(Press-News.org) Peking University, June 27, 2025: To overcome the inherent challenge of translation termination interference caused by stop codon reprogramming in mammalian cells, researchers from Peking University led by Chen Peng from College of Chemistry and Molecular Engineering and Yi Chengqi from School of Life Sciences have developed a novel codon expansion strategy that enables precise incorporation of noncanonical amino acids (ncAAs) without perturbing natural genetic codes. This innovative approach utilizes post-transcriptionally modified RNA codons—distinct from all 64 standard genetic codons—within targeted transcripts to encode ncAAs in mammalian systems. This work establishes a versatile platform for expanding the genetic code in mammalian cells, paving the way for advanced protein engineering and functional studies in complex biological systems. These findings were published in Nature on June 25, 2025, under the title "RNA codon expansion via programmable pseudouridine editing and decoding."
Why it matters:
The site-specific incorporation of non-canonical amino acids (ncAAs) provides new opportunities to tailor protein functions with custom chemistries. Traditional genetic code expansion (GCE) strategies achieve ncAA incorporation by reassigning stop codons as “blank” codons, which is not fully orthogonal to endogenous translation termination, limiting its precision and scope in cellular contexts. This RCE method utilizes bio-orthogonally assigned pseudouridine-modified codons (ΨCodons: ΨGA, ΨAA, or ΨAG) at designated mRNA transcripts for ncAA incorporation in mammalian cells. The RCE platform integrates a programmable guide RNA, an engineered decoder tRNA, and a specific aminoacyl-tRNA synthetase to achieve highly selective decoding of ΨCodons. These advances establish a robust strategy that employs pseudouridine as a post-transcriptional “letter,” creating new RNA codons for targeted protein engineering and expanding the genetic code in eukaryotic systems.
Methodology:
In this study, researchers established an RNA codon expansion (RCE) platform to assign pseudouridine (Ψ)-modified RNA codons (ΨCodons: ΨGA, ΨAA, ΨAG) as novel “blank” codons for non-canonical amino acid (ncAA) incorporation in mammalian cells, independent of endogenous codon usage. The RCE system is comprised of three essential components: a programmable guide RNA for targeted ΨCodon installation, a specifically engineered decoder tRNA ((ΨGA)-tRNAPyl, (ΨAA)-tRNAPyl, or (ΨAG)-tRNAPyl) for ΨCodon recognition, and a dedicated aminoacyl-tRNA synthetase for decoding. Each decoder tRNA demonstrated a strong preference for its corresponding ΨCodon over native codons, ensuring orthogonality within the mammalian translatome.
Ribosome profiling and proteomic analyses revealed that RCE(ΨGA) achieves high specificity for ncAA incorporation, while preserving the endogenous UGA stop codon, which constitutes approximately 52% of stop codons in the human genome. Furthermore, the three ΨCodon–decoder tRNA pairs were shown to be mutually orthogonal, enabling the site-specific incorporation of multiple ncAAs with distinct side chains into mammalian proteins. Importantly, the RCE platform was also compatible with conventional GCE systems, allowing for dual ncAA incorporation within single cells.
Key findings:
- The RCE system enables programmable encoding and decoding of modified RNA codons, achieving high translatome-wide specificity for ncAA incorporation and minimizing disruption to endogenous translation termination.
- Each ΨCodon–decoder tRNA pair operates orthogonally, facilitating the precise incorporation of multiple, chemically diverse ncAAs into proteins of interest in mammalian cells.
- This methodology offers new opportunities for the precise investigation and modulation of protein function, supporting both fundamental research and potential therapeutic applications.
This study establishes RCE as a robust and versatile platform for programmable genetic code expansion in eukaryotic systems, enabling precise site-specific protein modification and functional studies in complex biological settings.
*This article is featured in PKU News "Why It Matters" series. More from this series.
: https://www.nature.com/articles/s41586-025-09165-x
Written by: Yi chengqi, Chen Peng
Edited by: Zhang Jiang
Source: College of Chemistry and Molecular Engineering, Peking University
END
RNA codon expansion via programmable pseudouridine editing and decoding
2025-06-27
ELSE PRESS RELEASES FROM THIS DATE:
Post-diagnosis emergency department presentation and demographic factors in malignant skin cancers
2025-06-27
Background and objectives
Emergency department (ED) presentations are associated with higher cancer mortality. This study aimed to investigate the prevalence, frequency, and risk factors in Australian patients diagnosed with malignant skin cancers.
Methods
This data-linkage cohort study examined adult patients presenting to the ED at the Royal Melbourne and Western Health hospitals within 12 months of a malignant skin cancer diagnosis. Multivariable logistic and Poisson regressions were used to analyze factors influencing the prevalence and frequency of ED presentations.
Results
A total ...
A new genetic tuner for embryo development
2025-06-27
The research was led by Dr Irène Amblard and Dr Vicki Metzis from the Development and Transcriptional Control group, in collaboration with LMS facilities and the Chromatin and Development and Computational Regulatory Genomics groups.
All cells contain the same DNA but must turn specific genes ‘on’ and ‘off’ – a process known as gene expression – to create different body parts. The cells in your eyes and arms harbour the same genes but ‘express’ them differently to become each body part. The work focused on the gene Cdx2. The duration of Cdx2 expression helps to determine where and when a cell produces ...
Insurance churn and the COVID-19 pandemic
2025-06-27
About The Study: In this study, the Families First Coronavirus Response Act was associated with a significantly decreased risk of losing health insurance for individuals enrolled in the Medicaid program.
Corresponding Author: To contact the corresponding author, Sarah P. Shubeck, MD, MS, email shubeck@bsd.uchicago.edu.
To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/
(doi:10.1001/jamahealthforum.2025.1467)
Editor’s Note: Please see the article for additional information, including other authors, author contributions and affiliations, ...
Postpartum Medicaid use in birthing parents and access to financed care
2025-06-27
About The Study: The results of this study suggest that extending Medicaid coverage for 12 months postpartum was associated with expanded opportunities for greater access to Medicaid-financed medical and behavioral health care. Both prevention and ongoing treatment of chronic conditions may help mitigate key adverse outcomes. The findings may help policymakers and public health officials understand how extended coverage affects access to Medicaid-financed care.
Corresponding Author: To contact the corresponding author, Jonas J. Swartz, MD, MPH, email jonas.swartz@duke.edu.
To ...
Manufacturing chemicals via orthogonal strategy, making full use of waste plastic resources in real life
2025-06-27
Peking University, June 27, 2025: Addressing the challenge of waste plastics treatments, the scientific community has been pursuing innovative solutions. Recently, Peking University researchers led by Ma Ding from College of Chemistry and Molecular Engineering, in collaboration with Xu Shutao from Dalian Institute of Chemical Physics, Chinese Academy of Sciences, uncovered how complex plastic mixtures can be utilized based on the differences in the physical and chemical properties of the components with the aids of NMR technique and catalytic approaches. This work provides a new treatment ...
Study overturns long-held belief about shape of fish schools
2025-06-27
For 50 years, scientists believed that schools of fish would save the most energy by swimming in flat diamond formations. Recently, a team of researchers at Princeton and Harvard ran an experiment to check this assumption.
It turns out that, contrary to what models predicted, fish don’t swim in diamonds. They swim in a dynamic pattern that the researchers call a ladder, where they’re staggered in three dimensions like an echelon of fighter jets.
The research team, led by Radhika Nagpal, professor of robotics at Princeton, adapted computer vision software originally developed to track individual animal movements to collect the first 3D data ...
Precision oncology Organ Chip platform accurately and actionably predicts chemotherapy responses of patients suffering from esophageal adenocarcinoma
2025-06-27
By Benjamin Boettner
(BOSTON) — Esophageal adenocarcinoma (EAC), one of two major forms of esophageal cancer, is the sixth most deadly cancer worldwide for which no effective targeted therapy exists. Patients need to rely on chemotherapy as a standard-of-care, which is started ahead of surgical interventions as a so-called “neoadjuvant chemotherapy” (NACT) in the hope to shrink or control tumors. However, most patients become resistant to certain NACTs, leading to poor outcomes.
Given the utter lack of therapeutic alternatives, responders and non-responders alike, continue to receive one of the available chemotherapies without knowing whether ...
Verify the therapeutic effect of effective components of lycium barbarum on hepatocellular carcinoma based on molecular docking
2025-06-27
Background and objectives
In recent years, it has been found that Lycium barbarum can repair liver damage and promote liver regeneration. Additionally, the polysaccharides contained in Lycium barbarum have anticancer properties and can induce apoptosis in cancer cells. Molecular docking, a mature computer-aided method, is widely used in drug discovery. This study aimed to verify the efficacy of active ingredients of Lycium barbarum in the treatment of liver cancer ...
Early intervention changes trajectory for depressed preschoolers
2025-06-27
Depression affects 1%-2% of children younger than 13 in the U.S. and can arise as early as age 3, but a specialized therapeutic intervention can help preschool-aged children find relief from this condition — with benefits lasting at least four years, according to a new study led by researchers at Washington University School of Medicine in St. Louis.
The researchers, led by Joan Luby, MD, the Samuel and Mae S. Ludwig Professor of Psychiatry at WashU Medicine, and Mei Elansary, MD, an attending developmental behavioral pediatrician at Boston Medical Center, measured the long-term ...
HonorHealth Research Institute presents ‘monumental’ increase in survivability for patients suffering ultra-low blood pressure
2025-06-27
NEW YORK, N.Y. — June 27, 2025 — An 8-year HonorHealth Research Institute clinical trial, using non-surgical techniques, showed 86% of patients with a type of usually fatal low blood pressure known as ‘structural shock’ survived at least 3 months, while 73% survived at least 6 months, according to a study presented here at a major heart convention.
“That’s a spectacular improvement. This appears to be a monumental step forward,” said David G. Rizik, M.D., head of the Scottsdale, Ariz.-based Research Institute’s Cardiovascular Research Division.
Dr. ...