Scientists crack the CRISPR code for precise human genome editing

Scientists crack the CRISPR code for precise human genome editing
Illustration of the CRISPR/Cas9 genome editing system. Credit: Nigel Hawtin for the Francis Crick Institute

Scientists at the Francis Crick Institute have discovered a set of simple rules that determine the precision of CRISPR/Cas9 genome editing in human cells. These rules, published in Molecular Cell, could help to improve the efficiency and safety of genome editing in both the lab and the clinic.

Despite the wide use of the CRISPR system, rational application of the technology has been hindered by the assumption that the outcome of genome editing is unpredictable, resulting in random deletions or insertions of DNA regions at the target site.

Before CRISPR can be safely applied in the clinic, scientists need to make sure that they can reliably predict precisely how DNA will be modified.

"Until now, editing with CRISPR has involved a lot of guesswork, frustration and trial and error," says Crick group leader Paola Scaffidi, who led the study. "The effects of CRISPR were thought to be unpredictable and seemingly random, but by analysing hundreds of edits we were shocked to find that there are actually simple, predictable patterns behind it all. This will fundamentally change the way we use CRISPR, allowing us to study gene function with greater precision and significantly accelerating our science."

By examining the effects of CRISPR genome editing at 1491 target sites across 450 genes in , the team have discovered that the outcomes can be predicted based on simple rules. These rules mainly depend on one genetic 'letter' occupying a particular position in the region recognized by the 'guide RNA' to direct the molecular scissors, Cas9 .

Guide RNAs are synthetic molecules made up of around 20 genetic letters (A,T,C,G), designed to bind to a specific section of DNA in the target gene. Each genetic letter has a complementary partner—A binds to T and C binds to G—which stick together a bit like Velcro. The guide RNA is like the 'hook' side of Velcro, designed to stick to the 'loop' side on the target gene.

Guided by the RNA molecule, the Cas-9 enzyme scans along the genome until it finds the region of interest. When the RNA guide matches the correct DNA sequence, it sticks like Velcro and Cas9 cuts through the DNA. The DNA is broken three letters from the end of the target sequence, and bits of genetic code are then inserted or deleted, seemingly haphazardly, when the cell attempts to repair the break.

In this study, the researchers found that the outcome of a particular gene edit depends on the fourth letter from the end of the RNA guide, adjacent to the cutting site. The team discovered that if this letter is an A or a T, there will be a very precise genetic insertion; a C will lead to a relatively precise deletion and a G will lead to many imprecise deletions. Thus, simply avoiding sites containing a G makes genome editing much more predictable.

"We were amazed to discover that the rules that determine the outcome of CRISPR human genome editing are so simple," says Dr. Anob Chakrabarti, Wellcome Trust clinical Ph.D. fellow in the Crick's Bioinformatics and Computational Biology lab and joint-first author of the study. "By bearing these rules in mind when designing our guide RNAs, we can maximise the chances of getting the desired outcome of a specific gene edit—which is particularly important in a clinical context."

The team also discovered that how 'open' or 'closed' the target DNA is also affects the outcome of gene editing. Adding compounds that force DNA to open up—allowing Cas9 to scan the genome—led to more efficient editing, which could help when modifications need to be introduced in particularly closed genes.

"The good news is that regardless of the tissue of origin—which influences the degree of DNA 'openness' at specific genes—target regions containing an A or T at the key position show common editing," says Paola. "This means that, if we carefully select the target DNA, we can be pretty confident that we'll see the same effect in different tissues."

Josep Monserrat, Crick Ph.D. student in the Cancer Epigenetics lab and joint-first author of the study, says: "We hadn't previously appreciated the significance of DNA openness in determining the efficiency of CRISPR editing. This could be another factor to consider when aiming to edit a gene in a specific way. We are excited to observe that distinct cell types share common editing at precise target regions, and hope translation of our findings will be beneficial across disciplines."


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Largest study of CRISPR-Cas9 mutations creates prediction tool for gene editing

More information: Molecular Cell (2018). DOI: 10.1016/j.molcel.2018.11.031
Journal information: Molecular Cell

Citation: Scientists crack the CRISPR code for precise human genome editing (2018, December 13) retrieved 23 April 2019 from https://phys.org/news/2018-12-scientists-crispr-code-precise-human.html
This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.
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Dec 13, 2018
Forward, forward with our plan.......

Once the Republican Gene can be identified, the Republican race can be eradicated.

Dec 13, 2018
If so, Can you change 1 Dog Breed Progeny into Different type in the Future ?
It is only then can laymen trust it (I am saying Laymen).

Dec 13, 2018
Forward, forward with our plan.......

Once the Republican Gene can be identified, the Republican race can be eradicated.

Unnecessary. A III-Party Creation would do that.

Dec 13, 2018
This comment has been removed by a moderator.

Dec 13, 2018
Can you Find out with Gene Editing, Why ALL Birds shove their Eggs underneath their Belly ?
Try Sequential Gene Deletion to discover it.
https://www.youtu...xfu_sL1M

Dec 13, 2018
Forward, forward with our plan.......

Once the Republican Gene can be identified, the Republican race can be eradicated.

"We don't need the fetal body parts from babies to achieve scientific and medical achievements because we have alternatives that can do it," Rep. Jim Jordan said.
https://www.polit...-1029635

Dec 13, 2018
Used to take a bunch of big expensive experiments to do stuff like this.

Now you can do it in your basement.

This is scary. But predictable. We can no longer afford nutjobs. It's time to start figuring out how to fix this unless you like horror stories. As if a mass shooting every week wasn't one.

Dec 14, 2018
As if a mass shooting every week wasn't one.


That's the price of the thoroughly corrupt Republican Party's political and financial support from the NRA. They will tell you it is the price of the 2nd Amendment. Of course if you are stupid enough to believe this is about the 2nd amendment, and not the money, you probably also believe every mass shooter and scumbag murderer are exactly what the Founding Fathers were hoping to protect when they wrote the 2nd Amendment to protect "a well-regulated militia."

Dec 14, 2018
My interpretation of the 2nd Amndnt is based on actually reading the entire two paragraphs.
Then putting it into context with the FF's original intentions. But then I have actually read the Federalist & Anti-Federalist Papers & James Madison's Notes.
The 2nd is specifically to allow the individual States of the Union, the right to muster, arm, train & maintain organized Militia under State Command.
This was already obsolete by the time of the War of Northern Aggression. As well as a slew of other amendments that have become obsolete by the Centennial.
Instead of simply scrapping the old bird? Replacing it with a document that covers the issues important to this century & the next? We, The People, keep pretending the earlier versions of the US Constitution still have any relevance for modern life.

Oh & Mark, that is not the NRA's money slipped to the GOP. The NRA is as effectively bankrupt of funds as of morals.
All that money is surreptitious Russian & Saudi funding.

Dec 14, 2018
A well regulated militia being necessary to the security of a free state, the right of the people to keep and bear arms shall not be infringed.


Your interpretation is at least plausible.

It says right there "[a] well regulated militia" and "being necessary to the security of a free state." I don't see how arming every idiot age 18 and older is going to accomplish that objective and in fact, it is clearly counterproductive to "the security of a free state." How are little to no regulations supposed to be the same as well-regulated? This can't be what the FF intended. About the surreptitious Russian & Saudi funding, it sounds like a crazy conspiracy theory, but I have to wonder what Maria Butina would think.

"Maria Butina, the cofounder of the mysterious Russian gun-rights group called 'Right to Bear Arms' . . . "'took steps to develop relationships with American politicians.'"

https://www.gq.co...rvatives

Dec 14, 2018
Yes, the FF's intended that each State was Sovereign within an all inclusive Federal structure. The Governors would reward political supporters with appointments as militia officers for each District & Unit.

Then, during the Civil War, many of the appointee's, at best, were disappointing. Especially when they were commanding against Academy graduates or at least not total wash-outs.

Which, to an nonredeemable cynic such as myself? Is why it is so damn hilarious when the self-righteous bombast of their patriotism & moral zeal.

Don't know if you've noticed but "A Great Silence" has fallen on the fascists & their repunlican stooges?
Hey! I claim dibs on "A Great Silence" for my next history book title.

No longer do you hear them droning on endlessly for
"States Rights",
"Liberty For All"
"Restore The Original Constitution"

- cont'd -

Dec 14, 2018
That's the price of the thoroughly corrupt Republican Party's political and financial support from the NRA. They will tell you it is the price of the 2nd Amendment. Of course if you are stupid enough to believe this is about the 2nd amendment, and not the money, you probably also believe every mass shooter and scumbag murderer are exactly what the Founding Fathers were hoping to protect when they wrote the 2nd Amendment to protect "a well-regulated militia."
At the time the Bill of Rights was written, the nascent US was not going to be large and powerful as it is today; in those days, the US was going to be a small player on a rather large stage, and the Founders didn't want to stick the people with a bunch of taxes for an army. It would be over a hundred years before we started to gain the power we have today, and the colonists who were winning the Revolutionary War wanted to be a porcupine for any invading power.

Do we need that today? Probably not.

Dec 14, 2018
To get back to the original thread, it's not so much that gene editing has been made easy. It's that this technology (CRISPR etc.) enables anybody with a computer and a little knowledge of biological lab procedure to make any damn thing they can come up with.

I'll quote William Gibson: the street finds its own uses for technology. The point is, what are the motives and goals of the users? And how do you find some nutjob making Captain Trips in his basement because jebus told him it's time for armageddon when he was listening to his rice krispies whisper?

Dec 14, 2018
- cont'd -

Now the Hypocrites of the Right attack every voice of reason.
They deny the first paragraph of the 2nd Amt. Deny Citizens & Immigrants of Civil Rights & Human Dignity. They seek to delete the 1st Amt & the Emoluments Clause.

These copperheads & quislings, as agents of foreign powers, have deliberately sabotaged the national, state & local voting system.

I am so far too the left as I consider marxists to be right-wing fascist pigs.

To my own amazement?
I actually feel sympathy for the hard-working, true patriots of the beleaguered agents of the FBI, CIA, DoD, DoS & other acronym gov agencies agencies. Struggling against the onslaught of the right/evangelist betrayal.

I even feel sorry for John Kelly. Who, after a fine career serving his country. Has to retire in bitter defeat by the trumpsterfire crime family.

Perhaps someone should whisper in Melania's ear?
"Consider the fine example set by Edith Wilson as Acting President..."

I won't tell!

Dec 14, 2018
Perhaps someone should whisper in Melania's ear?
"Consider the fine example set by Edith Wilson as Acting President..."
My wife's reaction to the red xmas trees was classic. She had one word: "REDRUM"

I nearly laughed myself sick.

Dec 14, 2018
Ha. CRISPR/Cas is now truly "cutting edge" technology.

"change ... Progeny".

What are you on about? CRISPR/Cas has many potential uses, but the article discuss the most promising, medical genome editing. It is not a tool for *massive change in an entire populations genome*, which is what evolution do.

Nature has obviously always done that, and humans have done it with breeding. Go study evolution, if you somehow missed biology class, there are much study material on the internet say.


Dec 14, 2018
To get back to the original thread, it's not so much that gene editing has been made easy. It's that this technology (CRISPR etc.) enables anybody with a computer and a little knowledge of biological lab procedure to make any damn thing they can come up with.


Possibly, but I don't think CRISPR is the key technology, the ability to make the next plague has been there for a long time now. It is good to discuss risks, less good to attach undue scare to key technological advances. How many nuclear bombs have been dropped on people versus how many nuclear plants have we seen? How many chemical gas attacks have been levied on people versus how many tons of food has been saved by pesticides? Etcetera.

[Insane US gun owner voice:] "It is not CRISPR that kills people, it is the absence of CRISPR that kills them right now." /Sorry, I could not help myself due to the insanity of the sideshow topic,

Dec 14, 2018
@torbjorn, I can't find the quote you're referring to. Can you help?

Dec 14, 2018
@torbjorn, I can't find the quote you're referring to. Can you help?


Did you mean "cutting edge" or "change ... Progeny" or insane gun owner joke 'quote'? The first is just quoting a common idiom, the later is abstracted from the second comment of the thread, the third is just me being tired after gym class so my funny bone is funny tickled.

Dec 26, 2018
CRISPR-Cas9 is becoming a pre-requisite tool in genome editing market. The programmable capacity of the Cas9 enzyme is now transforming varied fields of medical research, industrial and animal biotechnology etc.

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