Review
Oncology
Qunli Xiong, Yaguang Zhang
Summary: Small RNAs are short RNA molecules that play various important roles in cells. Different types of small RNAs, such as miRNA, piRNA, siRNA, and tsRNA, have diverse functions. Current research suggests that small RNAs can be modified, affecting their stability and nuclear export, and these modifications are relevant to cellular processes like biogenesis, cell proliferation, and differentiation. This review focuses on the molecular characteristics and cellular functions of small RNAs and their modifications, as well as techniques for reliable detection. The potential clinical applications of small RNA modifications in the diagnosis and treatment of conditions like cancer are also discussed.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2023)
Review
Medicine, Research & Experimental
Yirong Wu, Siyao Zhan, Yizhou Xu, Xiangwei Gao
Summary: This review summarizes the regulatory roles and significance of several types of RNA modifications in cardiovascular diseases, as well as the interplay between RNA modifications and noncoding RNA, epigenetics. It also focuses on potential therapeutic strategies utilizing RNA modifications in treating CVDs.
Article
Mathematics
Saima Rashid, Aasma Khalid, Omar Bazighifan, Georgia Irina Oros
Summary: This paper establishes integral inequalities for P-convex functions using a generalised fractional integral operator based on Raina's function, presenting Hermite-Hadamard type inequality and a novel parameterized auxiliary identity. By deriving Ostrowski type inequalities for functions with absolute values as P-convex mappings using the auxiliary identity, the robustness and efficiency of the suggested scheme in matrices and Fox-Wright generalised hypergeometric functions are verified. The obtained outcomes exhibit classical convex and harmonically convex functions, corroborated by Riemann-Liouville fractional integral.
Review
Cell Biology
Zeyidan Jiapaer, Dingwen Su, Lingyang Hua, Helge Immo Lehmann, Priyanka Gokulnath, Gururaja Vulugundam, Shannan Song, Lingying Zhang, Ye Gong, Guoping Li
Summary: In this review, the current knowledge about RNA modifications and their roles in aging-related diseases is summarized. A catalog of RNA modifications on different RNA species is provided. Understanding the regulation and roles of RNA modifications can contribute to the development of novel diagnostics and therapeutics for aging-related diseases.
Editorial Material
Cell Biology
Marta Montes, Maite Huarte
Summary: A new study reveals that increased reactive oxygen species in cancer cause widespread, sequence-specific modifications of guanines in microRNA seed regions, altering their target genes and impacting tumorigenesis.
NATURE CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ricardo Castro-Hernandez, Tea Berulava, Maria Metelova, Robert Epple, Tonatiuh Pena Centeno, Julia Richter, Lalit Kaurani, Ranjit Pradhan, M. Sadman Sakib, Susanne Burkhardt, Momchil Ninov, Katherine E. Bohnsack, Markus T. Bohnsack, Ivana Delalle, Andre Fischer
Summary: This study used methylated RNA immunoprecipitation sequencing to investigate the role of N6-methyladenosine (m6A) in synaptic plasticity during cognitive decline. It was found that m6A levels decrease in aged animals and Alzheimer's disease (AD) patients. Common m6A changes were observed in transcripts related to synaptic function, and reduced m6A levels were shown to impair synaptic protein synthesis and function. These findings suggest that m6A RNA methylation plays a role in cognitive decline associated with aging and AD.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Chemistry, Multidisciplinary
Jing Mo, Xiaocheng Weng, Xiang Zhou
Summary: With increasing research interest, more than 170 types of chemical modifications of RNA have been characterized. These modifications do not alter the primary sequence of RNA but modulate gene activity. Developing innovative labeling and detection methodologies is crucial for understanding the biological significance and clinical prospects of RNA modifications.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Zhangli Su, Ida Monshaugen, Arne Klungland, Rune Ougland, Anindya Dutta
Summary: This study identified abundant non-microRNA-small RNAs in bladder cancer tumor samples. The modifications in small RNAs, especially tRFs and rRFs, can be captured as mismatches by TGIRT sequencing. Both the modifications and the non-microRNA-small RNAs should be explored as potential biomarkers for bladder cancer detection or follow-up.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Emma Wilkinson, Yan-Hong Cui, Yu-Ying He
Summary: RNA modifications play important roles in regulating RNA metabolism and gene expression, serving as key signaling machineries in cellular stress responses and disease pathogenesis. Their roles in response to cellular stressors are context- and cell-type-dependent, impacting various diseases including cancer, neurologic disorders, and metabolic diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Marta Jedynak-Slyvka, Agata Jabczynska, Roman J. Szczesny
Summary: Mitochondria, known as the powerhouses of cells, play crucial roles in energy production, apoptosis, calcium homeostasis, and regulation of the immune response. Abnormalities in mitochondria can lead to severe diseases, making it important to study their functions and physiological consequences. Despite progress in understanding RNA processing in mitochondria, there are still many unknowns and controversies in the field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Shijie Chen, Jin Zeng, Liping Huang, Yi Peng, Zuyun Yan, Aiqian Zhang, Xingping Zhao, Jun Li, Ziting Zhou, Sidan Wang, Shengyu Jing, Minghua Hu, Yuezhan Li, Dong Wang, Weiguo Wang, Haiyang Yu, Jinglei Miao, Jinsong Li, Youwen Deng, Yusheng Li, Tang Liu, Dabao Xu
Summary: A novel prognostic gene signature based on 3 RMWs was established in this study, which was validated through qPCR analysis, GEO datasets, and independent OS tissues, showing that high-risk patients had poor overall survival and the prognostic signature was an independent prognostic factor for OS. Functional studies revealed that pathways related to tumor, metabolism, cell cycle, and immune were associated with high risk.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Viktoriia A. Arzumanian, Georgii Dolgalev, Ilya Y. Kurbatov, Olga Kiseleva, Ekaterina Poverennaya
Summary: The building blocks for RNA molecules have a larger diversity than the standard four nucleotides due to post-transcriptional biochemical modifications. These modifications, both essential for RNA functions and functioning as dynamic markings, form the epitranscriptome. Over 300 distinct RNA modifications from all three life domains have been identified, but most reviews only cover a few well-established modifications. This study provides a comprehensive overview of the current research status on the epitranscriptome, analyzing the available information for all known RNA modifications and describing the current status of research on most RNA modifications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Correction
Cell Biology
Junchao Shi, Yunfang Zhang, Dongmei Tan, Xudong Zhang, Menghong Yan, Ying Zhang, Reuben Franklin, Marta Shahbazi, Kirsty Mackinlay, Shichao Liu, Bernhard Kuhle, Emma R. James, Liwen Zhang, Yongcun Qu, Qiwei Zhai, Wenxin Zhao, Linlin Zhao, Changcheng Zhou, Weifeng Gu, Jernej Murn, Jingtao Guo, Douglas T. Carrell, Yinsheng Wang, Xuemei Chen, Bradley R. Cairns, Xiang-lei Yang, Paul Schimmel, Magdalena Zernicka-Goetz, Sihem Cheloufi, Ying Zhang, Tong Zhou, Qi Chen
Summary: A correction notice has been published for this paper, please refer to the link for more details.
NATURE CELL BIOLOGY
(2021)
Article
Medicine, General & Internal
Chung-Ming Huang, Yu-Chia Chen, I-Lu Lai, Hong-Da Chen, Po-Hao Huang, Siang-Jyun Tu, Ya-Ting Lee, Ju-Chen Yen, Chia-Li Lin, Ting-Yuan Liu, Jan-Gowth Chang
Summary: Hyperuricemia and gout are common metabolic disorders with increasing incidence worldwide. This study found that RNA modifications, editing, and splicing play roles in gout development, and the findings may contribute to the development of new diagnostic and therapeutic strategies.
FRONTIERS IN MEDICINE
(2022)
Review
Cardiac & Cardiovascular Systems
Christine M. Loescher, Anastasia J. Hobbach, Wolfgang A. Linke
Summary: This review provides an overview of the changes in cardiac titin properties at a molecular level, including the role isoform diversity and post-translational modifications play in regulating myocardial function, and discusses the importance of this regulation imbalance in heart disease.
CARDIOVASCULAR RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Chao Liu, Hongbin Liu, Haobo Zhang, Lina Wang, Mengjing Li, Feifei Cai, Xiuge Wang, Li Wang, Ruidan Zhang, Sijie Yang, Wenwen Liu, Yu Liang, Liying Wang, Xiaohui Song, Shizhen Su, Hui Gao, Jing Jiang, Jinsong Li, Mengcheng Luo, Fei Gao, Qi Chen, Wei Li, Zi-Jiang Chen
Summary: Klinefelter syndrome may originate from paternal USP26 gene mutations, leading to the production of XY aneuploid spermatozoa. These research findings are crucial for understanding the origin and inheritance of KS.
Correction
Cell Biology
Junchao Shi, Yunfang Zhang, Dongmei Tan, Xudong Zhang, Menghong Yan, Ying Zhang, Reuben Franklin, Marta Shahbazi, Kirsty Mackinlay, Shichao Liu, Bernhard Kuhle, Emma R. James, Liwen Zhang, Yongcun Qu, Qiwei Zhai, Wenxin Zhao, Linlin Zhao, Changcheng Zhou, Weifeng Gu, Jernej Murn, Jingtao Guo, Douglas T. Carrell, Yinsheng Wang, Xuemei Chen, Bradley R. Cairns, Xiang-lei Yang, Paul Schimmel, Magdalena Zernicka-Goetz, Sihem Cheloufi, Ying Zhang, Tong Zhou, Qi Chen
Summary: A correction notice has been published for this paper, please refer to the link for more details.
NATURE CELL BIOLOGY
(2021)
Article
Cell Biology
Junchao Shi, Yunfang Zhang, Dongmei Tan, Xudong Zhang, Menghong Yan, Ying Zhang, Reuben Franklin, Marta Shahbazi, Kirsty Mackinlay, Shichao Liu, Bernhard Kuhle, Emma R. James, Liwen Zhang, Yongcun Qu, Qiwei Zhai, Wenxin Zhao, Linlin Zhao, Changcheng Zhou, Weifeng Gu, Jernej Murn, Jingtao Guo, Douglas T. Carrell, Yinsheng Wang, Xuemei Chen, Bradley R. Cairns, Xiang-lei Yang, Paul Schimmel, Magdalena Zernicka-Goetz, Sihem Cheloufi, Ying Zhang, Tong Zhou, Qi Chen
Summary: Shi et al. profiled small non-coding RNAs (sncRNAs) through PANDORA-seq, identifying tissue-specific transfer RNA- and ribosomal RNA-derived small RNAs, as well as sncRNAs with dynamic changes during induced pluripotent stem cell reprogramming.
NATURE CELL BIOLOGY
(2021)
Article
Chemistry, Medicinal
Xiaochuan Liu, Jun Yuan, Xudong Zhang, Lin Li, Xiaoxia Dai, Qi Chen, Yinsheng Wang
Summary: The increased expression of ATF3 protein in tamoxifen-resistant breast cancer cells is correlated with drug resistance and is regulated by the downregulation of YTHDF2. This leads to increased stability of ATF3 mRNA and subsequently enhances drug resistance. These findings suggest ATF3 and YTHDF2 as potential therapeutic targets for overcoming drug resistance in cancer cells.
CHEMICAL RESEARCH IN TOXICOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Qi Chen, Xudong Zhang, Junchao Shi, Menghong Yan, Tong Zhou
Summary: tsRNA, derived from tRNA cleavage, are ancient small RNAs with versatile roles in fundamental biological processes. These roles stem from sequence conservation, RNA modifications, and protein-binding abilities, suggesting the need for expanding tsRNA research into broader areas for precision medicine.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Letter
Peripheral Vascular Disease
Liwen Zhang, Yuzhu Li, Jian Wang, Cheng Hong, Wenju Lu, Yongcun Qu, Stephen M. Black, Qi Chen, Tong Zhou, Wanzhu Jin, Enkui Duan, Haiyang Tang, Ying Zhang
Article
Cell Biology
Junchao Shi, Tong Zhou, Qi Chen
Summary: This article discusses recent approaches for discovering sncRNAs, limitations associated with sncRNA expression analyses, and emerging methods for direct and simultaneous detection of multiple RNA modifications.
NATURE CELL BIOLOGY
(2022)
Article
Developmental Biology
Linkai Zhu, Tong Zhou, Rajan Iyyappan, Hao Ming, Michal Dvoran, Yinjuan Wang, Qi Chen, R. Michael Roberts, Andrej Susor, Zongliang Jiang
Summary: By using high-resolution ribosome fractionation and low-input ribosome profiling, we have defined the translational landscapes of bovine oocytes and preimplantation embryos. We discovered four modes of translational selectivity in early embryo development and found a strong translational selection of low-abundance transcripts involved in metabolic pathways and lysosomes. These findings provide important insights into the translational regulation during bovine preimplantation development.
Article
Environmental Sciences
Jingwei Liu, Junchao Shi, Rebecca Hernandez, Xiuchun Li, Pranav Konchadi, Yuma Miyake, Qi Chen, Tong Zhou, Changcheng Zhou
Summary: Exposure to plastic-associated endocrine disrupting chemicals (EDCs) increases the risk of chronic diseases and negatively affects the metabolic health of offspring. Paternal exposure to the phthalate DCHP leads to insulin resistance and impaired insulin signaling in F1 offspring, with changes in sperm tsRNA/rsRNA landscape playing a role in the intergenerational transmission of metabolic disorders. Moreover, paternal DCHP exposure also induces sex-specific transgenerational adverse effects in F2 offspring, causing glucose intolerance in female descendants. These findings enhance our understanding of chemical-induced intergenerational and transgenerational effects on human health.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Developmental Biology
Qi Chen
Summary: Emerging evidence suggests that mammalian sperm carry various types of RNAs that can respond to the paternal environment and mediate the transmission of specific phenotypes to offspring. This offers the potential for programming offspring characteristics during embryonic development. The study also discusses the challenges and opportunities in understanding the mechanisms of sperm RNA-mediated epigenetic inheritance and the potential applications in improving animal production and human health.
REPRODUCTION FERTILITY AND DEVELOPMENT
(2023)
Letter
Biochemical Research Methods
Andrew D. Holmes, Patricia P. Chan, Qi Chen, Pavel Ivanov, Laurence Drouard, Norbert Polacek, Mark A. Kay, Todd M. Lowe
Editorial Material
Endocrinology & Metabolism
Xudong Zhang, Qi Chen
Summary: A new study shows that exposure of pregnant mice to bisphenol A, an endocrine disrupting chemical, leads to multi-transgenerational inheritance of obesity in their descendants (up to six generations). This effect is dependent on CTCF-mediated chromatin reorganization in sperm, which results from altered DNA methylation, RNA modification, and long-range chromatin interactions.
NATURE REVIEWS ENDOCRINOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xueli Chen, Ru Ma, Wei Zhang, Ginger Qinghong Zeng, Qianying Wu, Ajiguli Yimiti, Xinzhao Xia, Jiangtian Cui, Qiongwei Liu, Xueer Meng, Junjie Bu, Qi Chen, Yu Pan, Nancy Xiaonan Yu, Shouyan Wang, Zhi-De Deng, Alexander T. Sack, Myles Mc Laughlin, Xiaochu Zhang
Summary: Previous studies have shown correlations between alpha oscillations and working memory (WM) retention, but causal evidence has been lacking. Conventional tACS cannot modulate brain oscillations within the short retention subprocess, making it unsuitable for demonstrating causal evidence for parietal alpha oscillations in WM retention. In this study, we developed an online phase-corrected tACS system that allowed precise modulation of brain oscillations and used it to show a causal link between parietal alpha oscillations and WM retention.
