BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Gene-editing

The Miracle of CRISPR/Cas9 in Gene Editing

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On April 5, 2017

In Student Post

Some scientists say, “you can do anything with CRISPR” and others are absolutely astonished and amazed.

CRISPR can rapidly change any gene in any animal or plant with ease. It can fix genetic diseases, fight viruses, sterilize mosquitos and prepare organs for transplant. The possibilities are endless – and the prospect of designer babies isn’t far off.

https://en.wikipedia.org/wiki/CRISPR#/media/File:Crispr.png

Dead Cas9 can fix a single base pair typo in DNA’s genetic instructions. It can convert a C-G into a T-A pair. Also, we can attach fluorescent tags to dead Cas9 so researchers can locate and observe DNA or RNA in a living cell. Dead Cas9 can also block RNA Polymerase from turning on a gene, in CRISPRi. In CRISPRa, a protein that turns on genes is fused to dead Cas9.

CRISPR can be used for anything involving cutting DNA. It guides molecular scissors (Cas9 enzyme) to a target section of DNA & works to disable or repair a gene, or insert something new.

Many scientists have been thinking of improvements for this miracle gene editor. RNA Biologist Gene Yeo compares the original Cas9 to a Swiss army knife with only one application – a knife. He says that by bolting other proteins and chemicals to the blade, they transformed the knife into a multifunctional tools.

CRISPR/Cas9 is special because of its precision. It is much easier to manipulate and use compared to other enzymes that cut DNA. By using “guide RNA” it can home in on any place selected by the researcher by chemically pairing with DNA bases.

While Cas9 does have some problems, scientists definitely see the potential for greatness with a few tweaks. They wanted to ensure permanent single base pair changes, and they increased that from 15 to 75 percent. Liu used a hitchhiking enzyme called cytidine deaminase.

Scientists researched chemical tags on DNA called epigenetic marks. When scientists placed the epigenetic marks on some genes, activity shot up. This provided evidence that the mark boosts gene activity.

Case can also revolutionize RNA biology. The homing ability of CRISPR/Cas9 is what makes this seem possible. It was found that Cas9 could latch on to mRNA.

CRISPR/Cas9 was first found in bacteria as a basic immune system for fighting viruses. It zeroes in on and shreds the viral DNA. Half of bacteria have CRISPR immune systems, using enzymes beyond Cas9.

Overall scientists predict that in the next few years, results will be amazing. The many ways of using CRISPR will continue to multiply and we will see where science takes us.

Source: https://www.sciencenews.org/article/crispr-inspires-new-tricks-edit-genes

Other Sources: https://www.neb.com/tools-and-resources/feature-articles/crispr-cas9-and-targeted-genome-editing-a-new-era-in-molecular-biology

Anti-CRISPR Proteins: What are they and can they be beneficial?

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On April 5, 2017

In Student Post

NIH Image Gallery Image Link

Understanding CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

For many bacteria, one line of defense against viral infection is the RNA guided “immune system” known as CRISPR-Cas. This particular complex is unique because of its ability to recognize viral DNA and trigger its destruction. Scientists have used CRISPR to degrade sections of viral RNA and use the CRISPR systems to remove unwanted genes from an organism. CRISPR proteins have also been studied with the hope of eliminating serious disease and illnesses. However, this CRISPR system does not always work do to anti-CRSPR proteins that inhibit the complex from working properly.

Research 

According to an article on ScienceDaily, researchers have finally discovered how these anti-CRISPR proteins work! Research done by biologist Gabriel C. Lander from the Scripps Research Institute, discovered that anti-CRISPR proteins work by inhibiting CRISPR’s ability to identify and attack viral genomes. Just like there are different CRISPR systems, there are multiple anti-CRISPR proteins as well. One in particular mimics DNA to throw the CRISPR-guided detection machine off its course. Scientists have been able to further discover certain aspects of CRISPR and anti-CRISPR systems by using a high-resolution imaging technique called cryo-electron microscopy. They have discovered that the CRISPR surveillance complex analyzes a virus’s genetic material to see where it should attack by having proteins within the complex wrap around the CRISPR RNA, exposing specific sections of bacterial RNA. These sections of RNA then scan viral DNA, looking for genetic sequences they recognize. Lander describes these proteins as being very clever because they “have evolved to target a crucial piece of the CRISPR machinery. If bacteria were to mutate this machinery to avoid viral attacks, the CRISPR system would cease to function.” Therefore, CRISPR systems cannot avoid anti-CRISPR proteins without completely chancing the mechanism used to recognize DNA. Another type anti-CRISPR protein works a bit differently. Based on its location and negative charge, this anti-CRISPR protein acts as a DNA mimic, fooling CRISPR into binding this immobilizing protein, rather than an invading viral DNA.

Can Anti-CRISPR Proteins be beneficial?

Researchers are saying that the understanding of how these anti-CRISPR proteins work are extremely important! According to an article on GEN, the discovery and understanding of anti-CRISPR proteins actually allows researchers to have greater control over gene-edits. In this article, Dr. Sontheimer, a professor in the RNA The RNA Therapeutics Institute at UMass Medical School, expressed how “CRISPR/Cas 9 is a good thing because it introduces specific chromosome breaks that can be exploited to create genome edits, but because chromosome breakage can be hazardous, it is possible to have too much of a good thing, or to have it go on for too long.” Anti-CRISPR proteins can be beneficial and work as an off switch for CRISPR, therefore advancing gene editing!

 

 

 

The Grey Area of Human Gene Editing

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On March 1, 2017

In Student Post

The process of Human Gene Editing developed with the goal to prevent future generations from suffering from genetic diseases present in past generations, like our own. Human gene editing, provided it is done only to the correct disease, alters the DNA in embryos, eggs, and sperm to the when reproduction occurs, the gene for the disease or disability is not inherited. However, two weeks ago the National Academies of Sciences and Medicine issued a report stating that human gene editing is being used to enhance people’s health or abilities. This is considered unethical according to organizers of a Global Summit on human gene editing.

Human gene editing has been given a “yellow light” because the process is not yet approved to be done on people. There are high hopes that diseases caused by only 1 genetic mutation such cystic fibrosis and Huntington’s disease will be eliminated due to this process. Unfortunately diseases that are caused by more than one genetic mutation, such as autism or schizophrenia, are not curable by this process.

National Cancer Institute

Gene Editing on humans is such a controversial topic right now: is it ethical to change genes? should the practice be used to change physical appearances? Ultimately, if Human Gene Editing is approves, who decides when it becomes too much, or unethical. This grey area is presented to be somewhere between when it is appropriate to help aid the life of a human, ridding them of a disease, and when enhancements are made.

 

More CRISPR Improvements

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On May 1, 2016

In Student Post

Crispr-Cas9 is a genome editing tool that is creating a whole lot of buzz in the science world. It is the newest faster, cheaper and more accurate way of editing DNA.  Crispr- Cas9 also has a wide range of potential applications. It is a unique technology that enables geneticists and medical researchers to edit parts of the genome by cutting out, replacing or adding parts to the DNA sequence.  The CRISPR-Cas9 system consists of two key molecules that introduce a mutation into the DNA. The first Molecule is an enzyme called Cas9. Cas9 acts as a pair of scissors that can cut the two strands of DNA at a specific location in the genome so that bits of DNA can be added or removed.  The second is a piece of RNA called guide RNA or gRNA. This consists of a small piece of pre-designed RNA sequence located within a longer RNA scaffold. The scaffold part binds to DNA and the pre-designed sequence guides Cas9 to the right part of the genome. This makes sure that the Cas9 enzyme cuts at the right point in the genome.Screen Shot 2016-04-10 at 4.50.55 PM

CRISPR-Cas9 is efficient compared to previous gene-editing techniques, but there’s still plenty of room for improvement. CRISPR is less efficient when employing the cellular process of homology-directed DNA repair, or HDR, as opposed to nonhomologous end joining.  Jacob Corn, the scientific director of the Innovative Genomics Initiative at the University of California, Berkeley, and his colleagues have come up with a way to improve the success rate of homology-directed repair following CRISPR-Cas9. “We have found that Cas9-mediated HDR frequencies can be increased by rationally designing the orientation, polarity and length of the donor ssDNA to match the properties of the Cas9-DNA complex,” the researchers wrote in their paper, “We also found that these donor designs, when paired with tiled catalytically inactive dCas9 molecules, can stimulate HDR to approximately 1%, almost 50-fold greater than donor alone.”

“Our data indicate that Cas9 breaks could be different at a molecular level from breaks generated by other targeted nucleases, such as TALENS and zinc-finger nucleases, which suggests that strategies like the ones we are using can give you more efficient repair of Cas9 breaks,” coauthor Christopher Richardson, a postdoc in Corn’s lab, said in a statement.

Original Article:

http://www.the-scientist.com/?articles.view/articleNo/45159/title/More-CRISPR-Improvements/

Other Addtional Helpful Links:

http://www.yourgenome.org/facts/what-is-crispr-cas9

 

Should We Use It: Crispr-Cas 9 Edition

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On April 13, 2016

In Student Post

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https://www.youtube.com/watch?v=7C20s4eAGtU

Arguably the greatest thing to happen to genetics since the Human Genome Project, Crispr-Cas 9 has been getting a lot of attention.  The Los Angeles Times wrote an article approximately 4 months ago discussing the ins and outs of the new gene editing breakthrough.  The concept of editing genes is nothing new for scientists.  They’ve been doing it since the 1970s.  So many people are asking “What makes Crispr so special?”  The answer is convenience.  Crispr-Cas 9, although still filled with flaws, is the easiest gene editing tool to use out there right now.  Scientists from UC Irvine and UC San Diego have used it on mosquitoes to fight malaria and scientists have begun to use it on human embryos as well.  Crispr is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats which is a relatively complicated way of saying “gene editing tool.”  What Crispr does is it can target certain parts of a strand of DNA and “delete” them from the strand.  In reality they aren’t being “deleted” but “turned off” so RNA doesn’t code it and begin to manufacture proteins for it.  But the real question is why certain people are against gene editing.  Everyone’s seen the movie GATTACA where gene editing is not only commonplace, but discriminatory.  However in today’s world, the fear is much more strongly rooted than a fear of “geneticism” (genetic rascism).  Using Crispr on viable human embryos to edit genes may have undesired effects.  The turning off/on of one gene could result in the unintentional turning on/off of another.  Also, many scientists believe that a parent making decisions for an unborn child can be unethical and unfair if the child did not want those changes to be made.  And who knows, maybe in the future with the continuous use of Crispr and the development of more complex gene editing tools, “geneticism” could be a reality.

Other articles pertaining to Crispr are linked here and here for more information on the subject.

The New and Improved CRISPR-Cas9

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On April 13, 2016

In Student Post

The CRISPR-Cas9 genome editing system has transformed into an even better version of itself. A new, elegant technique, coined by researches at the Broad Institute of MIT and Harvard and the McGovern Institute for Brain Research at MIT, has resolved one of the most reoccurring technical issues in genome editing.

https://commons.wikimedia.org/wiki/File:Crystal_Structure_of_Cas9_in_Complex_with_Guide_RNA_and_Target_DNA.jpg

Primarily, the CRISPR-Cas9 system works to specifically modify a cell’s DNA. CRISPR is dependent on protein Cas9, as it is specialized for cutting DNA. The DNA, at a location identified by a RNA’s sequence matching the target site, is altered by Cas9. Though it very efficient at cutting its target sites, there is a large complication in the process. Once the Cas9 is inside the cell, it can also bind and cut additional sites that are not targeted. Because of this, undesired edits are produced which can alter gene expression or kill off a gene completely. These setbacks can lead to cancer or other problems. Feng Zhang, along with his colleagues at MIT, reported that by just changing 3 out of the approximately 1,400 amino acids composing the Cas9 enzyme from S. pyogenes, a considerable reduction of “off-target editing” to undetectable levels are observed.

This newfound information was derived from studying the structure of the Cas9 protein. Since DNA is negatively charged, it binds to a positively charged groove in the Cas9 protein. The scientists predicted that by replacing some of the positively charged amino acids with a neutral charge, there would be a decrease in binding to “off target” sequences than to “on target” sequences. By mutating three amino acids, their technique proved to be successful.

The team is calling this newly-engineered enzyme “enhanced S. pyogenes Cas9” or “eSpCas9.” It’ll be particularly useful for genome editing that requires precise specificity and it is said to be available for researches worldwide.

I believe that this newfound resolution for the CRISPR-Cas9 genome editing hurtle is a huge game changer. This charge-changing approach might also be able to be used for other experiments involving RNA-guided DNA targeting enzymes. Ethical and societal concerns have also risen due to the idea of rapid and efficient genome editing. The eSpCas9 is highly beneficial in the scientific community, however there is a lot more research needed to be done in order to be used clinically.

 

Original article can be found here.

CRISPR: Is Science Going Too Far?

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On April 13, 2016

In Student Post

CRISPR is a some-what new genetic tool in the field of science to edit human embryos. Using CRISPR, scientists can edit the genes of organisms more precisely than ever before. It uses RNA and an enzyme that slices up invading virusesF. One use of this new technology is to fix mutations that cause genetic diseases.

Crispr

https://en.wikipedia.org/wiki/CRISPR

Ethical concerns arose in April of 2015 when Chinese research used CRISPR to edit nonviable human embryos. In addition, some fear that the use of CRISPR to give the embryo traits not found in their genetic code can lead to a obsessive gene culture like the one found in Gattaca. This ethical debates caused scientists to meet at an international summit hosted by the United States National Academies of Sciences and Medicines, where the scientists discussed the ethical concerns of CRISPR but agreed to continue researching it cautiously.

In addition, some argue that using CRISPR for gene editing defeats the sacredness of the human genome and is unnatural. To this point, Sarah Chan from the EuroStemCell argues, “There is nothing sacred or sacrosanct about the genome as such. The human genome – the genome of humanity as a whole, and the unique individual genome we each possess – is merely the product of our evolutionary history to date”. From this point of view, the genome is merely a record of one’s history, but to some religious groups it is a symbol of life which should not be tainted with.

So readers, what do you think? Should we use this tool to help cure treatable diseases, or does this new technology cross the line between scientific mechanisms and morality? What type of genes should this new tool be allowed to edit?

 

Other sources

https://www.sciencenews.org/article/year-review-breakthrough-gene-editor-sparks-ethics-debate

http://www.sciencemag.org/news/2016/04/crispr-debate-fueled-publication-second-human-embryo-editing-paper

http://www.wired.com/2015/12/stop-dancing-around-real-ethical-problem-crispr/

http://www.eurostemcell.org/commentanalysis/ethics-changing-genes-embryo

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