CRISPR Cas9 A-Z



Pharma IQ
03/14/2017

The CRISPR tool has attracted worldwide attention from the R&D industry in regards to its capabilities for gene editing.

CRISPR alongside the use of the Cas9 protein enables the ability to target a specific section of a gene sequence and edit it – by deleting and sometimes replacing the function with a new element. 

Pharma IQ presents this A-Z of one of the market's most affordable gene editing technique. 

Activating gene expression 

This is the process in which genetic information is transferred into a useful gene product. CRISPR cas 9 has been used in various studies to perform gene activation. 

B

Battles (Patent)

Over the last few years, a patent ownership battle between University of California and Broad Institute of MIT and Harvard has been taking place to decide who governs the IP concerning CRISPR.

C

Cas9 

An RNA guided nuclease that is attached to the CRISPR technique. This protein causes the double strand break to effectively cut the DNA. 

E

Ethical minefield

The topic of CRISPR gene editing has encountered an array of ethical concerns including those regarding off target mutations from the technique which could lead to death. Also, the possibility of the technique being used for non medicinal purposes for example for genetic enhancement has fuelled debate. Work has been laid for clinical trials to be run concerning cancer treatments in human embryos. 

D

Docking system  (cas9 ) 

The process of identifying an apt binding area for a target protein. 2

F

FINGERs ( Zinc) 

Zinc Finger Nucleases are DNA binders that enable gene editing through double strand breaks. CRISPR Cas9 is deemed as more efficient in targeting than this technique.

G

Genome Editing - Phenotypes

Gene editing is the process of altering the expression behaviour of a gene. 

H
Homology directed repair

This is a repair progress which is naturally occurring for nucleic acids that can assist with genome modification. 

I

Induced Pluripotent Stem Cells (IPSCs)

In 2016, CRISPR was used to edit genes in IPSCs – these are skin cells that can be reverted into pluripotent stem cells that can then be turned into almost any cell.

J

Dr. Jennifer Doudna

Dr.Doudna of UC Berkeley has been at the front of CRISPR Cas 9’s progression publishing groundbreaking findings in regards to the technique’s application. 

K

Knockout 

The process of removing the bit of DNA that is causing a certain phenotype activity. 

L

Light controlled genome editing

MIT researchers managed to develop the gene editing technique so that it is responsive to light. For example editing only occurs with target cells in the presence of ultraviolet light. 

M

Mutations / mutagenesis

The process of transforming an organism’s genetic information. 

N

Neurodegeneration

CRISPR has seen positive traction within the study of neurodegenerative conditions such as Alzheimer’s, Huntingdon’s  and Parkinson’s disease. 

O

Off target effects 

As genomes are large in size with multiple binding sites for Cas 9, it is an often occurrence that the protein can miss the target and cut the wrong part of the DNA. 

P

Parasites

CRISPR is being applied to advance a range of biotechnologies including those in plants, livestock to improve food production and in insects to halt the spread of parasites.

R

RNA guided 

Synthetic RNA which is tailored for Cas9 binding and coding to identify the target genome that needs to be modified. 8 

S

Strand break 

Pathway recovery post double strand break.

T

TALENS

Transcriptor Activator like Effector Nuclease- enzymes that can cut specific DNA. CRISPR Cas9 is also deemed as more efficient in targeting than this technique.

U

US Panel 

U.S. Patent and Trademark Office in early 2017 reached a ruling in the ownership dispute between Broad Institute of MIT and Harvard and the University of California, Berkeley (UC). The decision deemed that the patents granted to the Broad institute of MIT and Harvard regarding the application of CRISPR to eukaryotic genomes do not interfere with claims of UC Berkeley. Through this, a way was cleared for UC Berkeley regarding the general use of the technique in any type of cell ( outside of eukaryotic cells). 9, 10

V
Vivo/vitro / vectors 

In vivo- testing that is conducted in an organism ( cell/body) 

X

X files 

In vitro – testing that is conducted in a culture container. 

The plot of its recent series finale featured the use of CRISPR-Cas 9. 

Y

Yang 

Sheng Yang and Junjie Yang recently assisted in a paper looking at multi gene editing with CRISPR Cas9 in the Escherichia coli genome. The project found a few strategies to counter off target occurrences.

Z

Dr Feng Zhang

The Zhang lab has also been instrumental to the progression of the CRISPR technique. Dr Feng Zhang is a core member of the Broad Institute and MIT. The CRISPR patents he has acquired are assigned jointly to the Institute and MIT. 

Resources 

1. https://www.omicsonline.org/open-access/ethical-issues-in-genome-editing-using-crisprcas9-system-2155-9627-1000266.php?aid=70914 

2. https://books.google.ie/books?id=_kV0AgAAQBAJ&pg=PA261&lpg=PA261&dq=Genomics+docking+site+definition&source=bl&ots=ZYhp7o2Cci&sig=M9_vIakMSKNIlkNi23EmQm48uxI&hl=en&sa=X&ved=0ahUKEwjLhJmp78bSAhWnCsAKHR0EBjUQ6AEIOTAF#v=onepage&q=Genomics%20docking%20site%20definition&f=false 

3. http://www.cell.com/biophysj/abstract/S0006-3495(14)00938-2?cc=y= 

4. http://www.sigmaaldrich.com/life-science/zinc-finger-nuclease-technology/learning-center/what-is-zfn.html 

5. http://www.the-scientist.com/?articles.view/articleNo/46810/title/Using-CRISPR-to-Edit-Genes-in-Induced-Pluripotent-Stem-Cells/ 

6. https://sites.tufts.edu/crispr/genome-editing/homology-directed-repair/ 

7. http://news.mit.edu/2016/using-light-control-genome-editing-0825 

8. https://www.addgene.org/crispr/guide/ 

9. http://www.xconomy.com/boston/2017/02/15/patent-judges-crispr-ruling-for-broad-leaves-daylight-for-berkeley/ 

10. http://news.berkeley.edu/2017/02/15/patent-office-determines-uc-broad-institute-patent-claims-on-crispr-cas9-genome-editing-are-separately-patentable/

11. https://www.broadinstitute.org/crispr/journalists-statement-and-background-crispr-patent-interfer