DOE News
    Doe Science news source
    The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
    • 2017-06-21 13:00:29
    • Article ID: 676793

    Researchers Find New Mechanism for Genome Regulation

    Berkeley Lab study could have implications for improving gene therapy

    • Credit: Amy Strom/Berkeley Lab

      Liquid-like fusion of heterochromatin protein 1a droplets in the embryo of a fruit fly.

    • Credit: Amy Strom/Berkeley Lab

      Shown is purified heterochromatin protein 1a forming liquid droplets in an aqueous solution. On the right side, two drops fuse together over time.

    • Credit: Amy Strom/Berkeley Lab

      Mouse fibroblast cells expressing HP1alpha, the human version of heterochromatin protein 1a. A technique that highlights edges between two liquid phases reveals the liquid droplets in the nucleus.

    The same mechanisms that quickly separate mixtures of oil and water are at play when controlling the organization in an unusual part of our DNA called heterochromatin, according to a new study by researchers at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab).

    Researchers studying genome and cell biology provide evidence that heterochromatin organizes large parts of the genome into specific regions of the nucleus using liquid-liquid phase separation, a mechanism well known in physics but whose importance for biology has only recently been revealed. 

    They present their findings June 21 in the journal Nature, addressing a long-standing question about how DNA functions are organized in space and time, including how genes are regulated to be silenced or expressed.

    “The importance of DNA sequences in health and disease has been clear for decades, but we only recently have come to realize that the organization of sections of DNA into different physical domains or compartments inside the nucleus is critical to promote distinct genome functions,” said study corresponding author, Gary Karpen, senior scientist at Berkeley Lab's Biological Systems and Engineering Division.

    The long stretches of DNA in heterochromatin contain sequences that, for the most part, need to be silenced for cells to work properly. Scientists once thought that compaction of the DNA was the primary mechanism for controlling which enzymes and molecules gain access to the sequences. It was reasoned that the more tightly wound the strands, the harder it would be to get to the genetic material inside.

    That mechanism has been questioned in recent years by the discovery that some large protein complexes could get inside the heterochromatin domain, while smaller proteins can remain shut out.

    In this new study of early Drosophila embryos, the researchers observed two non-mixing liquids in the cell nucleus: one that contained expressed genes, and one that contained silenced heterochromatin. They found that heterochromatic droplets fused together just like two drops of oil surrounded by water.

    In lab experiments, researchers purified heterochromatin protein 1a (HP1a), a main component of heterochromatin, and saw that this single component was able to recreate what they saw in the nucleus by forming liquid droplets.

    "We are excited about these findings because they explain a mystery that's existed in the field for a decade," said study lead author Amy Strom, a graduate student in Karpen's lab. "That is, if compaction controls access to silenced sequences, how are other large proteins still able to get in? Chromatin organization by phase separation means that proteins are targeted to one liquid or the other based not on size, but on other physical traits, like charge, flexibility, and interaction partners."

    The Berkeley Lab study, which used fruit fly and mouse cells, will be published alongside a companion paper in Nature led by UC San Francisco researchers, who showed that the human version of the HP1a protein has the same liquid droplet properties, suggesting that similar principles hold for human heterochromatin.

    Interestingly, this type of liquid-liquid phase separation is very sensitive to changes in temperature, protein concentration, and pH levels.

    "It's an elegant way for the cell to be able to manipulate gene expression of many sequences at once," said Strom.

    Other cellular structures, including some involved in disease, are also organized by phase separation.

    "Problems with phase separation have been linked to diseases such as dementia and certain neurodegenerative disorders," said Karpen.

    He noted that as we age, biological molecules lose their liquid state and become more solid, accumulating damage along the way. Karpen pointed to diseases like Alzheimer's and Huntington's, in which proteins misfold and aggregate, becoming less liquid and more solid over time.

    "If we can better understand what causes aggregation, and how to keep things more liquid, we might have a chance to combat these types of disease," Strom added.

    The work is a big step forward for understanding how DNA functions, but could also help researchers improve their ability to manipulate genes.

    “Gene therapy, or any treatment that relies on tight regulation of gene expression, could be improved by precisely targeting molecules to the right place in the nucleus,” says Karpen. “It is very difficult to target genes located in heterochromatin, but this understanding of the properties linked to phase separation and liquid behaviors could help change that and open up a third of the genome that we couldn’t get to before.” 

    This includes targeting gene-editing technologies like CRISPR, which has recently opened up new doors for precise genome manipulation and gene therapy.

    Karpen and Strom have joint appointments at UC Berkeley's Department of Molecular and Cell Biology. Other study co-authors include Mustafa Mir and Xavier Darzacq at UC Berkeley, and Alexander Emelyanov and Dmitry Fyodorov at the Albert Einstein College of Medicine in New York. 

    The National Institutes of Health and the California Institute for Regenerative Medicine helped support this work.

    ###

    Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel Prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit www.lbl.gov.

    DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

    • other-fb
    • other-tw
    X
    X
    X
    • Filters

    • × Clear Filters
    A New Collider Concept Would Take Quantum Theories to an Extreme

    A New Collider Concept Would Take Quantum Theories to an Extreme

    A new idea for smashing beams of elementary particles into one another could reveal how light and matter interact under extreme conditions that may exist on the surfaces of exotic astrophysical objects, in powerful cosmic light bursts and star explosions, in next-generation particle colliders and in hot, dense fusion plasma.

    Unexpected observation of ice at low temperature, high pressure questions ice, water theory

    Unexpected observation of ice at low temperature, high pressure questions ice, water theory

    Scientists at Oak Ridge National Laboratory studying super-cold states of water discovered a pathway to the unexpected formation of dense, crystalline phases of ice thought to exist beyond Earth's limits. Their findings, reported in Nature, challenge accepted theories and could lead to better understanding of ice found on other planets, moons and elsewhere in space.

    New Argonne Battery Design Offers ​"Solid" Advantage

    New Argonne Battery Design Offers ​"Solid" Advantage

    In a new study from the U.S. Department of Energy's (DOE) Argonne National Laboratory, researchers have identified a new boundary layer that emerges between a lithium metal anode and a lithium transition metal oxide (LLZO) electrolyte, potentially leading to improved battery stability.

    Laser Focus Shines Light on How Nanoparticles Form

    Laser Focus Shines Light on How Nanoparticles Form

    Titan supercomputer tells origin story of nanoparticle size distributions with large-scale simulations.

    In a first, researchers identify reddish coloring in an ancient fossil - a 3-million-year-old mouse

    In a first, researchers identify reddish coloring in an ancient fossil - a 3-million-year-old mouse

    Researchers have for the first time detected chemical traces of red pigment in an ancient fossil - an exceptionally well-preserved mouse, not unlike today's field mice, that roamed the fields of what is now the German village of Willershausen around 3 million years ago.

    Improving Isotope Supply for a Cancer-Fighting Drug

    Improving Isotope Supply for a Cancer-Fighting Drug

    Production of actinium-227 ramps up for use in a drug to fight prostate cancer that has spread to bone.

    Extracting Signs of the Elusive Neutrino

    Extracting Signs of the Elusive Neutrino

    Scientists use software to "develop" images that trace neutrinos' interactions in a bath of cold liquid argon.

    Machine learning speeds modeling of experiments aimed at capturing fusion energy on Earth to rapidly predict behavior of plasma that fuels fusion reactions

    Machine learning speeds modeling of experiments aimed at capturing fusion energy on Earth to rapidly predict behavior of plasma that fuels fusion reactions

    Release describes application of machine learning form of artificial intelligence to predict the behavior of fusion plasma.

    Record-shattering underwater sound

    Record-shattering underwater sound

    A team of researchers has produced a record-shattering underwater sound with an intensity that eclipses that of a rocket launch. The intensity was equivalent to directing the electrical power of an entire city onto a single square meter, resulting in sound pressures above 270 decibels.

    CosmoGAN: Training a Neural Network to Study Dark Matter

    CosmoGAN: Training a Neural Network to Study Dark Matter

    A Berkeley Lab-led research group is using a deep learning method known as generative adversarial networks to enhance the use of gravitational lensing in the study of dark matter.


    • Filters

    • × Clear Filters
    Ames Laboratory names James Morris Chief Research Officer

    Ames Laboratory names James Morris Chief Research Officer

    Dr. James Morris has been named Chief Research Officer at the Department of Energy's (DOE) Ames Laboratory. His appointment follows an extensive search and will be effective June 17, 2019.

    Four scientists at PPPL awarded national and international honors

    Four scientists at PPPL awarded national and international honors

    Feature profiles four PPPL scientists who have received high honors.

    Brookhaven's Mircea Cotlet Named a Battelle "Inventor of the Year"

    Brookhaven's Mircea Cotlet Named a Battelle "Inventor of the Year"

    The global science and technology organization Battelle recognized materials scientist Mircea Cotlet of Brookhaven Lab's Center for Functional Nanomaterials for his research in applying self-assembly methods to control the interfaces between nanomaterials and other light-interacting components.

    Berkeley Lab Project to Pinpoint Methane 'Super Emitters'

    Berkeley Lab Project to Pinpoint Methane 'Super Emitters'

    Methane, a potent greenhouse gas that traps about 30 times more heat than carbon dioxide, is commonly released from rice fields, dairies, landfills, and oil and gas facilities - all of which are plentiful in California. Now Berkeley Lab has been awarded $6 million by the state to find "super emitters" of methane in an effort to quantify and potentially mitigate methane emissions.

    Cryogenics equipment maker licenses ORNL auto-fill method for more efficient liquid helium use

    Cryogenics equipment maker licenses ORNL auto-fill method for more efficient liquid helium use

    Advanced Research Systems has licensed an ORNL technology designed to automatically refill liquid helium used in laboratory equipment for low-temperature scientific experiments, which will reduce downtime, recover more helium and increase overall efficiency.

    New Argonne coating could have big implications for lithium batteries

    New Argonne coating could have big implications for lithium batteries

    In a new discovery, scientists at the U.S. Department of Energy's (DOE) Argonne National Laboratory have developed a new cathode coating by using an oxidative chemical vapor deposition technique. The new coating can keep the battery's cathode electrically and ionically conductive and ensures that the battery stays safe after many cycles.

    Argonne's Chain Reaction Innovations appoints first advisory council

    Argonne's Chain Reaction Innovations appoints first advisory council

    World-class energy leaders will offer their expertise to Chain Reaction Innovations (CRI), the entrepreneurship program at the U.S. Department of Energy's Argonne National Laboratory, as part of a new Advisory Council announced today. CRI has named 14 Advisory Council members, including investors, industry experts and business executives, to help guide its growth and strategy.

    ORNL, Lincoln Electric to Advance Large-Scale Metal Additive Manufacturing Technology

    ORNL, Lincoln Electric to Advance Large-Scale Metal Additive Manufacturing Technology

    The new agreement builds upon ORNL and Lincoln Electric's previous developments by extending additive technology to new materials, leveraging data analytics and enabling rapid manufacture of metal components in excess of 100 pounds per hour.

    Students from Minnesota and Massachusetts Win DOE's 29th National Science Bowl(r)

    Students from Wayzata High School in Plymouth, Minnesota, won the 2019 U.S. Department of Energy (DOE) National Science Bowl(r) (NSB) today in Washington, D.C. In the middle school competition, students from Jonas Clarke Middle School in Lexington, Massachusetts, took home first place.

    Five new innovators join Chain Reaction Innovations in third cohort

    Five new innovators join Chain Reaction Innovations in third cohort

    Five new innovators will be joining Chain Reaction Innovations (CRI), the entrepreneurship program at the U.S. Department of Energy's (DOE's) Argonne National Laboratory, as part of the elite program's third cohort. Announced on Monday, April 22, these innovators were selected following an extensive national solicitation process and two-part pitch competition, with reviews from industry experts, investors, scientists and engineers.


    • Filters

    • × Clear Filters
    Laser Focus Shines Light on How Nanoparticles Form

    Laser Focus Shines Light on How Nanoparticles Form

    Titan supercomputer tells origin story of nanoparticle size distributions with large-scale simulations.

    Improving Isotope Supply for a Cancer-Fighting Drug

    Improving Isotope Supply for a Cancer-Fighting Drug

    Production of actinium-227 ramps up for use in a drug to fight prostate cancer that has spread to bone.

    Extracting Signs of the Elusive Neutrino

    Extracting Signs of the Elusive Neutrino

    Scientists use software to "develop" images that trace neutrinos' interactions in a bath of cold liquid argon.

    Slow Charge Generation Plays Big Role in Model Material for Solar Cells

    Slow Charge Generation Plays Big Role in Model Material for Solar Cells

    Insight about energy flow in copper-based material could aid in creating efficient molecular electronics.

    Capturing Energy Flow in a Plasma by Measuring Scattered Light

    Capturing Energy Flow in a Plasma by Measuring Scattered Light

    First measurements of heat flux in plasmas experientially sheds light on models relying on classical thermal transport.

    Artificial Intelligence and Deep Learning Accelerate Efforts to Develop Clean, Virtually Limitless Fusion Energy

    Artificial Intelligence and Deep Learning Accelerate Efforts to Develop Clean, Virtually Limitless Fusion Energy

    The Fusion Recurrent Neural Network reliably forecasts disruptive and destructive events in tokamaks.

    Spin Flipper Upends Protons

    Spin Flipper Upends Protons

    The spin direction of protons was reversed, for the first time, using a nine-magnet device, potentially helping tease out details about protons that affect medical imaging and more.

    Splitting Water Fast! Catalyst Works Faster than Mother Nature

    Splitting Water Fast! Catalyst Works Faster than Mother Nature

    Design principles lead to a catalyst that splits water in a low pH environment, vital for generating solar fuels.

    Sea Quark Spin Surprise!

    Sea Quark Spin Surprise!

    Antiquark spin contribution to proton spin depends on flavor, which could help unlock secrets about the nuclear structure of atoms that make up nearly all visible matter in our universe.

    The Weak Side of the Proton

    The Weak Side of the Proton

    A precision measurement of the proton's weak charge narrows the search for new physics.


    Spotlight

    ILSAMP Symposium showcases benefits for diverse students, STEM pipeline
    Monday May 20, 2019, 12:05 PM

    ILSAMP Symposium showcases benefits for diverse students, STEM pipeline

    Argonne National Laboratory

    Integrating Scientific Computing into Science Curricula
    Monday May 13, 2019, 11:05 AM

    Integrating Scientific Computing into Science Curricula

    Brookhaven National Laboratory

    Students from Minnesota and Massachusetts Win DOE's 29th National Science Bowl(r)
    Monday April 29, 2019, 02:05 PM

    Students from Minnesota and Massachusetts Win DOE's 29th National Science Bowl(r)

    Department of Energy, Office of Science

    DOE's Science Graduate Student Research Program Selects 70 Students to Pursue Research at DOE Laboratories
    Friday April 12, 2019, 03:05 PM

    DOE's Science Graduate Student Research Program Selects 70 Students to Pursue Research at DOE Laboratories

    Department of Energy, Office of Science

    Young Women's Conference in STEM seeks to change the statistics one girl at a time
    Thursday March 28, 2019, 03:05 PM

    Young Women's Conference in STEM seeks to change the statistics one girl at a time

    Princeton Plasma Physics Laboratory

    Students team with Argonne scientists and engineers to learn about STEM careers
    Tuesday March 12, 2019, 05:05 PM

    Students team with Argonne scientists and engineers to learn about STEM careers

    Argonne National Laboratory

    Lynbrook High wins 2019 SLAC Regional Science Bowl competition
    Wednesday February 13, 2019, 02:05 PM

    Lynbrook High wins 2019 SLAC Regional Science Bowl competition

    SLAC National Accelerator Laboratory

    Equipping the next generation for a technological revolution
    Thursday January 24, 2019, 01:05 PM

    Equipping the next generation for a technological revolution

    Argonne National Laboratory

    Chemistry intern inspired by Argonne's real-world science
    Friday January 18, 2019, 05:05 PM

    Chemistry intern inspired by Argonne's real-world science

    Argonne National Laboratory

    Chasing a supernova
    Friday January 18, 2019, 04:05 PM

    Chasing a supernova

    Argonne National Laboratory

    Argonne intern streamlines the beamline
    Tuesday January 08, 2019, 02:05 PM

    Argonne intern streamlines the beamline

    Argonne National Laboratory

    Research on Light-Matter Interaction Could Lead to Improved Electronic and Optoelectronic Devices
    Thursday October 11, 2018, 04:00 PM

    Research on Light-Matter Interaction Could Lead to Improved Electronic and Optoelectronic Devices

    Rensselaer Polytechnic Institute (RPI)

    Innovating Our Energy Future
    Wednesday October 03, 2018, 07:05 PM

    Innovating Our Energy Future

    Oregon State University, College of Engineering

    Physics graduate student takes her thesis research to a Department of Energy national lab
    Tuesday October 02, 2018, 03:05 PM

    Physics graduate student takes her thesis research to a Department of Energy national lab

    University of Alabama at Birmingham

    Friday September 21, 2018, 01:05 PM

    "Model" students enjoy Argonne campus life

    Argonne National Laboratory

    Writing Code for a More Skilled and Diverse STEM Workforce
    Thursday September 06, 2018, 01:05 PM

    Writing Code for a More Skilled and Diverse STEM Workforce

    Brookhaven National Laboratory

    New graduate student summer school launches at Princeton Plasma Physics Laboratory
    Tuesday September 04, 2018, 11:30 AM

    New graduate student summer school launches at Princeton Plasma Physics Laboratory

    Princeton Plasma Physics Laboratory

    The Gridlock State
    Friday August 31, 2018, 06:05 PM

    The Gridlock State

    California State University (CSU) Chancellor's Office

    Meet Jasmine Hatcher and Trishelle Copeland-Johnson
    Friday August 31, 2018, 02:05 PM

    Meet Jasmine Hatcher and Trishelle Copeland-Johnson

    Brookhaven National Laboratory

    Argonne hosts Modeling, Experimentation and Validation Summer School
    Friday August 24, 2018, 11:05 AM

    Argonne hosts Modeling, Experimentation and Validation Summer School

    Argonne National Laboratory

    Students affected by Hurricane Maria bring their research to SLAC
    Wednesday August 22, 2018, 01:05 PM

    Students affected by Hurricane Maria bring their research to SLAC

    SLAC National Accelerator Laboratory

    Brookhaven Lab Pays Tribute to 2018 Summer Interns
    Wednesday August 22, 2018, 10:05 AM

    Brookhaven Lab Pays Tribute to 2018 Summer Interns

    Brookhaven National Laboratory

    Changing How Buildings Are Made
    Monday August 20, 2018, 12:05 PM

    Changing How Buildings Are Made

    Washington University in St. Louis

    CSUMB Selected to Host Architecture at Zero Competition in 2019
    Thursday August 16, 2018, 12:05 PM

    CSUMB Selected to Host Architecture at Zero Competition in 2019

    California State University, Monterey Bay

    Department of Energy Invests $64 Million in Advanced Nuclear Technology
    Friday July 20, 2018, 03:00 PM

    Department of Energy Invests $64 Million in Advanced Nuclear Technology

    Rensselaer Polytechnic Institute (RPI)

    Professor Miao Yu Named the Priti and Mukesh Chatter '82 Career Development Professor
    Thursday July 19, 2018, 05:00 PM

    Professor Miao Yu Named the Priti and Mukesh Chatter '82 Career Development Professor

    Rensselaer Polytechnic Institute (RPI)

    2018 RHIC & AGS Annual Users' Meeting: 'Illuminating the QCD Landscape'
    Tuesday July 03, 2018, 11:05 AM

    2018 RHIC & AGS Annual Users' Meeting: 'Illuminating the QCD Landscape'

    Brookhaven National Laboratory

    Argonne welcomes <em>The Martian</em> author Andy Weir
    Friday June 29, 2018, 06:05 PM

    Argonne welcomes The Martian author Andy Weir

    Argonne National Laboratory

    Creating STEM Knowledge and Innovations to Solve Global Issues Like Water, Food, and Energy
    Monday June 18, 2018, 09:55 AM

    Creating STEM Knowledge and Innovations to Solve Global Issues Like Water, Food, and Energy

    Illinois Mathematics and Science Academy (IMSA)

    Professor Emily Liu Receives $1.8 Million DoE Award for Solar Power Systems Research
    Friday June 15, 2018, 10:00 AM

    Professor Emily Liu Receives $1.8 Million DoE Award for Solar Power Systems Research

    Rensselaer Polytechnic Institute (RPI)

    Celebrating 40 years of empowerment in science
    Thursday June 07, 2018, 03:05 PM

    Celebrating 40 years of empowerment in science

    Argonne National Laboratory

    Introducing Graduate Students Across the Globe to Photon Science
    Monday May 07, 2018, 10:30 AM

    Introducing Graduate Students Across the Globe to Photon Science

    Brookhaven National Laboratory

    Students from Massachusetts and Washington Win DOE's 28th National Science Bowl(r)
    Wednesday May 02, 2018, 04:05 PM

    Students from Massachusetts and Washington Win DOE's 28th National Science Bowl(r)

    Department of Energy, Office of Science

    The Race for Young Scientific Minds
    Thursday April 12, 2018, 07:05 PM

    The Race for Young Scientific Minds

    Argonne National Laboratory

    Q&A: Al Ashley Reflects on His Efforts to Diversify SLAC and Beyond
    Wednesday March 14, 2018, 02:05 PM

    Q&A: Al Ashley Reflects on His Efforts to Diversify SLAC and Beyond

    SLAC National Accelerator Laboratory

    Insights on Innovation in Energy, Humanitarian Aid Highlight UVA Darden's Net Impact Week
    Thursday February 15, 2018, 12:05 PM

    Insights on Innovation in Energy, Humanitarian Aid Highlight UVA Darden's Net Impact Week

    University of Virginia Darden School of Business

    Ivy League Graduate, Writer and Activist with Dyslexia Visits CSUCI to Reframe the Concept of Learning Disabilities
    Friday February 09, 2018, 11:05 AM

    Ivy League Graduate, Writer and Activist with Dyslexia Visits CSUCI to Reframe the Concept of Learning Disabilities

    California State University, Channel Islands

    Photographer Adam Nadel Selected as Fermilab's New Artist-in-Residence for 2018
    Wednesday January 17, 2018, 12:05 PM

    Photographer Adam Nadel Selected as Fermilab's New Artist-in-Residence for 2018

    Fermi National Accelerator Laboratory (Fermilab)

    Fermilab Computing Partners with Argonne, Local Schools for Hour of Code
    Wednesday January 17, 2018, 12:05 PM

    Fermilab Computing Partners with Argonne, Local Schools for Hour of Code

    Fermi National Accelerator Laboratory (Fermilab)

    Q&A: Sam Webb Teaches X-Ray Science from a Remote Classroom
    Wednesday December 20, 2017, 01:05 PM

    Q&A: Sam Webb Teaches X-Ray Science from a Remote Classroom

    SLAC National Accelerator Laboratory

    The Future of Today's Electric Power Systems
    Monday December 18, 2017, 01:05 PM

    The Future of Today's Electric Power Systems

    Rensselaer Polytechnic Institute (RPI)

    Supporting the Development of Offshore Wind Power Plants
    Monday December 18, 2017, 12:05 PM

    Supporting the Development of Offshore Wind Power Plants

    Rensselaer Polytechnic Institute (RPI)

    Stairway to Science
    Tuesday October 03, 2017, 01:05 PM

    Stairway to Science

    Argonne National Laboratory

    After-School Energy Rush
    Thursday September 28, 2017, 12:05 PM

    After-School Energy Rush

    Argonne National Laboratory

    Bringing Diversity Into Computational Science Through Student Outreach
    Thursday September 28, 2017, 10:05 AM

    Bringing Diversity Into Computational Science Through Student Outreach

    Brookhaven National Laboratory

    From Science to Finance: SLAC Summer Interns Forge New Paths in STEM
    Thursday September 21, 2017, 03:05 PM

    From Science to Finance: SLAC Summer Interns Forge New Paths in STEM

    SLAC National Accelerator Laboratory





    Showing results

    0-4 Of 2215