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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
ContactHiroe YonedaSenior Specialist in Project Planning and OutreachNanoLSI Administration OfficeNano Life Science Institute (WPI-NanoLSI)Kanazawa UniversityKakuma-machi, Kanazawa 920-1192, JapanEmail: [email protected]: +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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Dongfa Group’s Gas Scenario + Digital Twin Technology, Leads the Industry with New AI Trend

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–Highlights of the 2024 Exhibition
SHANGHAI, May 23, 2024 /PRNewswire/ — From May 17 to 19, 2024, China(Shanghai) International Metrology Measurement Technology and Equipment Exhibition was held at the Shanghai World Expo Exhibition and Convention Center. Dongfa Group participated in the exhibition, showcasing its latest research achievements. At the expo, Chairman Liu Ming of Dongfa Group conducted the lighting ceremony and announced the official launch of the “Smart Gas Comprehensive Supervision Platform,” demonstrating the convenience and efficiency achieved through the smart management of municipal gas meters.

Dandong Dongfa (Group) Co., Ltd., established in 1962 and headquartered in Singapore, was formerly known as Dandong Thermal Instrument Co., Ltd. As an integrated group company engaged in research, production, and operations, Dongfa Group is dedicated to the development and application of instruments and meters. Its product range includes IC card gas meters, wired direct-reading remote diaphragm gas meters, wireless direct-reading remote diaphragm gas meters, NB-IoT IoT meters, and ultrasonic gas meters. These products incorporate the technical features of similar domestic and international products, offering high accuracy, reliability, and stability, making the company a leading smart gas meter manufacturer in China.
At the expo, Dongfa Group showcased its Smart Gas Comprehensive Supervision Platform, which integrates AI, IoT, cloud computing, and big data. This platform connects the topological structure of all aspects of gas operations and consolidates all relevant data involved in production management and operation maintenance. This integration enhances the comprehensive research and development and operational maintenance capabilities of the big data governance system.
At the same time, Dongfa Group is empowering comprehensive management and control with digital twins, AI, and big data. By leveraging digital twins, AI models, and 5G technology as data elements, the company is constructing a unified citywide network and a digital twin map of the gas pipeline network. This enables deep integration of AI monitoring, pressure and leakage detection, smart terminals, and other sensing devices with gas operations, ensuring the comprehensive safety and supply of urban gas.
Digital twin gas technology not only provides auxiliary support for pipeline design, but also plays a crucial role in intelligent emergency response and precise distribution. Especially in the operation of gas stations, it enables comprehensive real-time monitoring, intelligent integrated operation scheduling, proactive warning, emergency event command plans, and other effects, thereby improving the efficiency and safety of gas management.
However, there have been numerous incidents of data leakage involving smart AI devices in recent years. Sensitive data is being collected or even sold by malicious actors, leading to the disclosure of confidential information, resulting in significant economic losses and even legal risks.
To ensure the security of both enterprise and user data, Dongfa Group utilizes Digital Envelope technology to encrypt and decrypt data packets during data collection and distribution. This approach combines the advantages of both symmetric and asymmetric encryption technologies for secure information transmission, enabling fast, efficient, and secure encryption and decryption processing for the smart gas digital business sector. This ensures the security and integrity of data during transmission.
Visitors at the expo showed strong interest in the new products and technologies exhibited by Dongfa Group. Dongfa Group has always been committed to driving the development of the smart instrumentation industry through technological innovation. Through this exhibition, the company not only showcased its technical prowess but also strengthened communication and collaboration with industry peers. Looking ahead, they aim to join hands in opening a new chapter in the smart instrumentation industry.
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QNAP S3-compatible Storage Solution “QuObjects” Certified as Veeam® Ready – Object with Immutability

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TAIPEI, May 23, 2024 /PRNewswire/ — QNAP® Systems, Inc., a leading computing, networking, and storage solution innovator, today announced that its S3-compatible object storage solution “QuObjects” has qualified as Veeam® Ready – Object with Immutability, applicable for QNAP NAS with QTS and QuTS hero operating systems. This certification underscores the reliability of QuObjects as a secure object backup solution for enterprises, enhancing data management efficiency and upmost security.

QuObjects is the S3 object storage solution for QNAP NAS, boasting read/write speeds 20 times faster than conventional cloud services, along with a highly flexible and scalable architecture to ensure efficient transmission and flexibility in object storage. From object service development to demanding workloads like machine learning and data lakes, QuObjects assists enterprises in achieving diverse application needs with higher cost effectiveness.
QuObjects supports Object Lock to ensure data immutability, further safeguarding against ransomware threats, cyberattacks, or human error. Coupled with access controls and authentication features, it provides comprehensive protection for object data security.
Jimmy Tam, Product Manager of QNAP, stated “Data security is critical for enterprises. With QuObjects certified by Veeam Ready – Object with Immutability, we empower organizations leveraging Veeam solutions to confidently opt for QNAP NAS for on-prem S3 object storage and backup, enjoying rapid transmission, extensive scalability, and steadfast security.”
QNAP is the preferred partner for Veeam object backup solutions. Learn more at Veeam Ready Object Partner and QNAP QuObjects- S3 Object Storage.
For more information and to view the full QNAP NAS lineup, please visit www.qnap.com.
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Tencent Announces Winners of Flagship CarbonX Program to Combat Climate Change

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SHENZHEN, China, May 23, 2024 /PRNewswire/ — Tencent (00700.HK) is awarding 13 exceptional teams that won the first phase of its groundbreaking CarbonX Program, which is aimed at boosting promising new climate technologies. The winners, which emerged from a pool of 30 finalists and more than 300 initial applications, will receive a total of around RMB 100 million (US$14 million) in financial support from Tencent. It showcases the company’s commitment to driving sustainable social innovations in the fight against climate change.

CarbonX was launched in March 2023 to advance the next generation of low-carbon technologies. Tencent has committed RMB 200 million (US$28 million) in catalytic funding over the next three years to innovative ideas that might otherwise languish or fail to gain traction.
CarbonX’s first phase focused on carbon capture, utilization, and storage (CCUS), as well as technology-based carbon removal. These solutions were chosen for their unique ability to curb emissions from hard-to-abate industries such as steel and cement, mitigate the continued reliance on fossil fuels, and reduce legacy emissions created from decades of industrialization.
Backed by Tencent’s mission of Tech for Good and an alliance of like-minded industry partners, CarbonX aims to help these cutting-edge technologies make the leap from the research or early startup stage to commercial scale. The ultimate goal is supporting them in making a significant impact toward the targets outlined in the Paris Agreement, which includes a 45 percent reduction in emissions by 2030 and achieving net-zero emissions by 2050.
Dr. Hao Xu, Tencent’s Vice President of Sustainable Social Value and Head of Tencent’s Carbon Neutrality Lab, said: “Technology innovation serves as the driving force to accelerate our progress toward achieving carbon neutrality. CarbonX program is aimed at fostering the growth of these technologies, driving positive impact across society, and laying the groundwork for a more sustainable future.”
Professor Jerry Yan, Chair Professor of the Hong Kong Polytechnic University and Co-chairman of the CarbonX expert committee, said: “To pave the path for a greener economy, we must champion the development of cutting-edge low-carbon technologies. Just as solar and wind power were nurtured in their infancy, emerging solutions like CCUS and tech-based carbon removal demand our early support.”
The program assembled a panel of experts from academia, industries, and the investor community as the jury, and welcomed submissions from diverse participants across three distinct tracks:
CarbonX Lab: Designed to incubate research institutions, universities, or labs that bring in game-changing climate solutionsCarbonX Accelerator: Designed to accelerate the growth of climate-tech startups that exhibit commercialization potentialCarbonX Infrastructure: Designed to support capacity building to facilitate industry developmentThe finalists comprise four projects from the Lab track, six from the Accelerator track, and three from the Infrastructure track. These projects explore innovative solutions, such as using steel slag to capture and store carbon directly from furnace exhaust, converting CO2 into sustainable aviation fuel and valuable chemicals through electrochemical reactions or microorganisms, and employing new approaches to directly capture CO2 from the atmosphere with the hope of slashing the cost to less than US$150 per ton.
Meanwhile, Tencent is also collaborating with Tsinghua University to develop a comprehensive system of Measure, Reporting and Verification (MRV) tools to accurately gauge progress toward decarbonization.
Aside from receiving financial and advisory support, several projects will also have the opportunity to collaborate with industry partners and test their research beyond the laboratory setting.
Building upon the success of the first phase, Tencent is poised to launch the second iteration of CarbonX globally as early as later this year in pursuit of early-stage climate tech innovation.

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