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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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Madison Liquidators Launches Office Essentials to Highlight Necessities Nationwide

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January 7, 2025

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MADISON, Wis., Jan. 7, 2025 /PRNewswire/ — Madison Liquidators, a trusted name in online office furniture solutions, is excited to announce the launch of its Office Essentials campaign, a targeted initiative to help businesses and individuals create productive, ergonomic, and stylish work environments. The Office Essentials campaign focuses on providing high-quality, affordable office furniture basics tailored to the needs of modern workplaces. Madison Liquidators aims to simplify the shopping experience for office must-haves while delivering exceptional value to customers.

Some of the major highlights of the Office Essentials Campaign will include curated product lines, special promotions, as well as expert guidance. Curated product lines feature handpicked selections of office desks, chairs, storage solutions, and accessories from top brand partners. Expert guidance will be the crowning force in the essentials campaign as Madison Liquidators has always prioritized customer service. With this in mind, the expert guidance focus of the campaign offers personalized support from the company’s customer support team to help shoppers find the perfect solutions for their space and budget.

The Office Essentials campaign is an excellent time for businesses large and small to optimize their office space with everything they need to create a productive office space. This means the campaign will feature common items such as l-shape desks, ergonomic office chairs, storage cabinets, and conference tables. This will provide offices not only an incentive to update their spaces with quality office furniture but also to help new businesses understand other items necessary to office productivity like monitor arms, laptop stands, desk accessories, and keyboard trays.

The Office Essentials campaign is live now, with new products and deals updated on the Madison Liquidators website. The homepage has a tab dedicated to Office Essentials for shoppers to quickly navigate the essentials.  Since 2015, Madison Liquidators has been a leading provider of office furniture and solutions, offering a vast inventory of high-quality products to businesses and individuals nationwide. Known for its dedicated customer service, Madison Liquidators is dedicated to enhancing workspaces with furniture that marries efficiency with employee comfort and well-being.

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BSI Financial Services SVP Allen Price Joins IMN Home Equity Investment Advisory Board

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January 7, 2025

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IRVING, Texas, Jan. 7, 2025 /PRNewswire/ — BSI Financial Services, a national mortgage fintech platform, today announced that Allen Price has been selected to join the IMN Home Equity Investment Advisory Board. Price, who serves as senior vice president of sales, client and transaction management at BSI Financial Services, is the first mortgage servicing executive appointed to the Board.

The IMN Home Equity Investment Advisory Board is comprised of thought leaders and key stakeholders from servicing, capital markets, HEI originations and rating agency organizations who are dedicated to advancing the primary and secondary markets through innovation and strategic collaboration. Price’s position on the Advisory Board reflects BSI Financial’s growing prominence in the HEI space. BSI is a rated servicer that provides both full and backup servicing and asset management for rated and non-rated HEI backed securitizations, as well as non-securitized HEI assets. BSI Financial also services traditional home equity lines of credit (HELOC) and closed-end second lien loan products.

“I am deeply honored to join the IMN Home Equity Investment Advisory Board and to collaborate with such an accomplished group of mortgage and capital markets professionals,” Price said. “This opportunity allows me to continue to provide thought leadership and innovation to this very important and growing sector while bringing to the table BSI Financial’s unique perspective and expertise in servicing HEI assets.”

BSI Financial’s proprietary technology stack, including Libretto and BSI ASSET360, differentiates the company from other servicers. Libretto automates daily quality control, reducing processing errors and identifying potential issues before they impact customers. BSI ASSET360 provides lenders and investors with real-time visibility into asset status and performance. These systems help build consumer, originator, regulatory and investor confidence in the growing HEI sector.

BSI Financial has experienced substantial growth in its servicing portfolio of HEI assets. The company now services approximately $2.1 billion in unpaid principle balances across 22,000 units, establishing itself as a servicing industry leader in the home equity investment asset class.  

“Building world-class servicing operational processes to support the unique and bespoke nature of HEI assets that will provide homeowners with greater financial flexibility is exactly what BSI is all about,” said Harold Lewis, President and COO of BSI Financial Services.

For more information about BSI Financial Services and its contributions to the HEI market, visit https://bsifinancial.com/lender_landing_hei.html.

About BSI Financial Services 
BSI Financial Services is leading the evolution of mortgage servicing for originators, investors, and homeowners using a mortgage fintech platform. The company brings together a talented team with long mortgage industry expertise, scalable digital capabilities, and deep regulatory understanding. BSI Financial is one of the fastest-growing mortgage servicers across the industry and currently services nearly $50 billion in mortgages. The company is approved as a servicer by Fannie Mae, Freddie Mac, FHA, VA, and USDA, approved as an issuer by Ginnie Mae, and rated by S&P, Fitch and DBRS as a servicer. For more information, visit www.bsifinancial.com

PRESS CONTACT FOR BSI:
Mary McGarity
Strategic Vantage Marketing & Public Relations
203-260-5476
MaryMcGarity@StrategicVantage.com

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BLAZE® POS Integrates with Sage to Streamline Accounting for Enterprise Cannabis Retailers

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January 7, 2025

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Streamlining Cannabis Retail Accounting with Automation and Real-Time Financial Insights

LOS ANGELES, Jan. 7, 2025 /PRNewswire/ — BLAZE®, a leading cannabis software platform, announces its integration with Sage, the leader in accounting, financial, HR, and payroll technology for small and mid-sized businesses. This integration enables efficient accounting workflows and enhanced financial visibility across several retail locations.

With this integration, cannabis retailers can complete daily accounting tasks with just a few clicks. The integration, facilitated by Alembic Computer Services, Inc.’s software connector, also provides detailed, store-level financial data across multiple states, empowering enterprise retailers to make informed decisions and scale effectively.

Completed purchase orders are seamlessly converted into vendor bills, with new vendors automatically added to the system. Daily sales and COGS data are mapped by product type and synced directly to Sage Intacct, ensuring accurate financial records while saving time and reducing errors.

Key Benefits of the Integration:

Simplify Daily Accounting: Automate transaction postings and reconciliations to streamline workflows.Location-Based Insights: Offers detailed views of financial performance across individual stores.Compliance-Ready Reporting: Ensures accuracy and meets regulatory requirements.

“Cannabis retail enterprises face unique accounting challenges as they scale,” said Chris Violas, CEO of BLAZE. “Our integration with Sage Intacct is a key part of our vision to empower enterprise cannabis retailers with seamless tools for managing their bookkeeping. By implementing automation, we’re providing businesses with a faster, more efficient way to close their books, enabling them to focus on growth and delivering exceptional customer experiences.”

This collaboration highlights BLAZE’s commitment to providing innovative tools that meet the evolving needs of the cannabis industry.

For more information, visit the BLAZE + Sage Integration Page

About BLAZE®
Founded in 2015 by technology and cannabis entrepreneurs, BLAZE powers cannabis retail operations with intuitive technology solutions. The award-winning BLAZE software suite provides point-of-sale, delivery, e-commerce, mobile apps, and integrated payments to cannabis retailers across North America. Built for enterprise-level retailers, BLAZE continues to set the gold standard for customer service and innovation. BLAZE has ranked in the Inc. 5000 Fastest Growing Private Companies in 2023 and 2024 and recently received the Kind Award for Best POS in Canada and a Cannatech Innovation Award for Scan to Shop.

Contact: Press@blaze.me

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