differs from DNA in that it’s only one strand, rather than two, meaning it looks like just a half of a ladder. To build an RNA molecule, one part of the CRISPR acts as a template, and proteins called polymerases to swoop in to construct an RNA molecule that is “complementary” to that template, meaning the two strands’ bases would fit together like puzzle pieces. For example, a G in the DNA molecule would get transcribed as a C in the RNA.

Each snippet of CRISPR RNA contains a copy of a repeat and a spacer from a CRISPR region of DNA, according to a 2014 review by Jennifer Doudna and Emmanuelle Charpentier, published in the journal Science. The crRNA interacts with the Cas9 protein and another kind of RNA, called “trans-activating crRNA” or tracrRNA, in order to help bacteria fend off viruses.

Cas9: The Cas9 protein is an enzyme that cuts foreign DNA. The protein binds to crRNA and tracrRNA, which together guide Cas9 to a target site on the virus’s DNA strand where the protein will make its cut. The target DNA that the Cas9 will cut through is complementary to a 20-nucleotide stretch of the crRNA, where a “nucleotide” is a building block of DNA that contains one base.

Using two separate regions or “domains” on its structure, Cas9 cuts both strands of the DNA double helix, making what is known as a “double-stranded break,” according to the 2014 Science article.

There is a built-in safety mechanism that ensures that Cas9 doesn’t just cut just anywhere in a genome. Short DNA sequences are known as “protospacer adjacent motifs,” or PAMs, serve as tags and sit adjacent to the target DNA sequence. If the Cas9 complex doesn’t see a PAM next to its target DNA sequence, it won’t cut. This is one possible reason that Cas9 doesn’t ever attack the CRISPR region in bacteria, according to a 2014 review published in Nature Biotechnology.

Key Components Of CRISPR

How CRISPR Works As A Genome-Editing Tool

Genomes encode a series of messages and instructions within their DNA sequences, and genome editing involves changing those sequences, thereby changing the messages they contain. This can be done by inserting a cut or break in the DNA and tricking a cell’s natural DNA repair mechanisms into introducing the targeted changes. CRISPR-Cas9 provides a means to do so.

In 2012, two pivotal research papers were published in the journals Science and PNAS, describing how the bacterial CRISPR-Cas9 could be used to chop up any DNA, not just that of viruses. In this way, the natural CRISPR system could be transformed into a simple, programmable genome-editing tool.

To direct Cas9 to snip a specific region of DNA, scientists can simply change the sequence of the crRNA, which binds to a complementary sequence in the target DNA, the studies concluded.In the 2012 Science article, Martin Jinek and his colleagues further simplified the system by fusing crRNA and tracrRNA to create a single “guide RNA.” Thus, genome editing requires only two components: a guide RNA and the Cas9 protein.

“Operationally, you design a stretch of 20 base pairs that match a gene that you want to edit,” and from there, one can figure out what the complementary crRNA sequence would be, George Church, a professor of genetics at Harvard Medical School, told Live Science. Church emphasized the importance of making sure that the nucleotide sequence is found only in the target gene and nowhere else in the genome.

“Then the RNA plus the protein [Cas9] will cut — like a pair of scissors — the DNA at that site, and ideally nowhere else,” Church explained. Once the DNA is cut, the cell’s natural repair mechanisms kick in and work to piece the DNA back together, and at this point, edits can be made to the genome. There are two ways this can happen:

According to Huntington’s Outreach Project at Stanford University, one repair method involves gluing the two cuts back together. This method, known as “non-homologous end joining,” tends to introduce errors where nucleotides are accidentally inserted or deleted, resulting in mutations that could disrupt a gene.

In the second method, the break is fixed by filling in the gap with a sequence of nucleotides. In order to do so, the cell uses a short strand of DNA as a template. Scientists can supply the DNA template of their choosing, thereby writing-in any gene they want, or correcting a mutation.

Who Discovered CRISPR?

Scientists originally discovered the CRISPRs in bacteria in 1987, but they didn’t initially understand the biological significance of the DNA sequences, and they didn’t yet call them “CRISPRs,” according to Quanta Magazine. Yoshizumi Ishino and colleagues at Osaka University in Japan first found the characteristic nucleotide repeats and spacers in the gut microbe Escherichia coli, and as the technology for genetic analysis improved in the 1990s, other researchers found CRISPRs in many other microbes.

Francisco Mojica, a scientist at the University of Alicante in Spain, was the first to describe the distinct characteristics of CRISPRs and found the sequences in 20 different microbes, according to a 2016 report in the journal Cell. At one point, he dubbed the sequences “short regularly spaced repeats” (SRSRs), but he later suggested that they be called CRISPRs instead. The term CRISPR first appeared in a 2002 report, published in the journal Molecular Microbiology and authored by Ruud Jansen of Utrecht University, with whom Mojica had been in correspondence.

In the following years, scientists also discovered Cas genes and the function of Cas enzymes, and they figured out that the spacers in CRISPRs came from invasive viruses, Quanta reported.

Among these pioneering researchers was Jennifer Doudna, a professor of biochemistry, biophysics and structural biology at the University of California, Berkeley, who went on to share the 2020 Nobel Prize in chemistry with Emmanuelle Charpentier, director of the Max Planck Unit for the Science of Pathogens. The two scientists are credited with adapting the bacterial CRISPR/Cas system into a handy gene-editing tool, Live Science previously reported.

Charpentier initially discovered tracrRNA while studying the bacteria Streptococcus pyogenes, which causes a range of diseases from tonsillitis to sepsis. Having uncovered tracrRNA as a previously unknown component of the CRISPR/Cas system, Charpentier began collaborating with Doudna to recreate that system in a test tube. In 2012, the team published their seminal work in the journal Science, announcing that they’d successfully simplified the molecular scissors into a gene-editing tool.

Some thought that biochemist Feng Zhang of the Broad Institute might also earn the Nobel for his own, separate work with the CRISPR system, Science Magazine reported. Zhang demonstrated that the CRISPR system works in mammalian cells, and based on this work, the Broad Institute earned the first patent for the use of CRISPR gene-editing technology in eukaryotes, or complex cells with nuclei to hold their DNA.

CRISPR Gene in E.Coli

How Has CRISPR Been Used?

In 2013, researchers in the labs of Church and Zhang published the first reports describing the use of CRISPR-Cas9 to edit human cells in an experimental setting. Studies conducted in a lab dish and animal models of human disease have demonstrated that the technology can effectively correct genetic defects. Examples of such diseases include cystic fibrosis, cataracts, and Fanconi anemia, according to a 2016 review article published in the journal Nature Biotechnology. These studies have paved the way for therapeutic applications in humans.

In the realm of medicine, CRISPR has been tested in early-stage clinical trials as cancer therapy and as a treatment for an inherited disorder that causes blindness. It’s also been investigated as a strategy for preventing the spread of Lyme disease and malaria from viral vectors to people, and it’s also been studied in animal models of HIV as a way to rid infected cells of the virus, Live Science previously reported. One research team in China attempted to treat a human patient’s HIV using CRISPR, and while the treatment wasn’t successful in curing the infection, the gene therapy also didn’t cause any harmful effects, Live Science reported.

“I think the public perception of CRISPR is very focused on the idea of using gene editing clinically to cure disease,” said Neville Sanjana of the New York Genome Center and an assistant professor of biology, neuroscience, and physiology at New York University. “This is no doubt an exciting possibility, but this is only one small piece.”

CRISPR technology has also been applied in the food and agricultural industries to engineer probiotic cultures and to vaccinate industrial cultures (yogurt, for example) against viruses. It is also being used in crops to improve yield, drought tolerance, and nutritional properties.

One other potential application is to create gene drives, a genetic engineering technique that increases the chances of a particular trait passing on from parent to offspring; this kind of genetic engineering derives from a natural phenomenon, where specific versions of genes are more likely to be inherited. Eventually, over the course of generations, the trait spreads through entire populations, according to the Wyss Institute. Gene drives could be used for various applications, such as eradicating invasive species or reversing pesticide and herbicide resistance in crops, according to a 2014 report published in the journal Science.

During the COVID-19 pandemic, the CRISPR-Cas9 system has been used to develop various diagnostic tests for viral infection, BBC News reported.

In addition, CRISPR has recently been used in the following ways:

  • In April 2017, a team of researchers released research in the journal Science that they had programmed a CRISPR molecule to find strains of viruses, such as Zika, in blood serum, urine and saliva.
  • On Aug. 2, 2017, scientists revealed in the journal Nature that they had removed a heart disease defect in an embryo successfully using CRISPR.
  • On Jan. 2, 2018, researchers announced that they may be able to stop fungi and other problems that threaten chocolate production using CRISPR to make the plants more resistant to disease.
  • On April 16, 2018, researchers upgraded CRISPR to edit thousands of genes at once, according to research published by the journal BioNews.

However, despite its wide range of uses, the tool is not without its drawbacks.

“I think the biggest limitation of CRISPR is it is not a hundred percent efficient,” Church told Live Science. That means, in a given experiment, CRISPR may successfully edit only a percentage of the targeted DNA. According to the 2014 Science article by Doudna and Charpentier, in a study conducted in rice, gene editing occurred in nearly 50% of the cells that received the Cas9-RNA complex. Meanwhile, other analyses have shown that depending on the target, editing efficiencies can reach as high as 80% or more.

The technology can also create “off-target effects” when DNA is cut at sites other than the intended target. This can lead to the introduction of unintended mutations. Furthermore, Church noted, even when the system cuts on target, there is a chance of not getting a precise edit. He called this “genome vandalism.”

Potential Risks And Ethical Concerns Of Using CRISPR

The many potential applications of CRISPR technology raise questions about the ethical merits and consequences of tampering with genomes. And in particular, a slew of ethical debates flared up in 2018 when He Jiankui, formerly a biophysicist at the Southern University of Science and Technology in Shenzhen, announced that his team had edited DNA in human embryos and thus created the world’s first gene-edited babies.

He was subsequently sentenced to three years in prison and fined 3 million yuan ($560,000) for practicing medicine without a license, violating Chinese regulations on human-assisted reproductive technology and fabricating ethical review documents, Live Science previously reported. But even after his sentencing, He’s experiments raised questions about how the use of CRISPR should be regulated going forward, especially given that the technology is still fairly new.

Illegal experimentation in human embryos represents an extreme misuse of CRISPR, of course, but even seemingly ethical uses of the technology could carry risks, scientists say.

In general, making genetic modifications to human embryos and reproductive cells such as sperm and eggs is known as germline editing. Since changes to these cells can be passed on to subsequent generations, using CRISPR technology to make germline edits has raised a number of ethical concerns.

Variable efficacy, off-target effects, and imprecise edits all pose safety risks. In addition, there is much that is still unknown to the scientific community. In a 2015 article published in Science, David Baltimore and a group of scientists, ethicists, and legal experts note that germline editing raises the possibility of unintended consequences for future generations “because there are limits to our knowledge of human genetics, gene-environment interactions, and the pathways of disease (including the interplay between one disease and other conditions or diseases in the same patient).”

In the 2014 Science article, Oye and colleagues point to the potential ecological impact of using gene drives. An introduced trait could spread beyond the target population to other organisms through crossbreeding. Gene drives could also reduce the genetic diversity of the target population, potentially hampering its ability to survive.

Other ethical concerns are more nuanced. Should we make changes that could fundamentally affect future generations without having their consent? What if the use of germline editing veers from being a therapeutic tool to an enhancement tool for various human characteristics?

To address these concerns, the National Academies of Sciences, Engineering, and Medicine put together a comprehensive report with guidelines and recommendations for genome editing.

Although the National Academies urge caution in pursuing germline editing, they emphasize “caution does not mean prohibition.” They recommend that germline editing be done only on genes that lead to serious diseases and only when there are no other reasonable treatment alternatives.

Among other criteria, they stress the need to collect data on the health risks and benefits and to maintain continuous oversight during clinical trials. They also recommend that, after a trial concludes, trial organizers should follow up with the participants’ families for multiple generations to see what changes persist in the genome over time.

Source: By Aparna Vidyasagar, Nicoletta Lanese – Live Science

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