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and to develop commercial uses for sound recordings, worries that NIH is overemphasizing the new approach “The decision to abandon the ES resource in favor of making simple knockouts is a mistake” Skarnes says “You still want to make conditionals through the ES route” See how CRISPR runs Using the genome-engineering tool to alter a fertilized egg is a quicker and more efficient way to engineer a mouse than the traditional route which starts by modifying an embryonic stem cell K Sutliff/Science CRISPR researchers are now refining the technique to do knockins with greater efficiency But that entails tinkering with the mechanisms that cells use to repair broken DNA which are critical to their health “I’m cautious about overmanipulation of biology to increase efficiency” says Steve Murray who helps run JAX’s contribution to the Knockout Mouse Phenotyping Program (KOMP2) which is part of the international consortium “We’re waiting in the wings for the wizards in the field to help us with this” CRISPR stands for “clustered regularly interspaced short palindromic repeats” which is a description of the prokaryotic genetic material from which it was derived It uses what’s called a guide RNA to send biological scissors—usually the CRISPR associated protein Cas9—to a precise spot in a genome Once Cas9 enzymatically makes the cut the cell tries to heal the wounded DNA One repair mechanism leads to knockouts whereas the second leads to knockins “All CRISPR does is cut the DNA” Wiles says “Everything else is the cell repair system and that’s what we’re hitching on to” The cell’s standard response is to try to paste the double-stranded DNA back together at the break points This often requires eating away or adding a few bases—the As Cs Ts and Gs that make up DNA—which leads to insertions or deletions In effect the repair effort introduces typos into the DNA text disabling the gene MIT’s Jaenisch was the first to show the power of CRISPR for producing mouse knockouts In a 2 May 2013 paper in Cell that appeared 5 months after researchers first showed CRISPR could work in mammalian cells he and co-workers reported that the technique successfully disrupted five genes in a single set of mouse ES cells something that was not possible before More important they showed that they could bypass ES cells altogether and simultaneously knock out two genes in single-celled mouse zygotes or fertilized eggs No longer would researchers have to modify ES cells and painstakingly breed several generations of mice to produce an animal that carried the mutant gene in its egg or sperm cells And researchers who wanted mice with two mutations would no longer have to interbreed single mutants and go through a similarly time-consuming cumbersome process to arrive at progeny with the altered germ line As the title of Jaenisch’s paper declared triumphantly “One-step generation of mice carrying mutations in multiple genes” Since then more than 500 papers have detailed how CRISPR can both knock out and knock in genes in mice “The impact it’s had is enormous” says Jaenisch who in 1974 created the first transgenic mouse “It’s really changed the time and efficiency of getting these engineered animals” adds biochemist Tak Mak of the University of Toronto in Canada who was also a pioneer in the mouse-mutating business Mak estimates it’s about 30% cheaper to engineer a mouse with CRISPR than with ES cells bringing his average cost down to about $100000 CRISPR works in every strain of mouse whereas ES-cell technology is mostly limited to one inbred strain Stanton Short / Jennifer L Torrance courtesy of the Jackson Laboratory CRISPR’s impact is measured in more than savings The ease and speed of the technique makes it possible to engineer mice on the fly to solve specific puzzles like one that C C Hui of the Hospital for Sick Children in Toronto recently confronted: a knockout in which the missing gene didn’t have any observable effect Hui realized that the knocked-out gene was linked to another gene that might be compensating for it He took the problem to Lauryl Nutter who oversees mouse making at the Centre for Phenogenomics in Toronto She used CRISPR to mutate the offending gene in a zygote from the original knockout “We got the zygote injected it with CRISPR-Cas9 and 8 weeks later he had a double mutant on the ground” Nutter says “That would have taken years with ES cells” The revolution is not limited to making mice with germline mutations CRISPR has allowed investigators to mutate several suspected cancer genes simultaneously in the somatic cells of adult mice for example CRISPR knockins have also corrected disease-causing gene defects in adult mice such as the mutations that cause hemophilia and sickle cell anemia And several groups plan to inject CRISPR into a developing mouse; the goal is to create mutations that act as barcodes and allow scientists to track cell lineages as they differentiate Mousemaking outfits like the Centre for Phenogenomics and JAX expect that CRISPR will vastly expand the range of mutants they produce “Now I can take a really exotic mouse that has three genetic modifications and modify it again” JAX’s Wiles says “We couldn’t do sequential modification with ES cells We could breed a mouse with two modifications with another that had two modifications and the alleles scattered like the wind It would take years to get all four modifications” Wiles says this likely won’t affect JAX’s bottom line “Instead of shipping thousands of boxes with one variety we will have hundreds of boxes with tens of varieties” On one front however the CRISPR revolution is faltering Three months after his lab’s first CRISPR report Jaenisch and co-workers published a second paper in Cell that suggested CRISPR could easily perform more complex genetic surgery knocking in chunks of DNA rather than simply disabling genes As a demonstration they used CRISPR to knock fluorescent tags into mouse zygotes which lighted up whenever a specific gene was turned on They also created conditional mutants which are key to many research efforts including the knockout consortium Conditionals get around a barrier to making knockouts About one-third of mouse genes are essential for embryonic growth; the mouse is never born if they are disabled from the start So researchers working with ES cells cleverly designed a system called Cre-Lox recombination that knocks out genes only after the mouse has developed enough to survive their loss It requires adding extra DNA: Lox sequences flanking the targeted gene plus a Cre gene which can be turned on to produce an enzyme that modifies the DNA between the Lox sites Using CRISPR to insert this same system into zygotes Jaenisch’s team reported making conditional mice with relatively “high efficiency”—about 16% of the zygotes led to mouse pups with the correct mutations Skarnes is one of many researchers bowled over by Jaenisch’s initial reports but he was disappointed when he tried to take the technique into his own lab “It looked from his papers that this was going to be straightforward and I was quite confident this would make ES obsolete” Skarnes says “What was disappointing is none of us could reproduce at the efficiencies reported by Jaenisch … It works at 1% or 2% at JAX and a lot of projects are failing It’s really not proven to be a robust method” Related article There are several reasons why a CRISPR cut more readily leads to a knockout than a knockin To create knockins with CRISPR researchers introduce stretches of “donor” DNA—anything from a few bases to an entire gene—designed to integrate at the break points created by Cas9 Splicing in the donor DNA requires that its ends match or are “homologous” with the damaged DNA A process of homologous-directed repair (HDR) then stitches the ends together The knockout repair mechanism which is called nonhomologous end joining can happen at any stage in the cell division cycle and occurs quickly HDR in contrast mainly happens in one phase of the cell cycle and is far slower Some genes such as those Jaenisch selected for his initial knockin experiments are also more conducive to HDR than others “The paper reported what we found” Jaenisch says “Now we see there are issues” To others CRISPR’s limitations raise questions about the knockout mouse consortium’s decision to abandon ES cell technology Launched in 2003 the project has created a repository of mutant ES cells most of them conditionals for nearly 18000 genes Any researcher can order a cell line and spend a year or more making a needed knockout mouse It has also bred 5011 mutant mouse strains that have germ line transmission of the knockout This summer as part of KOMP2 NIH decided to extend the tally of live knockouts to 8000 funding JAX the University of California Davis and Baylor College of Medicine in Houston Texas to do the work But it specified that the knockouts should be made using CRISPR alone Colin Fletcher a mouse geneticist at NIH’s National Human Genome Research Institute in Rockville Maryland who oversees KOMP2 says advisers endorsed the switch to CRISPR “You can’t cling to the old technology” Fletcher says “A lot of people have abandoned the ES cell repository and on the other hand a lot of people have come in to the field because of the new technology People are voting with their feet People are putting much more effort into making conditional alleles with CRISPR rather than making ES cells” Skarnes who has just moved from Wellcome to the JAX genomic medicine branch in Farmington Connecticut calls the shift premature But he concedes that researchers will “eventually” figure out how to tweak CRISPR so that it makes conditional mutant mice with high efficiency One route is to block an enzyme crucial to nonhomologous end joining Another is to enhance a protein critical to the HDR process that makes knockins possible Still other investigators have toyed with lengthening the cell-cycle phase that is most favorable to that repair process zapping zygotes with electric pulses to aid the entry of the CRISPR-Cas9 construct and creating mutant Cas9s called “nickases” that only break a single DNA strand and preferentially induce HDR Whatever CRISPR’s shortcomings appear to be at this point Wiles emphasizes that its potential for engineering mice should not be underestimated “There is a massive number of things CRISPR can do that people are just beginning to grasp” he says “We’re really at the very very early phases of development and the tool has infinite possibilities”” Tonsing said. poor working conditions and wages and child labour." said Modi." 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