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    "original_url": "https:\/\/www.nytimes.com\/2026\/09\/17\/science\/crispr-gene-editing-vipr.html?emc=edit_nn_20260918&nl=the-morning&segment_id=226681",
    "parsed_content": "AdvertisementSKIP ADVERTISEMENTSupported bySKIP ADVERTISEMENTThe Next Gene-Editing Technology May Also Be the OldestScientists have discovered a powerful gene-targeting system in viruses. Billions of years old, VIPR seems to predate CRISPR and may be even more effective.Listen \u00b7 7:49 min Share full articleMicrographs of a virus that carries VIPR proteins, a gene-editing defense system in nature, found in viruses themselves.Credit...Santiago Lopez\/University of California, BerkeleyBy Carl ZimmerSept. 17, 2026Leer en espa\u00f1olSign up for Science Times Get stories that capture the wonders of nature, the cosmos and the human body. Get it sent to your inbox.Over the past decade, the gene-editing technology known as CRISPR has become a familiar scientific tool, used to create lifesaving cures, make more productive crops, and even engineer allergy-free dogs.But scientists didn\u2019t invent CRISPR from scratch. They discovered it in bacteria and other microbes, which use it as a defense against invading viruses. On Thursday, scientists reported that they had found another gene-editing defense in nature, this one in viruses themselves.This system, called VIPR, appears to be more than four billion years old, and it seems be the evolutionary ancestor of CRISPR, the researchers wrote in two papers published in Science.It may prove to be the more powerful gene-editing tool, with certain advantages over CRISPR. VIPR seems able to target a wider variety of genetic sequences, allowing it to alter more of the genome.AdvertisementSKIP ADVERTISEMENTAnd these molecules are smaller, making them potentially easier to deliver into cells.\u201cThe incredibly small size of VIPR makes these systems transformative tools for genome engineering,\u201d said Philip Kranzusch, a microbiologist at Harvard Medical School who was not involved in the research.Jennifer Doudna, a biochemist at the University of California, Berkeley, who is an author of the studies, shared the Nobel Prize in 2020 for harnessing the power of CRISPR. After that breakthrough, she began wondering how the natural version of the gene editor evolved.\u201cIt had to come from somewhere,\u201d she recalled thinking. \u201cMaybe it was being used to do something else before, and maybe there\u2019s still evidence of what it might have been doing.\u201dCRISPR is made up of proteins and RNA molecules that join together to shred viral genes. The RNA molecule consists of a sequence of building blocks that exactly matches the gene sequences of certain viruses.The RNA locks on to viral genes, and the protein it has brought along cuts the DNA strand, disabling the virus.AdvertisementSKIP ADVERTISEMENTSince the first CRISPR systems were discovered in the 1990s, scientists have found them in an ever-growing number of microbes.By comparing their genes, scientists have gained insight into CRISPR\u2019s evolution. In 2024, researchers concluded that the common ancestors of all living things carried CRISPR molecules.But where did this DNA-shredding defense come from?When biologists try looking back that far, the picture gets fuzzy. It\u2019s like peering through a telescope: The farther away you look, the blurrier the stars become.ImageJennifer Doudna, a biochemist at the University of California, Berkeley, who shared the Nobel Prize in 2020 for harnessing the power of CRISPR.Credit...Anastasiia Sapon for The New York TimesTwo years ago, Peter Yoon, then a graduate student working with Dr. Doudna, set out to build a better telescope. Instead of examining CRISPR genes, he studied the molecules encoded by those genes.AdvertisementSKIP ADVERTISEMENTA gene serves as a blueprint for a protein. When a gene mutates, the protein it encodes may also change \u2014 but sometimes, a gene mutation will have no effect. Its protein may still retain the same overall shape, even over billions of years.The shape of a protein determines the chemical reactions it can carry out. Once a protein evolves to do something, it usually just keeps doing it. \u201cNature is very lazy,\u201d said Dr. Yoon, who is now a member of the technical staff at Anthropic, the A.I. company.Working with Kenneth Loi, a graduate student, Dr. Yoon sifted through 2.3 million proteins, finding hundreds that had resembled CRISPR molecules but were not part of that gene-editing systems in microbes.No one had figured out what any of these CRISPR-like proteins were doing. But Dr. Yoon and Mr. Loi did discover one astonishing fact: Almost all of them came from viruses.\u201cIt was a total inversion of what we were expecting,\u201d Dr. Yoon said. CRISPR is a weapon that microbes like bacteria use against viruses. Now the scientists were finding viruses that seemed to carry a version of it themselves.AdvertisementSKIP ADVERTISEMENTDr. Kranzusch noted that this discovery would have been impossible just a few years ago. Artificial intelligence systems now allow scientists to uncover ancient connections between proteins that were hidden until now.\u201cIt\u2019s a beautiful demonstration of the power of these methods,\u201d he said.Dr. Yoon and his colleagues named these proteins VIPR and set out figuring out how they worked. That required running experiments on real viruses.On their list of candidates, they noticed a strain that Dr. Doudna happened to have stored in her lab freezer for other experiments.\u201cWe were so lucky,\u201d Mr. Loi said. \u201cWe just thawed the virus and infected some cells and said, \u2018Let\u2019s just see what we find.\u2019\u201dImageViruses with VIPR proteins that infect bacteria. \u201cYou can imagine VIPR is a gun that viruses are pointing at each other,\u201d Peter Yoon, who studied the proteins, said. Credit...Santiago Lopez\/University of California, BerkeleyThe infected cells made VIPR proteins, which then joined together with viral RNA molecules. And like CRISPR, these molecules targeted viral DNA, the researchers found.AdvertisementSKIP ADVERTISEMENTWhile CRISPR proteins chop up genes, VIPR proteins wrap around them. The effect is the same: The targeted genes shut down.Dr. Doudna and her students see in this biochemistry a weapon that viruses must be deploying against other viruses. \u201cThe whole thing starts to make sense,\u201d she said. \u201cThis is some kind of ancient viral warfare.\u201dThe idea is that when two viruses infect the same cell, they have to compete for control of the cell\u2019s molecular machinery. A virus that carries VIPR genes can shut down its rival. The triumphant virus alone gets to replicate within the host.Dr. Doudna and her colleagues propose that VIPR arose early in Earth\u2019s history, well over four billion years ago. As viruses competed to infect the first microbes, they battled one another with gene-targeting molecules. That struggle continues today.AdvertisementSKIP ADVERTISEMENTCRISPR arose from this viral weapon, the researchers suggest, when microbes seized the system for their own use. It\u2019s fairly common for viral genes to accidentally wind up in the genomes of their hosts. (Our own DNA is rife with them.)\u201cYou can imagine VIPR is a gun that viruses are pointing at each other,\u201d Dr. Yoon said. \u201cIf the bacteria just steal that, it becomes an immune system.\u201dIt remains to be seen if VIPR can be turned into a gene-editing tool. But its discovery has left scientists wondering if the long-running battle between viruses has produced other genetic weaponry not yet found.\u201cI would be very surprised if VIPR were the last unexpected targeting system we discover,\u201d said Rafael Pinilla-Redondo, a virologist at the University of Copenhagen who was not involved in the studies.Dr. Doudna said she felt humbled to think that an ancestor of gene-editing systems was sitting in her lab freezer for years: \u201cIt\u2019s a great reminder of how little we still understand about biology.\u201dAdvertisementSKIP ADVERTISEMENT",
    "published_at": "2026-09-17T18:00:08+00:00",
    "author_name": "Carl Zimmer",
    "site_name": "The New York Times",
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    "ai_headline": "The Next Gene-Editing Technology May Also Be the Oldest",
    "ai_simplified_title": "Scientists Discover VIPR Gene-Editing System in Viruses",
    "ai_excerpt": "Scientists have discovered VIPR, a powerful gene-targeting system in viruses that appears to predate CRISPR and may be even more effective. This ancient system, over four billion years old, could offer advantages over CRISPR due to its smaller size and wider targeting capabilities.",
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