The Triple Helix @ UChicago

Fall 2016

"CRISPR" by Jasmine Barnard


The scientific community is abuzz with the discovery and new use of CRISPR, a gene editing technique derived from an ancient prokaryotic anti-viral defense mechanism. CRISPR stands for ‘clustered regularly interspersed short palindromic repeats.’ Lets unpack that a bit. In the 1980’s researchers who were studying bacteria genomes noticed short lengths of DNA that repeated themselves over and over again, with “junk” DNA separating each repeat. These sequences were concentrated in several clusters throughout the genome, and seemed to have no purpose except to perplex scientists. Turns out, these regularly interspersed repeats were not a merely a fun byproduct of evolution run amok, but a part of an anti-virus defense system. 

In bacteria, this system consists of CRISPR sequences paired with Cas (CRISPR associated) proteins, a subset of proteins which form different complexes within the cell that perform various different functions in the CRISPR/Cas defense system. Cas enzymes can cleave invading viruses, Cas transcription complexes help transcribe sections of CRISPR in the bacteria’s genome, and Cas nuclease complexes recognize old viruses and dismantle them with the aid of guiding bits of CRISPR sequences. This process is triggered when a new bacteriophage (virus that infects bacteria) enters a cell, and is met by a Cas I complex, which cleaves the virus and removes bits of its nucleotides and inserts them into the bacterium’s genome as a “spacer”, or the junk DNA that separates CRISPR repeats. This spacer is then transcribed the next time the CRISPR length of DNA is transcribed by a Cas II complex, and the spacers are processed into crRNA bits, or lengths of RNA that can recognize its anti-parallel sequence in the original virus (all DNA and some RNA is double stranded, the anti-parallel strand is the opposite strand whose nucleotides match up perfectly with the first strand). These crRNA bits are incorporated into a Cas III complex. The crRNA bits guide the Cas III complex to the corresponding bacteriophage, where the complex then proceeds to chop up the offending virus into harmless bits. Essentially, the CRISPR sequences sit back and guide the Cas proteins in doing all the hard work. It may be helpful to think of CRISPR/Cas complexes as memory B cells in the human immune system. They both recognize old pathogens that they have come into contact with before, and work to destroy them before they can do any repeat damage. Cas proteins are like hit men, while CRISPR sequences in the DNA is the hit list. 

The reason the discovery and understanding of this mechanism is so exciting (besides the fact that hitmen proteins floating around a cell is cool in itself) is that homologous systems can be set up and utilized in mouse and human cells. A simplified version of this system has already been used in various research projects in order to remove or insert genes from target cells. This system consists of a human engineered CRISPR/Cas9 complex. Cas9 is a specific Cas protein from the bacteria Streptococcus pyogenes, a species you will be familiar with if you’ve ever had strep throat. Cas9 is a protein complex of endonuclease enzymes (nucleotide cutters) that is guided by bits of CRISPR sequences. Researchers can design a CRISPR/Cas9 complex to make nicks in DNA in order to insert synthetic DNA with the properties of their choosing, or completely remove preexisting lengths of DNA. This is particularly useful for gene knock-out experiments when studying genomes. 

The medical possibilities include developing therapies or preventative treatments against viral infections such as HIV, and possible genome editing that could cure genetic disorders. However, the implications can be frightening. This could be a step closer to human genetic enhancement, which brings with it a host of problems of inequality of access, moral issues that have to do with consent and unforeseen consequences, and humane use on both humans and animals. With every new scientific development comes new ethical quandaries that must be addressed, and the CRISPR/Cas9 complex is no different. 


[1] Barrangou, Rodolphe, Christophe Fremaux, and Hélène Deveau Deveau. "CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes." Science. AAAS, 23 Mar. 2007. Web. 
[2] Cong, Le, F. Ann Ran, and David Cox. "Multiplex Genome Engineering Using CRISPR/Cas Systems." Science. AAAS, 15 Feb. 2013. Web. 
[3] Doudna, Jennifer A., and Emmanuelle Charpentier. Science. AAAS, 28 Nov. 2014. Web. 
[4] Zhang, Sarah. "Everything You Need to Know About CRISPR, the New Tool That Edits DNA." Gizmodo. N.p., 06 May 2015. Web.

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