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Kanazawa University research: Chromatin Accessibility: A new avenue for gene editing

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KANAZAWA, Japan, Feb. 16, 2024 /PRNewswire/ — In a study recently published in Nature Genetics, researchers from Nano Life Science Institute (WPI-NanoLSI), Kanazawa University explore chromatin accessibility, i.e., endogenous access pathways to the genomic DNA, and its use as a tool for gene editing.

Our DNA is protected from unwanted external modifications by forming structures called nucleosomes that consist of threads of DNA wound around chunks of special proteins known as histones. This unique coiled shape prevents the access of undesirable molecules to a cell’s DNA. However, for vital genetic functions—such as DNA repair—the right set of proteins require access to these DNA fragments. This phenomenon known as ‘chromatin accessibility’ involves a privileged set of protein molecules, many of which are still unknown.

Now, researchers from Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, led by Yusuke Miyanari, have used advanced genetic screening methods to unravel chromatin accessibility and its pathways.

For the investigation the team used a combination of two technologies—CRISPR screening and ATAC-see. While the former is a method to suppress the function of a desired set of genes, the latter is a means to identify which ones are essential for chromatin accessibility. Thus, using this method all genes playing a crucial role in chromatin accessibility could be pinned down.

With the help of these assays, novel pathways and individual players involved in chromatin accessibility were uncovered—some playing a positive role and some negative. Of these, one particular protein, TFDP1, showed a negative effect on chromatin accessibility. When it was suppressed, a significant increase in chromatin accessibility was observed, accompanied by nucleosome reduction. A deeper dive into the mechanism of TFDP1 revealed that it functions by regulating the genes responsible for production of certain histone proteins.

The team then focused their study towards exploring biotechnological applications of their findings. After suppressing TFDP1, two different approaches were tried. The first approach involved gene editing using the CRISPR/Cas9 tool. This revealed that deletion of TFDP1 made the gene editing process easier. Now, most chromatin accessibility occurs in nucleosome-depleted regions or NDRs. However, by suppressing TFDP1 chromatin accessibility occurred not only in NDRs but across other regions as well. Secondly, the depletion of TFDP1 aided the process of converting regular cells into stem cells, a massive step forward in cellular transformation.

This study identified new chromatin accessibility pathways and channels for exploring its potential even further. “Our study shows the significant potential to manipulate chromatin accessibility as a novel strategy to enhance DNA-templated biological applications, including genome editing and cellular reprogramming,” conclude the researchers.

Background

CRISPR screening: CRISPR screening is a large-scale tool used to find genes involved in a particular function. In this method, genes from the entire genome can be deleted one at a time to investigate which ones play a role in any target pathway. The mechanisms and roles of the genes narrowed down are then understood further using biological assays. In this study the genes identified by CRISPR screening were subjected to ATAC-see to confirm their involvement with chromatin accessibility.

ATAC-see: Transposase-Accessible Chromatin with visualization (ATAC-see) is a technique whereby accessible DNA locations can be visualized and quantified. ATAC-see involves using an enzyme to insert fluorescent proteins into the DNA at accessible sites. This technique works within nucleosome-depleted regions but also beyond these regions. Hence, when such sites were visualized after running CRISPR screening, the researchers could understand which genes were affecting chromatin accessibility directly.

Reference

Satoko Ishii, Taishi Kakizuka, Sung-Joon Park, Ayako Tagawa, Chiaki Sanbo, Hideyuki Tanabe, Yasuyuki Ohkawa, Mahito Nakanishi, Kenta Nakai, Yusuke Miyanari. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nature Genetics, 2024. Published Feb 15, 2024

DOI :10.1038/s41588-024-01658-1

https://www.nature.com/articles/s41588-024-01658-1

Related figures

https://nanolsi.kanazawa-u.ac.jp/wp/wp-content/uploads/Fig.-1-1.png

Figure 1. a. Screening results of the players involved in chromatin accessibility analyzed by ATAC-see.

b. Successful reprogramming to stem cells (indicated by presence of TRA-1-60) after depletion of TFDP1 (right).

© 2024 Ishii, et al., Nature Genetics

Contact
Hiroe Yoneda
Senior Specialist in Project Planning and Outreach
NanoLSI Administration OfficeNano Life Science Institute (WPI-NanoLSI)
Kanazawa University
Kakuma-machi, Kanazawa 920-1192, Japan
Email: nanolsi-office@adm.kanazawa-u.ac.jp
Tel: +81 (76) 234-4555

About Nano Life Science Institute (WPI-NanoLSI), Kanazawa University

Understanding nanoscale mechanisms of life phenomena by exploring “uncharted nano-realms.”

Cells are the basic units of almost all life forms. We are developing nanoprobe technologies that allow direct imaging, analysis, and manipulation of the behavior and dynamics of important macromolecules in living organisms, such as proteins and nucleic acids, at the surface and interior of cells. We aim at acquiring a fundamental understanding of the various life phenomena at the nanoscale.

https://nanolsi.kanazawa-u.ac.jp/en/

About the World Premier International Research Center Initiative (WPI)

The WPI program was launched in 2007 by Japan’s Ministry of Education, Culture, Sports, Science and Technology (MEXT) to foster globally visible research centers boasting the highest standards and outstanding research environments. Numbering more than a dozen and operating at institutions throughout the country, these centers are given a high degree of autonomy, allowing them to engage in innovative modes of management and research. The program is administered by the Japan Society for the Promotion of Science (JSPS).

See the latest research news from the centers at the WPI News Portal: https://www.eurekalert.org/newsportal/WPI

Main WPI program site:  www.jsps.go.jp/english/e-toplevel

About Kanazawa University

As the leading comprehensive university on the Sea of Japan coast, Kanazawa University has contributed greatly to higher education and academic research in Japan since it was founded in 1949. The University has three colleges and 17 schools offering courses in subjects that include medicine, computer engineering, and humanities.

The University is located on the coast of the Sea of Japan in Kanazawa – a city rich in history and culture. The city of Kanazawa has a highly respected intellectual profile since the time of the fiefdom (1598-1867). Kanazawa University is divided into two main campuses: Kakuma and Takaramachi for its approximately 10,200 students including 600 from overseas.

http://www.kanazawa-u.ac.jp/e/

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Warhound Launches with $200 Million to Rebuild America’s Military Working Dog Supply, Using Advanced Genetics and Defense Technology

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Company will produce genetically enhanced working dogs that leverage cybernetics technology to improve health and performance while ending reliance on foreign suppliers

DALLAS and COSTA MESA, Calif., Oct. 23, 2026 /PRNewswire/ — Warhound, a new defense technology company conceived by American technology entrepreneurs Ben Lamm and Palmer Luckey emerged from stealth with a $200 million seed round. Warhound will rebuild America’s domestic supply of elite working dogs for U.S. military forces, law-enforcement, emergency first response teams—a critical national security resource that the U.S. has long relied on foreign countries to provide. Led by CEO David Spirk, the company will reduce dependence on a shrinking European supply chain and strengthen America’s ability to protect its own people, infrastructure, and national security interests.

Warhound is modernizing America’s working-dog program by delivering a vertically integrated program, combining Colossal’s enhanced genetics platform and secure biobanking capabilities of America’s top-performing dog arsenal, controlled delivery through cloning with best-in-class training and animal care. Through a partnership, all dogs will be equipped by Anduril’s advanced cybernetic Augments, software, and battlefield situational awareness. The company is backed by In-Q-Tel, Sequoia Capital, ARK Invest, Franklin Templeton, 8VC, USIT, Bob Nelsen, Breyer Capital, CAZ Investments, Neogenesis, Builders VC, and Lux Capital among others. Based in Texas, Warhound will operate under the guidance of the American Humane Society which will certify its training programs and support the reunification of retired military working dogs with their former handlers and adoption protocols.

“Palmer, Ben and the Warhound team are exceptional. Sequoia is proud to back them,” said Shaun Maguire, Partner at Sequoia Capital.

Warhound is bringing together Colossal’s breakthroughs in genetics, cloning, and animal biology with Anduril’s advanced defense technology to fundamentally change how America produces, trains, and protects its military working dogs. Colossal’s science will help produce healthier dogs with characteristics suited to demanding missions, while Anduril’s technology will give dogs and their handlers greater awareness and protection in the field.

“Every day, we ask dogs to put their lives on the line to protect ours. They detect explosives, protect our troops, and run toward dangers that most people are trained to run away from. Yet we’re still relying on outdated approaches to breeding and training these extraordinary animals, with too many never making it through the process. We have an opportunity to fundamentally change that. Colossal has spent years pioneering breakthroughs in genetics, cloning, and animal biology, and now we’re applying that science to give these dogs the best possible chance at a long, healthy life and a successful mission. If we’re going to ask man’s best friend to protect America, we owe it to them to use every tool at our disposal to protect them, too,” said Ben Lamm.

Since the Army established the K-9 Corps in 1942, military working dogs have served alongside America’s armed forces for more than 84 years—detecting threats, protecting service members and supporting missions worldwide. That program has evolved in The United States Department of War’s (DOW) Military Working Dog Program, which currently includes 2,200+ working dog teams that are operationally critical for detection and patrol work, and a critical part of the defense infrastructure of the country. More than 80% of U.S. military working dogs are currently acquired from Europe, creating a critical interdependency on foreign nations for an asset the Pentagon itself calls irreplaceable. That dependency is compounding: after a rigorous, roughly three-year acquisition-and-training pipeline, less than half of the dogs procured are ultimately deemed fit for service, meaning the U.S. must source and train roughly 200 dogs today to field 100 working animals tomorrow.

“Man’s best friend deserves man’s best tech,” said Palmer Luckey. 

David Spirk has been named the CEO of Warhound. As a veteran of the United States Marine Corps, he worked as an intelligence specialist with multiple deployments and ultimately served as the Deputy Associate Director of National Intelligence for Afghanistan and Pakistan at the Office of the Director of National Intelligence representing the Intelligence Community at the White House and on Capital Hill. He has an extensive background in the U.S. military, intelligence community, and federal data governance, specifically focused on scaling algorithmic warfare and creating data driven advantages. More recently, he was a Senior Counselor at Palantir Technologies where he focused on expanding the company’s software footprints across the U.S. government, allied international partners, and commercial sectors. Previously, he was appointed the First Chief Data Officer (CDO) for the Department of War, where he worked on accelerating the military’s data-driven capabilities and was the first CDO for the U.S. Special Operations Command (USSOCOM).

“Our long-term goal is simple: healthier dogs, better-prepared teams, and more service members and first responders coming home safely. Leading Warhound, and strengthening America’s working-dog capabilities, is an opportunity to apply my experience to a mission I care deeply about: protecting people and helping the animals who support them,” said David Spirk. “My focus is building a team that can turn scientific advances into capabilities that work in the field.”

Building Healthier, More Capable Working Dogs to Protect Both Dogs and People
The concept of Warhound was conceived years ago by Palmer and Ben after a discussion at Peter Diamandis’ Moonshots Summit. Military working-dog programs face a costly challenge: more than half of candidate dogs fail to complete training, while reliance on overseas breeders leaves the United States dependent on a constrained foreign supply chain. Warhound was created to improve that system—producing fewer dogs with a greater likelihood of remaining healthy, completing training, and succeeding in their missions.

Warhound dog-and-handler teams will also connect Anduril’s integrated capabilities—including eye and ear protection and Eagle Eye technology—will help safeguard working dogs, their handlers and the wider unit while supporting safer, more effective missions.

“For millennia, people have selectively bred dogs to be companions and helpmates. Modern biotechnology gives us a more precise way to shape some of their traits, thus improving both the work dogs do and their own health and well-being,” said Alta Charo, Warren P. Knowles Professor Emerita of Law and Bioethics at the University of Wisconsin–Madison. “The Warhound project offers the possibility of improving working dogs’ health and welfare while supporting the lifesaving work they do. But we still must look carefully at who benefits, what risks the animals bear, and how concern for animal welfare translates into practice through careful evaluation of the evidence, meaningful oversight, and responsibility for the dogs throughout their lives, including retirement. The American Humane Society brings valuable experience through its military working dog reunification efforts and Pups4Patriots program. That experience provides a foundation, but public trust has to be earned through the care we provide and the commitments we keep.”

Animal welfare is central to the program. By improving health, durability, and training success, Warhound will significantly reduce washouts, limit the number of dogs unnecessarily entering intensive training and enable safer, more effective missions. Technologies and therapeutics developed through the program will also be made available to all dogs and ultimately improve the health of all dogs, not only those serving alongside America’s service men and women. Together, these capabilities will establish a secure domestic supply of military working dogs while giving American service members healthier, more capable canine partners.

“Working dogs are extraordinary animals whose courage and loyalty save lives,” said Dr. Robin Ganzert, President and CEO of American Humane Society. “We owe these dogs a commitment to their well-being that matches their service to us. What excites me about Warhound is the opportunity to make health, welfare, and exceptional care fundamental to a working-dog program from the very beginning. Success means helping these dogs thrive throughout their lives—from training and active service to the loving, dignified retirement every canine hero deserves.”

Warhound is built to take today’s level of performance and make it better: using cutting edge engineering and technology, on American soil, from American companies, without the wait times, price volatility, or geopolitical exposure of a foreign supply chain.

About Warhound
Warhound is a Texas-based defense technology company building a secure domestic supply of healthier, more capable working dogs for the U.S. military, law enforcement and emergency responders. Conceived by Palmer Luckey and Ben Lamm, Warhound combines biotechnology licensed from Colossal Biosciences with advanced training and Anduril’s cybernetic augments and software. The company aims to reduce reliance on foreign suppliers, improve canine health and performance, and enhance safety for dogs and their handlers. Animal welfare is central to Warhound’s mission, with a commitment to lifelong care from birth through training, service and retirement. To follow along, please visit: warhound.com.

About Anduril
Anduril Industries is a defense technology company that builds autonomous systems and a common operating layer to give the United States and its allies a persistent advantage in sensing, decision-making, and force projection.

About the American Humane Society
The American Humane Society is the country’s first national humane organization and a global leader in animal welfare. Founded in 1877, American Humane has been at the forefront of protecting animals, rescuing them from cruelty, abuse, and natural disasters, and setting the gold standard in science-based welfare certifications. The organization oversees prominent programs including the iconic “No Animals Were Harmed®” film and television certification, the American Humane Certified™ farm and zoo standards, military working dog reunifications, and the Pups4Patriots™ service dog program. Learn more at americanhumane.org. 

About Colossal Biosciences
Colossal was founded by emerging technology and software entrepreneur Ben Lamm and world-renowned geneticist and serial biotech entrepreneur George Church, Ph.D., and is the first to apply CRISPR technology for the purposes of species de-extinction. Colossal creates innovative technologies for species restoration, critically endangered species protection and the repopulation of critical ecosystems that support the continuation of life on Earth. Colossal is accepting humanity’s duty to restore Earth to a healthier state, while also solving for the future economies and biological necessities of the human condition through cutting-edge science and technologies. To follow along, please visit: www.colossal.com.

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Best Version Media Names Chris Laurence Next CEO; Kevin O’Brien Transitions to CRO

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Leadership investment strengthens companywide execution and sharpens focus on Publisher success and revenue growth

BROOKFIELD, Wis., Oct. 23, 2026 /PRNewswire/ — Best Version Media (BVM), a local media and marketing company serving more than 1,300 communities across the United States and Canada, today announced that Chris Laurence has joined the company as Chief Executive Officer. Kevin O’Brien, who previously served as CEO, will transition to Chief Revenue Officer, focusing on leading BVM’s sales field and accelerating revenue growth.

The appointments reflect BVM’s investment in leadership to support its next stage of growth. By establishing dedicated executive leadership for the broader organization and the sales field, BVM is strengthening its ability to execute across the business while supporting its independent Publishers and the local businesses they serve.

“Our growth has brought us to a point where leading the overall company and leading our sales field each deserve a dedicated focus,” said O’Brien. “This transition allows me to concentrate on working with our sales leaders and Publishers, strengthening the field, and helping more local businesses connect with their communities. I’m excited to partner with Chris as we build on BVM’s momentum.”

Laurence brings experience as CEO, CFO, and COO of public, private, and private equity-backed companies, where he has led growth, operational improvement, and technology transformation. Before moving into operating roles, he was a general partner at Brentwood Associates, a Los Angeles-based private equity firm.

“BVM has built a powerful combination of community storytelling, local relationships, and marketing solutions for small businesses,” said Laurence. “I look forward to working with Kevin and the entire team to build on that foundation, strengthen how we operate, and support the success of our Publishers and clients.”

As CEO, Laurence will lead BVM’s overall strategy and operations, working with the team to scale operations and support the success of our Publishers and the local businesses they serve. As CRO, O’Brien will focus on sales leadership, Publisher growth, and revenue generation. Together, they will help advance BVM’s print and digital offerings and position the company for continued growth.

About Best Version Media

Founded in 2007, Best Version Media (BVM) connects local businesses with customers through community magazines, targeted digital advertising, and online presence management tools. Serving more than 1,300 communities across the United States and Canada, BVM’s network of independent Publishers builds relationships with local businesses and brings community stories to life. BVM is a portfolio company of H.I.G. Capital. To learn more, visit www.bestversionmedia.com.

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Dow and Small Caps Climb Weekly While Nasdaq Slips on Megacap Earnings Charges

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VANCOUVER, BC, Oct. 23, 2026 /PRNewswire/ — Stock Preachers News Commentary – Stocks closed a volatile earnings week with a split verdict: the Dow gained 0.64% and the Russell 2000 jumped 2.07%, while the Nasdaq Composite fell 0.45% and the S&P 500 slipped 0.22%. The VIX rose to 19.40 and the VXN climbed to 28.13 as traders weighed a wave of third-quarter results. Gold dropped 3.47% and silver fell 4.90% on the week, while WTI crude rose 3.74% on Thursday alone. The 10-year Treasury yield eased 11 basis points to 4.99%. Active Companies from around the markets with current developments this week include: Meta Platforms, Inc. (Nasdaq: META), Texas Instruments Incorporated (Nasdaq: TXN), RTX (NYSE: RTX), IBM (NYSE: IBM), and First Citizens BancShares, Inc. (Nasdaq: FCNCA).

Large-cap benchmarks diverged sharply this week. The Dow closed at 52,337.54, up 0.64% for the week despite a 1% drop on Friday, while the S&P 500 ended at 7,642.22, down 0.22% weekly after touching a week high of 7,770.40. The Nasdaq Composite settled at 26,022.45, down 0.45% on the week, dragged by a rough stretch for megacap tech following a batch of earnings reports.

The Russell 2000 was the standout, closing at 2,777.63 for a 2.07% weekly gain, outperforming its large-cap peers as investors rotated toward smaller names. RSI readings show the Nasdaq at 38.9 and the S&P 500 at 43.5, both in cooler territory, while the Dow’s RSI of 54.1 reflects its relative strength this week.

Volatility ticked higher into the weekend, with the VIX up 0.96 points for the week to 19.40 and the VXN up a full point to 28.13. In commodities, natural gas spiked 8.66% on Thursday alone even as it remained down 0.65% for the week, while copper rose 2.44% daily. The dollar firmed slightly against the euro, with EUR/USD down 0.24% on the week to 1.12.

The full report also breaks down key support and resistance levels for each index, additional earnings movers, and sentiment heading into next week’s sessions.

CONTINUED… Read this and more news for Meta Platforms, Inc. (Nasdaq: META), Texas Instruments Incorporated (Nasdaq: TXN), RTX (NYSE: RTX), IBM (NYSE: IBM), and First Citizens BancShares, Inc. (Nasdaq: FCNCA) at: https://stockpreachers.com/articles/small-caps-lead-big-tech-lags-as-earnings-season-shakes-the-tape/

In other industry developments and happenings in the market this week include:

Meta Platforms, Inc. (Nasdaq: META) Meta reported third-quarter revenue of $64.60 billion, up 26% year over year, but net income of $9.86 billion reflected a $9.89 billion charge tied to an agreement with 52 state attorneys general over teen mental health and social media litigation. Diluted EPS was $3.83, up 265% year over year; excluding the litigation charge, EPS would have been $7.40.

Operating margin fell to 20% from 40% a year earlier, while costs and expenses rose 68% to $51.61 billion. Capital expenditures, including finance lease payments, totaled $34.91 billion, and free cash flow was negative $2.12 billion for the quarter.

“We hit major milestones this quarter toward delivering personal superintelligence for everyone – including launching Muse and Muse Wonder, our first frontier model,” said Mark Zuckerberg, Meta founder and CEO. “Our investments are paying off, the core business is strong, and we’re seeing velocity across the board.” The company guided fourth-quarter revenue to a range of $73-76 billion and raised full-year 2026 total expense guidance to $175-179 billion. Read the release.

Texas Instruments Incorporated (Nasdaq: TXN) Texas Instruments reported third-quarter revenue of $6.06 billion, up 28% from a year earlier, with net income of $2.43 billion and earnings per share of $2.62. Operating profit rose 73% to $2.87 billion, and revenue increased 11% sequentially.

“Revenue increased 11% sequentially and 28% from the same quarter a year ago with continued broad growth in industrial, automotive and data center,” said Haviv Ilan, TI’s chairman, president and CEO. Trailing 12-month cash flow from operations was $9.9 billion, with free cash flow of $8.4 billion.

The company returned $5.8 billion to shareholders over the trailing 12 months and guided fourth-quarter revenue to a range of $5.80 billion to $6.30 billion, with earnings per share expected between $2.45 and $2.79. Read the release.

RTX (NYSE: RTX) RTX reported third-quarter sales of $25.0 billion, up 11% versus the prior year and 12% organically, with adjusted EPS of $2.26, up 33% from a year earlier. GAAP EPS was $1.89. Operating cash flow was $2.9 billion and free cash flow was $2.1 billion, with results including $0.25 of IEEPA cost recovery per share.

The company’s backlog reached a record $340 billion, including $176 billion commercial and $164 billion defense, after over $81 billion of new awards including Tomahawk and AMRAAM multi-year production contracts.

“Our strong execution and operational focus in the third quarter enabled RTX to deliver double-digit organic sales growth across commercial aerospace and defense,” said RTX Chairman and CEO Chris Calio. The company raised its full-year adjusted EPS outlook to $7.65-$7.75 and adjusted sales guidance to $97.0-$97.5 billion. Read the release.

IBM (NYSE: IBM) IBM reported third-quarter revenue of $17.1 billion, up 5% as reported and 6% at constant currency, with Software revenue up 8% and Infrastructure revenue up 4%. GAAP diluted earnings per share were $2.31, up 26% year over year, while operating (non-GAAP) EPS was $2.95, up 11%.

The company generated $4.0 billion in net cash from operating activities in the quarter and $3.0 billion in free cash flow, up $0.7 billion year over year. Year to date, free cash flow reached $7.8 billion.

“Disciplined execution throughout the quarter drove accelerated revenue growth and strong free cash flow,” said Arvind Krishna, IBM chairman, president and chief executive officer. IBM now expects full-year free cash flow to increase by more than $1 billion year over year, while continuing to guide constant currency revenue growth of four to five percent. Read the release.

First Citizens BancShares, Inc. (Nasdaq: FCNCA) First Citizens BancShares reported third-quarter net income of $606 million, down from $672 million in the linked quarter. Net income available to common stockholders was $577 million, or $51.23 per common share, a $63 million decrease from the prior quarter’s $640 million.

Net interest income rose to $1.70 billion, up $43 million from the linked quarter, while net interest margin declined 3 basis points to 3.07%. The company completed its BMO Branch Acquisition on September 4, 2026, assuming approximately $4.9 billion in deposits and acquiring approximately $650 million in loans.

“We returned $600 million to our stockholders through share repurchases and further optimized our balance sheet by repaying another $8.0 billion of the Purchase Money Note,” said Chairman and CEO Frank B. Holding, Jr. The board approved a new repurchase plan authorizing up to $1.2 billion of Class A common shares through 2027. Read the release.

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