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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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Fitterfly Healthtech and Ascensia Diabetes Care Launch a 21-Day Diabetes Management Program on World Diabetes Day

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MUMBAI, India, Nov. 14, 2024 /PRNewswire/ — This World Diabetes Day, on 14th November, Fitterfly Healthtech and Ascensia Diabetes Care are joining hands to launch a complimentary 21-day Diabetes Management Program for Ascensia’s glucometer users. This initiative aims to make diabetes care simpler and more effective for people, offering them personalised support, expert guidance, and easy-to-use tools.

For many, managing diabetes can feel overwhelming. Even with the right tools, knowing where to start can be challenging and confusing. That’s why this 21-day program is designed to help users get started on a wellness journey and build lasting habits, as 21 days is the time it takes to set a habit. By simply scanning a QR code on the warranty page of Ascensia’s glucometer, users can join the Fitterfly program and access diet plans, a 24/7 AI wellness coach, group sessions with diabetes experts, glucose tracking and insights, food diary tracking, assessments, and more. With each step, this structured support brings confidence and clarity, helping users feel truly in control of their health.

Albertraj Balraj, Country Head and Director at Ascensia Diabetes Care India Pvt Ltd., commented, “Glucometers and Self-Monitoring Blood Glucose (SMBG) play an important role in effective blood sugar monitoring. Through this partnership, we aim to offer people a 360° solution by combining our world-class glucometer with Fitterfly’s advanced tools and expert support to make diabetes management truly simple for everyone. We want people to approach diabetes care with confidence and without fear.”

Dr Arbinder Singal, CEO & co-founder of Fitterfly Healthtech, added, “Lifestyle management remains the first line of therapy for type 2 diabetes. Our collaboration with Ascensia makes it easy for people to take control of their health and get started on a journey to lower their blood sugar sustainably. By linking their glucometer to our Fitterfly app, users can track their readings, gain insights, and learn to manage diabetes with ease.”

This partnership is a true example of two brands joining forces to reduce the diabetes burden in the country.

To know more about Fitterfly’s Diabetes Programs, visit Fitterfly.

About Fitterfly

Fitterfly is a leading Indian healthtech company specialising in digital therapeutic programs for managing diabetes, obesity, and heart disease. Co-founded in 2016 by Dr Arbinder Singal and Shailesh Gupta, the Mumbai-based company employs over 200 professionals, including doctors, nutritionists, fitness experts, and technologists. Fitterfly aims to improve metabolic health by focusing on conditions like prediabetes, diabetes, obesity, hypertension, and heart disease. Fitterfly has significantly contributed to health technology research, publishing over 80 papers and winning numerous awards, including the Economic Times Healthtech Startup of the Year 2022. Fitterfly has raised $16.6 million in funding, with its last round in June 2022 led by Amazon with support from Fireside Ventures, 9 Unicorns, and Venture Catalysts.

About Ascensia Diabetes Care

Ascensia Diabetes Care is a global company focused entirely on helping people with diabetes. Our mission is to empower those living with diabetes through innovative solutions that simplify and improve their lives. We are home to the world-renowned CONTOUR® portfolio of blood glucose monitoring systems and the exclusive global distribution partner for the Eversense® Continuous Glucose Monitoring Systems from Senseonics. Ascensia is a member of PHC Group and was established in 2016 through the acquisition of Bayer Diabetes Care by PHC Holdings Corporation. Ascensia products are sold in more than 100 countries. Ascensia has around 1,400 employees and operations in 29 countries. For further information, please visit the Ascensia Diabetes Care website at www.ascensia.com.

Photo: https://mma.prnewswire.com/media/2553921/Fitterfly_Ascensia_Launch.jpg

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Eco-documentary A Chorus of Frogs officially launched

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NANJING, China, Nov. 14, 2024 /PRNewswire/ — Recently, the ecological documentary A Chorus of Frogs produced by Nanjing Newspaper Media Group was officially launched. The film told the story of Wang Ningjing, a post-95s Nanjing girl, who returned to the countryside to find the Chinese immaculate treefrog and shoot a documentary.

https://youtu.be/V8aI9PIFalA?si=Mcc6iP5FeAk3Y8OF

Wang Ningjing, the post-95s generation from Nanjing, is currently studying wildlife filmmaking in the UK. Professor Borzée Amaël from Nanjing Forestry University, who grew up in Madagascar, has been researching treefrogs over ten years.

Unlike most girls who like fairy tales, Wang has been passionate about creature and nature since childhood. Nanjing Hongshan Forest Zoo, not far from her home, was a place she often visited as a child.

“I see one. Is that it?……That one on the wheat. So beautiful!” The species’ breeding season is May and June. During this period, Professor Amaël conducted regular field surveys to locate populations of the treefrog, known for its unique calls that can be heard from a distance. The documentary began with Wang listening to the calls of the treefrog in the fields at night.

A Chorus of Frogs is positioned as an ecological and humanistic documentary. By following Wang Ningjing and Amer to explore the traces of the Chinese immaculate treefrog, it vividly tells the story of people and frogs.

Chinese path to modernization has the distinctive features of respecting nature, following its laws and protect it as well as promoting harmony between humans and nature. The harmonious coexistence between human and the environment is important not only to China but to the world as well.

Where does the Chinese immaculate treefrog go? I believe everyone will find their own answer after watching.

Nanjing Newspaper Media Group, a state-owned media group in Nanjing City, was established on December 17, 2002 with the approval from the National Press and Publication Administration. In recent years, the group has seized strategic opportunities for media convergence to develop a new type of mainstream media based on the Internet. Fully committed to mobile first, it has accelerated the establishment of all-media communication system. The group’s flagship brand, Zijinshan Video, focuses on short video creation, particularly the production of documentaries. It currently has more than 65 million followers across all platforms.

Video – https://www.youtube.com/watch?v=V8aI9PIFalA

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Avathon Partners with CP PLUS, Largest CCTV Manufacturer in India, to Enhance Public Safety while Strengthening Community Bonds

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PLEASANTON, Calif., Nov. 13, 2024 /PRNewswire/ — Avathon, provider of the leading AI platform for industrial operations, has partnered with CP PLUS, one of the largest manufacturers of CCTV cameras, to create safer, more connected societies by bundling Avathon’s computer vision technology with each camera. The companies are bringing Avathon’s computer vision AI capabilities to small and medium-sized businesses (SMBs) across India, turning their cameras into intelligent assets that enable more secure workplaces, factories and facilities.           

In today’s fast-paced world, it’s hard to keep an eye on every single detail, every minute of the day. Computer vision AI technology gives users the freedom and control to go about their daily lives knowing they will receive proactive alerts identifying safety and security issues in real time.

“Increasing demand for advanced public safety tools, smart home devices and integrated AI-powered cameras is fueling massive industry growth,” said Aditya Khemka, Managing Director, CP PLUS, a subsidiary of Aditya Group. “Our partnership with Avathon will help us to better deliver state-of-the-art AI-powered solutions that feature advanced functions like real-time anomaly detection and intelligent monitoring.”

Avathon’s computer vision AI automatically detects and alerts unsafe conditions and incidents in real time, allowing users to proactively take the right actions. Avathon enables business owners using valuable resources to monitor CCTV camera feeds to get back to focusing on operations. The company partners with OEM camera manufacturers by providing AI technology that enables end customers to quickly and accurately address processes, behaviors, and conditions that cause unacceptable risk. Through its partnership with CP PLUS, Avathon has democratized this technology, giving access to large organizations and small businesses alike.

CP PLUS is India’s leading surveillance brand with the most extensive portfolio in the entire global industry. Representing a major share of the Indian CCTV market, CP PLUS offers a range of products and services to meet the varied needs of government, commercial, residential, and industrial customers and its products are successfully deployed in every nook and corner of India and many countries across verticals and industry.

“AI cameras are paving the path forward in India toward smart-city initiatives and enhanced public safety improvements. In this sometimes disconnected world, it’s comforting to rely on a technology that instantly alerts users to potential dangers and other anomalies,” said Pervinder Johar, CEO of Avathon. “We’re proud to partner with CP PLUS to provide the AI innovations needed to push India to the leading edge of technological advancement.”

About Avathon

Avathon, a leader in Industrial AI, extends the life of critical infrastructure while advancing the journey toward full autonomy. Avathon’s Industrial AI platform empowers commercial and government customers with scalable, secure, and value-driven solutions that enhance efficiency and resilience across heavy industry.

Media contact:

Jon Ross
Sr. PR & Communications Manager
Avathon
jross@avathon.com

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SOURCE Avathon

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