Review
Cell Biology
Huake Cao, Yuechen Wang, Ning Zhang, Siyuan Xia, Pengfei Tian, Li Lu, Juan Du, Yinan Du
Summary: This article reviews the progress in RNA imaging and mapping RNA-protein interactions, with a focus on the precise CRISPR-Cas13-mediated method. This method has potential for real-time RNA imaging and recognition of RNA-protein interactions, and provides new ideas for optimizing the method.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Meng Li, Dan Li, Leiruo Lin, Panpan Wang, Wenxue Zhao
Summary: RNA-protein interactions are crucial for cellular regulation and disease. A new method has been developed to interfere with specific RNA-protein interactions, providing a better understanding of their roles in cellular processes. The tool described in this study demonstrates precise interference with a specific RNA-protein interaction, showing distinct effects on cell physiology.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lenzie Ford, Arun Asok, Arielle D. Tripp, Cameron Parro, Michelle Fitzpatrick, Christopher A. de Solis, Po-Tao Y. Chen, Neeva Shafiian, Luana Fioriti, Rajesh K. Soni, Eric R. Kandel
Summary: Biomolecular condensates, specifically ribonucleoprotein granules (RNPs), are critical for local protein synthesis and have important roles in synaptic plasticity and long-term memory. Proteins within RNPs contain low-complexity motifs (LCM), allowing for diverse protein-protein interactions. This study highlights the significance of protein-protein interactions mediated by the LCM of cytoplasmic polyadenylation element binding protein 3 (CPEB3) in regulating synaptic plasticity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Immunology
Anissa Guillemin, Anuj Kumar, Melanie Wencker, Emiliano P. Ricci
Summary: Innate immunity is the first line of defense against infections and tissue damage, and it relies on a dynamic and coordinated gene expression program. Transcriptional and post-transcriptional regulatory pathways, involving RNA-binding proteins and other effectors, play crucial roles in shaping the innate immune response. Recently, microRNAs and post-transcriptional modification of RNA bases have also emerged as essential players in this process.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Corinna J. Ulshoefer, Christina Pfafenrot, Albrecht Bindereif, Tim Schneider
Summary: CircRNAs have been extensively studied in recent years, revealing functional roles in various cell types and organisms. However, the specific interaction partners for most circRNAs remain unknown due to technical difficulties, presenting challenges in systematically studying circRNA-protein complexes.
Review
Biochemistry & Molecular Biology
Akio Masuda, Toshihiko Kawachi, Kinji Ohno
Summary: This article discusses the importance of protein-RNA interactions in mRNA transcription and processing, as well as the methods for detecting these interactions and their applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Vesper Burjoski, Anireddy S. N. Reddy
Summary: RNAs transmit information from DNA to encode proteins and regulate gene expression. Recent studies have uncovered a hidden landscape of RNA-protein interactions in plants. Application of modern techniques has led to the discovery of close to 2000 putative RNA-binding proteins in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Correction
Biochemical Research Methods
Wenkai Yi, Jingyu Li, Xiaoxuan Zhu, Xi Wang, Ligang Fan, Wenju Sun, Linbu Liao, Jilin Zhang, Xiaoyu Li, Jing Ye, Fulin Chen, Jussi Taipale, Kui Ming Chan, Liang Zhang, Jian Yan
Summary: A correction to the paper has been published.
Review
Pharmacology & Pharmacy
Jingyue Yan, Diana D. Kang, Gillian Turnbull, Yizhou Dong
Summary: RNA-binding proteins (RBPs) are crucial in RNA metabolism and alterations in the RBP-RNA network are related to cancer development. Various strategies, including small-molecule inhibitors and CRISPR-Cas9 technology, have been applied for RBP-based cancer therapies.
ADVANCED DRUG DELIVERY REVIEWS
(2022)
Article
Cell Biology
Rudian Zhang, Wenzhi Feng, Suhong Qian, Fei Wang
Summary: Autophagy plays an important role in regulating the meiosis-specific RNA-binding protein Rim4 and its associated transcripts in yeast meiosis. Rim4 enters the nucleus using a nuclear localization signal and loads its mRNA substrates before nuclear export. Active autophagy selectively spares the Rim4-mRNA complex in the cytoplasm, while degrading Rim4 during meiotic divisions in an Atg11-dependent manner, coinciding with the release of Rim4-bound mRNAs for translation. The conserved RNA recognition motifs (RRMs) of Rim4 are involved in stimulating Atg1 kinase and facilitating selective autophagy.
Article
Chemistry, Multidisciplinary
Huixin Luo, Wei Tang, Hongyu Liu, Xiangmei Zeng, William Shu Ching Ngai, Rui Gao, Heyun Li, Ran Li, Huangtao Zheng, Jianting Guo, Fangfei Qin, Gang Wang, Kexin Li, Xinyuan Fan, Peng Zou, Peng R. Chen
Summary: The interactions between RNA and proteins are crucial for cellular processes. This study developed a photocatalytic crosslinking strategy combined with mass spectrometry and RNA sequencing to study the composition and dynamics of protein-RNA interactions. The approach identified numerous RNA binding proteins in human cells and investigated the dynamic changes of RBPs in macrophage cells and their interactions with SARS-CoV-2 RNA.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Guoxu Song, Fei Zhang, Chunhong Tian, Xing Gao, Xiaoxiao Zhu, Dongdong Fan, Yong Tian
Summary: This study identified novel anti-CRISPR families that have the ability to inhibit Cas9 activity and even control genome editing post-translationally. By studying different Acr variants and developing chemically inducible control, new avenues for CRISPR-Cas9 applications have been established.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Plant Sciences
Mallesham Bulle, Vijay Sheri, Mahender Aileni, Baohong Zhang
Summary: The growing demand for food by the world population is expected to increase significantly by 2050. Both biotic and abiotic constraints severely affect agronomic productivity for food. Insect pests alone cause about 20% loss in crop yield every year globally. The use of chemical pesticides to control insect pests poses threats to human health and environmental sustainability. Therefore, innovative and environmentally friendly alternatives are needed to mitigate insect pest management strategies. Recent studies have shown that engineering chloroplasts with double-strand RNA (dsRNA) is an effective method to control western flower thrips and other pests. This biotechnological approach provides a promising solution for mitigating agronomic insect pests.
Review
Biochemistry & Molecular Biology
Maryam Nasiri-Aghdam, Texali C. Garcia-Garduno, Luis Felipe Jave-Suarez
Summary: Post-transcriptional modifications to coding and non-coding RNAs play a key role in influencing human mRNA and protein diversity, especially in cancer proliferation. CELF proteins have pleiotropic capabilities in RNA processing, impacting alternative splicing and transcript editing. Understanding the regulation of CELF functions, particularly through noncoding RNAs, is crucial for cancer research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Handong Huang, Lu Li, Kunming Wen
Summary: Long non-coding RNAs (lncRNAs) play crucial roles in cellular processes, particularly in the pathogenesis of diseases like cancer. Interactions between lncRNAs and RNA-binding proteins (RBPs) are essential for understanding cancer pathogenesis and developing effective therapies.
Article
Biochemistry & Molecular Biology
Shaoxiong Tian, Ge Yu, Huan He, Yu Zhao, Peilu Liu, Alan G. Marshall, Borries Demeler, Scott M. Stagg, Hong Li
Review
Biochemistry & Molecular Biology
Ge Yu, Yu Zhao, Hong Li
Article
Biochemical Research Methods
Travis H. Hand, Anuska Das, Mitchell O. Roth, Chardasia L. Smith, Uriel L. Jean-Baptiste, Hong Li
ACS SYNTHETIC BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Ge Yu, Yu Zhao, Shaoxiong Tian, Jay Rai, Huan He, John Spear, Duncan Sousa, Jinbo Fan, Hong-Guo Yu, Scott M. Stagg, Hong Li
SCIENTIFIC REPORTS
(2019)
Article
Multidisciplinary Sciences
Anuska Das, Travis H. Hand, Chardasia L. Smith, Ethan Wickline, Michael Zawrotny, Hong Li
NATURE COMMUNICATIONS
(2020)
Article
Genetics & Heredity
Travis H. Hand, Mitchell O. Roth, Chardasia L. Smith, Emily Shiel, Kyle N. Klein, David M. Gilbert, Hong Li
Summary: This study introduces a protein engineering method for selecting catalytically enhanced CRISPR-Cas9 variants by targeting a shortened protospacer within a toxic gene. By improving AceCas9 and SpyCas9, significant enhancements in catalytic efficiency were achieved, with noticeable improvement in gene insertion in human colon cancer cells facilitated by SpyCECas9.
Article
Multidisciplinary Sciences
Sagar Sridhara, Hemant N. Goswami, Charlisa Whyms, Jonathan H. Dennis, Hong Li
Summary: CRISPR-Cas-based virus detection assays, particularly those utilizing Type III-A CRISPR-Cas system, offer rapid and sensitive detection of viruses like SARS-CoV-2, making them potentially valuable tools for disease diagnosis.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Anuska Das, Hemant N. Goswami, Charlisa T. Whyms, Sagar Sridhara, Hong Li
Summary: CRISPR-based technology has revolutionized biomedicine through its applications in genome editing, therapeutics, and diagnostics. Recent studies have shown that CRISPR enzymes can also be used for nucleic acid detection by collateral and non-specific cleavage of viral DNA or RNA. The diverse compositions, self-foreign nucleic acid recognition mechanisms, usage of second messengers, and enzymology of CRISPR enzymes provide a wide range of diagnostic tools for further innovations. Structural biology plays a crucial role in understanding the activation mechanisms of these CRISPR enzymes.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Mitchell O. Roth, Hong Li
Summary: In this paper, the authors present a successful structure-guided approach to improve the genome-editing efficiency of CRISPR-CasX in Deltaproteobacteria and Planctomycetes.
Article
Biochemistry & Molecular Biology
Yu Zhao, Jay Rai, Hongguo Yu, Hong Li
Summary: This study characterized the structures and conformations of modified and pseudouridine-free ribosomes using electron cryomicroscopy. It found that pseudouridine stabilizes key functional motifs by establishing water-mediated close contacts with the phosphate backbone, while the absence of pseudouridine leads to abnormal inter-subunit movements.
Article
Biology
Yu Zhao, Jay Rai, Chong Xu, Huan He, Hong Li
Summary: AlphaFold-assisted CryoEM structure determination reveals the structure of the Bfr2-Lcp5 complex in the yeast 90S pre-ribosome. The complex interacts similarly to exosome factors Rrp6-Rrp47 and plays a role in regulating 90S transitions.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Sagar Sridhara, Jay Rai, Charlisa Whyms, Hemant Goswami, Huan He, Walter Woodside, Michael P. Terns, Hong Li
Summary: This study investigates the structure and activity of the Lactococcus lactis Csm complex in different functional states using cryoEM, functional assays, and comparative cross-linking. The results suggest that RNA binding influences the conformation and protein dynamics of the Csm complex.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Hemant N. Goswami, Jay Rai, Anuska Das, Hong Li
Summary: Cas7-11 is a Type III-E CRISPR Cas effector that can perform programmable RNA cleavage and has potential applications in RNA interference. The structure of Cas7-11 reveals its molecular basis for RNA processing and interference activities. This knowledge can be used to engineer a compact and programmable RNA interference tool.
Article
Chemistry, Physical
Anuska Das, Jay Rai, Mitchell O. Roth, Yuerong Shu, Megan L. Medina, Mackenzie R. Barakat, Hong Li
Summary: This study reports the conformational changes of Acidothermus cellulolyticus Cas9 along the reaction path, revealing the synchronized cutting mechanism of its two active sites. Altering the metal-coordination residues can change the metal specificity of Cas9.
Article
Biochemistry & Molecular Biology
Jana Sefcikova, Mitchell Roth, Ge Yu, Hong Li