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An Introduction to CRISPR Genome Engineering

Updated: Apr 3, 2023

DNA represents the fundamental molecular basis of life, providing the instructions for the development and functioning of nearly all living organisms. The discovery of DNA in the 1860s marked a seminal moment in the field of genetics and biology, and since then, extensive research efforts have been devoted to comprehending the intricacies of its structure and function. Despite the extensive work conducted over the past century and a half, manipulating DNA was considered a formidable challenge. Nevertheless, in the last two decades, innovative molecular tools, like CRISPR genetic engineering, have opened up new avenues for research and have enabled us the unprecedented ability to rewrite life itself.

Genome Engineering in A Nutshell

Genetic engineering is the process by which scientists can delete, add, or modify DNA sequences. Scientists use programmable DNA nucleases, like CRISPR, Zinc Finger Nucleases (ZFN), or TALENs, sometimes referred to as "molecular scissors," to rewrite DNA. Though, there are limitations to the types and extent of "rewriting" one can do, programmable DNA nucleases are revolutionizing the face of modern medicine, agriculture, diagnostics, forensics, space exploration, and more. It’s no wonder that Dr. Jennifer Doudna, UC Berkeley, and Dr. Emmanuelle Charpentier, Max Plank Institute, were awarded the Nobel Prize in Chemistry in 2020 for their work with CRISPR genome engineering.

Watch the video of our founder, Dr. Kris, below to learn some ways that CRISPR is being applied to change the world:

Where did CRISPR come from?

Though genome engineering isn’t a new field, it has recently become much more efficient and user-friendly with the discovery of CRISPR. Today, we use the word CRISPR to define the genome engineering technology as a whole. However, when it was first discovered in the 1980s, it was simply a puzzling repetitive sequence found in bacteria. The discovery of these repetitive sequences was made by Yoshizumi Ishino and later Francisco Mojica who coined the term CRISPR to stand for Clustered Regularly Interspaced Short Palindromic Repeats; quite literally a descriptor of how these odd sequences looked in bacteria.

It was not until decades later that Emmanuelle Charpentier who, along with her team of researchers, uncovered the purpose of these repetitive bacterial sequences. If scientists really shout "Eureka!" when they make a discovery, this moment would be one of the worthy ones. Charpentier and her team identified a key component to the functioning of the CRISPR system in bacteria, the guide RNA (gRNA). Surprisingly, the gRNA sequences were startlingly similar to bacteriophage genomes (bacteriophage = viruses that infect and kill bacteria).

Now, why would bacteria keep sequences of their invaders in their genome?

That was the million dollar question. With more work and in collaboration with Dr. Jennifer Doudna, the scientists continued to isolate the components of the CRISPR system and demonstrated that its purpose was to act as the bacterial immune system protecting the bacteria from invasion by pathogens.

Here's how the CRISPR systems works in bacteria to protect against invaders:

First, the bacterium detects the viral invader and subsequently activates the CRISPR system. The bacterium begins producing specific proteins called Cas proteins alongside an array of gRNAs. The Cas protein combines with a gRNA to form the Cas/gRNA complex which is able to detect the viral invader (using the gRNA) and cut the foreign DNA (using the Cas protein). Thus, the viral invader is rendered defunct by the bacterium's CRISPR system.

Figure 1. The main stages of CRISPR defense against invasion of a bacteriophage. [2]

Then, in 2012, the laboratories of Jennifer Doudna and Emanuelle Charpentier demonstrated that it was possible to repurpose the CRISPR system for gene editing and that same year Dr. Feng Zhang (MIT) and colleagues showed its utility in engineering the genomes of mammalian cells.

How does CRISPR genome engineering work?

To understand how CRISPR works, it’s important to grasp the basics of DNA and genes. The genetic code of nearly every organism on Earth is stored in DNA, which contains all the information needed to build and sustain life. Every organism—from plants to insects to humans—has a unique DNA code containing the instructions needed to build proteins. These proteins are what give each organism its unique traits and abilities, and proteins are essential for all forms of life. For example, proteins encoded in human DNA give us our ability to build strong bones, heal wounds, and lift heavy objects. In its most basic form, CRISPR is akin to molecular scissors that can cut DNA sequences, allowing scientists to remove, add, or modify specific sections of genetic code and thereby alter the function of proteins.

Let's get a little more technical

Gene editing works when you combine programmable DNA nucleases, like CRISPR/Cas9, with DNA repair. DNA repair processes are specific systems built into our cells that have evolved to maintain the fidelity of our genome. Their role is essential to prevent mutations from accumulating in our bodies over time due to sun exposure and other potential DNA mutagens. For example, high energy radiation from the sun leads DNA in our skin cells to break, also called a double-stranded DNA break (DSB). When a DSB forms, specific enzymes are recruited to the DNA break and lead to the activation of different DSB repair pathways. It is these repair pathways that can result in DNA deletions, additions, or modifications and therefore it is these pathways that must be activated to accomplish gene editing. While the sun or other mutagens create DNA breaks in the genome at random locations, programmable DNA nucleases, like CRISPR/Cas9, allow us instead to stimulate DNA repair at predetermined locations due to our ability site specifically induce DSBs. As a result, by using programmable DNA nucleases, we can direct where DNA repair occurs in the genome and therefore accomplish targeted genome editing.

3 lesser known ways CRISPR is changing the world

1) Catch criminals Scientists at the NIH use CRISPR to enrich DNA samples for specific regions called STRs (Short Tandem Repeats) which are highly variable between individuals. As a result, we can more easily identify the individuals who leave their DNA at crime scenes. ​

2) Fight climate change Scientists at Synthetic Genomics (Exxon Mobil) use CRISPR to develop algae for improved lipid production - the main component to biofuels. This may reduce our reliance on fossil fuels!

3) Explore space Astronauts successfully demonstrate DNA repair in space using CRISPR technology! The work could help us improve our capabilities for long-duration space travel. Trip to Mars anyone?

There has never been a better time to work in CRISPR Genome Engineering

CRISPR/Cas technology has ushered in a new era of genome engineering and molecular biology. It has become a crucial tool in basic and applied research for exploring new biological functions, improving disease models, developing novel therapeutics, and creating more accurate diagnostic tools. CRISPR/Cas has also entered the field of precision medicine, with successful use in human clinical trials in recent years. The growing number of CRISPR-based biotechs attests to the technology's immense potential, highlighting the increasing need for individuals with expertise in CRISPR/Cas and gene-editing technology. For those passionate about this field, now is an ideal time to deepen knowledge and develop unique skills that will be in high demand and contribute to advancing the fields of biology and precision medicine.



Kristina Tatiossian, PhD


CRISPR Classroom is disrupting STEM education and bringing learners closer to frontier scientific knowledge than previously possible. CRISPR Classroom, a new education technology start-up company, is the first-of-its-kind to use engaging storytelling to teach revolutionary innovations and make it digestible to the masses. Thanks to their high-impact content created in collaboration between scientists and veteran educators, CRISPR Classroom's courses are among the fastest growing biology training programs with rapid global adoption from learners from over 50 different countries. CRISPR Classroom is the merging of STEM innovation and education to create a well-oiled science education company that brings its users closer to frontier knowledge than ever before.

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