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
    Explaining Light-Nuclei Production in Heavy-Ion Nuclear Collisions

    Explaining Light-Nuclei Production in Heavy-Ion Nuclear Collisions

    Pairs of sub-atomic particles may catalyze reactions that happened moments after the Big Bang.

    Scientists hit pay dirt with new microbial research technique

    Scientists hit pay dirt with new microbial research technique

    Long ago, during the European Renaissance, Leonardo da Vinci wrote that we humans "know more about the movement of celestial bodies than about the soil underfoot." Five hundred years and innumerable technological and scientific advances later, his sentiment still holds true. But that could soon change. A new study in Nature Communications details how an improved method for studying microbes in the soil will help scientists understand both fine-grained details and large-scale cycles of the environment.

    STAR Gains Access to "Wimpy" Quarks and Gluons

    STAR Gains Access to "Wimpy" Quarks and Gluons

    Low-momentum (wimpy) quarks and gluons contribute to proton spin, offering insights into protons' behavior in all visible matter.

    Flipping the Script with Reverse D-Shaped Plasmas

    Flipping the Script with Reverse D-Shaped Plasmas

    Mirrored D shape demonstrates surprisingly high pressures in a tokamak, indicating a shape change may be in order for next-generation fusion reactors.

    Scientists make first high-res movies of proteins forming crystals in a living cell

    Scientists make first high-res movies of proteins forming crystals in a living cell

    Scientists have made the first observations of proteins assembling themselves into crystals, one molecule at a time, in a living cell. The method they used to watch this happen - an extremely high-res form of molecular moviemaking ­- could shed light on other important biological processes and help develop nanoscale technologies inspired by nature.

    Blue Pigment from Engineered Fungi Could Help Turn the Textile Industry Green

    Blue Pigment from Engineered Fungi Could Help Turn the Textile Industry Green

    A new biosynthetic production pathway developed by scientists at the Joint BioEnergy Institute could provide a sustainable alternative to conventional synthetic blue dye. The highly efficient fungi-based platform may also open the door for producing many other valuable biological compounds that are currently very hard to manufacture.

    Designer Frameworks for Refining Higher Octane Fuels

    Designer Frameworks for Refining Higher Octane Fuels

    Metal-organic frameworks designed with a topology-guided approach show higher efficiency than commercial benchmarks.

    Advanced NMR at Ames Lab Captures New Details in Nanoparticle Structures

    Advanced NMR at Ames Lab Captures New Details in Nanoparticle Structures

    Advanced nuclear magnetic resonance (NMR) techniques at the U.S. Department of Energy'sAmes Laboratory have revealed surprising details about the structure of a key group ofmaterials in nanotechology, mesoporous silica nanoparticles (MSNs), and the placement of their active chemical sites.

    Plants' Oil-Production Accelerator Also Activates the Brakes

    Plants' Oil-Production Accelerator Also Activates the Brakes

    UPTON, NY--Scientists studying plant biochemistry at the U.S. Department of Energy's Brookhaven National Laboratory recently made a surprising discovery: They found that a protein that turns on oil synthesis also activates a protein that puts the brakes on the same process. In a paper just published in the journal Plant Physiology, they describe how this seemingly paradoxical system keeps oil precursors perfectly balanced to meet plants' needs.

    A Trojan Horse for Fusion Disruptions

    A Trojan Horse for Fusion Disruptions

    Thin-walled diamond shells carry payloads of boron dust; the dust mitigates destructive plasma disruptions in fusion confinement systems.


    • Filters

    • × Clear Filters
    John Crane acquires division of Advanced Diamond Technologies, a company built on Argonne technology

    John Crane acquires division of Advanced Diamond Technologies, a company built on Argonne technology

    John Crane, a global provider of engineered products and services headquartered in Chicago, recently completed the purchase of Advanced Diamond Technologies (ADT), Industrial Division. ADT was founded in 2003 through the licensing of technology from the U.S. Department of Energy's (DOE's) Argonne National Laboratory.

    Energy Department to Invest $32 Million in Computer Design of Materials

    The U.S. Department of Energy announced that it will invest $32 million over the next four years to accelerate the design of new materials through use of supercomputers.

    Demarteau to head ORNL Physics Division

    Demarteau to head ORNL Physics Division

    The Department of Energy's Oak Ridge National Laboratory has named Marcel Demarteau as Physics Division Director, effective June 17.

    PPPL and Oak Ridge manage new DOE program designed to speed development of fusion energy with private-public partnerships

    PPPL and Oak Ridge manage new DOE program designed to speed development of fusion energy with private-public partnerships

    Feature describes PPPL role in innovative DOE program to promote public-private partnerships to speed development of fusion energy.

    ORNL welcomes seven new research fellows to Innovation Crossroads

    ORNL welcomes seven new research fellows to Innovation Crossroads

    Oak Ridge National Laboratory welcomed seven technology innovators to join the third cohort of Innovation Crossroads, the Southeast's only entrepreneurial research and development program based at a U.S. Department of Energy national laboratory.

    New DOE program connects fusion companies with national labs, taps ORNL to lead

    New DOE program connects fusion companies with national labs, taps ORNL to lead

    The Department of Energy has established the Innovation Network for Fusion Energy program, or INFUSE, to encourage private-public research partnerships for overcoming challenges in fusion energy development.

    Department of Energy Announces $75 Million for High Energy Physics Research

    The U.S. Department of Energy (DOE) announced $75 million in funding for 66 university research awards on a range of topics in high energy physics to advance knowledge of how the universe works at its most fundamental level.

    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.


    • Filters

    • × Clear Filters
    Deep Learning Reveals Mysteries of Deep Space

    Deep Learning Reveals Mysteries of Deep Space

    How do you determine the measurable "things" that describe the nature of our universe? To answer that question, researchers used CosmoFlow, a deep learning technique, running on a National Energy Research Scientific Computing Center supercomputer. They analyzed large, complex data sets from 3-D simulations of the distribution of matter to answer that question. The team showed that CosmoFlow offers a new platform to gain a deeper understanding of the universe.

    Explaining Light-Nuclei Production in Heavy-Ion Nuclear Collisions

    Explaining Light-Nuclei Production in Heavy-Ion Nuclear Collisions

    Pairs of sub-atomic particles may catalyze reactions that happened moments after the Big Bang.

    STAR Gains Access to "Wimpy" Quarks and Gluons

    STAR Gains Access to "Wimpy" Quarks and Gluons

    Low-momentum (wimpy) quarks and gluons contribute to proton spin, offering insights into protons' behavior in all visible matter.

    Flipping the Script with Reverse D-Shaped Plasmas

    Flipping the Script with Reverse D-Shaped Plasmas

    Mirrored D shape demonstrates surprisingly high pressures in a tokamak, indicating a shape change may be in order for next-generation fusion reactors.

    Designer Frameworks for Refining Higher Octane Fuels

    Designer Frameworks for Refining Higher Octane Fuels

    Metal-organic frameworks designed with a topology-guided approach show higher efficiency than commercial benchmarks.

    A Trojan Horse for Fusion Disruptions

    A Trojan Horse for Fusion Disruptions

    Thin-walled diamond shells carry payloads of boron dust; the dust mitigates destructive plasma disruptions in fusion confinement systems.

    Found: New Bismuth Compounds in Well-Known Systems of Two Elements

    Found: New Bismuth Compounds in Well-Known Systems of Two Elements

    Scientists discover an unexpected source of new materials, with potential for energy applications.

    Flowing for Function

    Flowing for Function

    A flowing magnetically responsive liquid seamlessly regulates the shape and properties of solids, letting them perform an array of jobs.

    Superconducting Films for Particle Acceleration

    Superconducting Films for Particle Acceleration

    Researchers demonstrated record accelerating cavity performance using a technique that could lead to significant cost savings.

    Parceling Particle Beams

    Parceling Particle Beams

    Beam chopper cuts accelerator-generated ion beams under highly demanding conditions.


    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