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Thursday, August 25, 2016

CRISPR Technology: Palindromic AHA!

      As we discussed last week, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are segments of prokaryotic DNA containing short repetitions of base sequences. 


       CRISPR’s powerful possibilities — even the controversial notions of creating “designer babies” and eradicating entire species — are stunning and sometimes disconcerting.

     So far CRISPR’s biggest impact has been felt in biology labs around the world. The inexpensive, easy-to-use gene editor has made it possible for researchers to delve into fundamental mysteries of life in ways that had been difficult or impossible. Developmental biologist Dr. Robert Reed likens CRISPR to a computer mouse.

       “You can just point it at a place in the genome and you can do anything you want at that spot.”
Anything, that is, as long as it involves cutting DNA. CRISPR/Cas9 in its original incarnation is a homing device (the CRISPR part) that guides molecular scissors (the Cas9 enzyme) to a target section of DNA. Together, they work as a genetic-engineering cruise missile that disables or repairs a gene, or inserts something new where it cuts.

      Even with all the genetic feats the CRISPR/Cas9 system can do, “there were shortcomings. There were things we wanted to do better,” says MIT molecular biologist Dr. Feng Zhang, one of the first scientists to wield the molecular scissors. From his earliest report in 2013 of using CRISPR/Cas9 to cut genes in human and mouse cells, Zhang has described ways to make the system work more precisely and efficiently.

      He isn’t alone. A flurry of papers in the last three years have detailed improvements to the editor. Going even further, a group of scientists, including Zhang, have dreamed up ways to make CRISPR do a toolbox’s worth of jobs.

      Turning CRISPR into a multitasker often starts with dulling the cutting-edge technology’s cutting edge. In many of its new adaptations, the “dead” Cas9

scissors can’t snip DNA. Broken scissors may sound useless, but scientists have upcycled them into chromosome painters, typo-correctors, gene activity stimulators and inhibitors and general genome tinkerers.

      “The original Cas9 is like a Swiss army knife with only one application: It’s a knife,”

      says Dr. Gene Yeo, an RNA biologist at the University of California, San Diego. But Yeo and other researchers have bolted other proteins and chemicals to the dulled blades and transformed the knife into a multifunctional tool.

      Zhang and colleagues are also exploring trading the Cas9 part of the system for other enzymes that might expand the types of manipulations scientists can perform on DNA and other molecules. With the expanded toolbox, researchers may have the power to pry open secrets of cancer and other diseases and answer new questions about biology.
     The genome is like a piano, says Dr. Jonathan Weissman, a biochemist at the University of California, San Francisco. “You can play a huge variety of different music with only 88 keys by how hard you hit the keys, what keys you mix up and the timing.” By dialing down or turning up the activity of combinations of genes at precise times during development, cells are coaxed into becoming hundreds of different types of body cells.

     For the last 20 years, researchers have been learning more about that process by watching when certain genes turn on and off in different cells. Gene activity is controlled by a large variety of proteins known as transcription factors. When and where a transcription factor acts is at least partly determined by chemical tags on DNA and the histone proteins that package it. Those tags are known collectively as epigenetic marks. They work something like the musical score for an orchestra, telling the transcription factor “musicians” which notes to hit and how loudly or softly to play. So far, scientists have only been able to listen to the music.

      With this new research, researchers can create molecules that will change epigenetic notes at any place in the score, Weissman says, allowing researchers to arrange their own music.
Epigenetic marks are alleged to be involved in addiction, cancer, mental illness, obesity, diabetes and heart disease. Scientists haven’t been able to prove that epigenetic marks are really behind these and other ailments, because they could never go into a cell and change just one mark on one gene to see if it really produced a sour note.

      The explosion of new ways to use CRISPR hasn’t ended. “The field is advancing so rapidly,” says Zhang. “Just looking at how far we have come in the last three and a half years, I think what we’ll see coming in the next few years will just be amazing,” according to an article published this week.

What a difference the past 4 years have made in epigenetics!



  1. Dr. Weissman's piano/genome metaphor was very helpful to me.

    The image of the scissors cutting the DNA helix reminds me of cutting a Mobius strip into one! Or into two looped strips if you do the "thirdsies" cut.

    The Swiss Army knife images peripherally pertain to one of tomorrow morning's Puzzleria! puzzles, the "Service With A Smirk Appetizer."


    1. I liked the piano analogy, too, Lego.

      I am enjoying the image of you cutting the cheese ;-).

  2. CRISPR is this decade's PCR, i.e., the defining bioscience innovation. My niece at Berkeley was lucky to get into a course with Jennifer Doudna.

  3. Replies
    1. More cross-pollination?

      A sad sight, indeed!

    2. Speaking of cross-whatever, what if you used CRISPR/Cas9 to create a cross between reindeer and lemmings? (Aren't lemmings also from Norway?) Or, just built a hybrid out of parts of roadkill, and arranged for it to be struck by lightning? IT'S ALIVE! OOPS!

    3. And, no, that wasn't a Gene Wilder reference.

    4. Beat me to it with the Gene Wilder reference. What a brilliant comedian!

      It's alive with lightning. It's dead with lightning. . .
      Which is it?

      I'd wrote this elsewhere but I am tired of all the loading. . .I thought the result was completely elegant. Getting there, not so much--IT was the destination, not the journey on this one. How did no one among us come upon this previously?!

    5. Wilder would have disagreed. Made a point of insisting he was an actor, not a clown.

      I liked the characters he played. But who knows what the real man was like? Two divorces and an affair with a married woman (Radner) suggest he may not have been quite as lovable as his on-screen personae, but who am I to judge?

    6. Brilliant actor. Sorry, Gene.

      Did not know any of his back story. . .Always enjoyed Gilda, the actress/comedienne (?)

    7. From what I understand, he went out singing Over the Rainbow. Well played.

    8. Listening to Ella's version of "Somewhere Over the Rainbow," -- very well-played, indeed, Paul.

  4. New post on "One-Syllable State of Maine Rocks: Underappreciated Silurian Age Stones" is now up.