Review
Biochemistry & Molecular Biology
Wuwen Zhang, Qinshi Wang, Yi Yang, Siyuan Zhou, Ping Zhang, Tongbao Feng
Summary: Exosomes play a crucial role in cell-cell communication within the cancer microenvironment. Exosomal long noncoding RNAs (lncRNAs) are key regulators in cancer development, involved in processes such as cancer cell proliferation, metastasis, drug resistance, and immunomodulation. Changes in exosomal lncRNAs levels often correlate with cancer occurrence and progression, making them valuable biomarkers for cancer diagnosis and prognosis.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Chu-Xiao Liu, Si-Kun Guo, Fang Nan, Yi-Feng Xu, Li Yang, Ling-Ling Chen
Summary: Exon back-splicing-generated circular RNAs can suppress PKR in cells. We synthesized immunogenicity-free RNA circles containing short dsRNA and found that they induce an immune response. Directly ligated circular RNAs efficiently suppress PKR activation.
Review
Peripheral Vascular Disease
Ji-Ru Zhang, Hai-Jian Sun
Summary: Hypertension, a multifactorial disorder, involves the dysregulation of vascular smooth muscle cells (VSMCs) which play a crucial role in the development of systemic hypertension and pulmonary arterial hypertension (PAH). Noncoding RNAs (ncRNAs) are emerging as novel modulators in the biological behaviors of VSMCs, with microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs being recommended as predictive biomarkers and therapeutic targets for hypertension and PAH.
HYPERTENSION RESEARCH
(2021)
Article
Cell Biology
Xiuchao Geng, Yuhao Zhang, Xiaomeng Lin, Zhaomu Zeng, Jun Hu, Liangchao Hao, Jianglong Xu, Xinjuan Wang, Hong Wang, Qiang Li
Summary: The delivery of circWDR62 through exosomes promotes TMZ-resistance and malignant progression in glioma by targeting the miR-370-3p/MGMT axis, providing a new therapeutic strategy. Exosomal circWDR62 in human serum may serve as a promising therapeutic target and prognostic marker for glioma therapy.
CELL DEATH & DISEASE
(2022)
Review
Oncology
Barbara Montico, Giorgio Giurato, Giovanni Pecoraro, Annamaria Salvati, Alessia Covre, Francesca Colizzi, Agostino Steffan, Alessandro Weisz, Michele Maio, Luca Sigalotti, Elisabetta Fratta
Summary: Cutaneous melanoma is an aggressive disease with high mortality rates and often unresponsive to conventional therapies. Recent studies have shown aberrant expression of different types of noncoding RNAs, with microRNAs being extensively studied, while circular RNAs and long noncoding RNAs in this tumor need further exploration.
MOLECULAR ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Dezhong Lv, Zhenghong Chang, Yangyang Cai, Junyi Li, Liping Wang, Qiushuang Jiang, Kang Xu, Na Ding, Xia Li, Juan Xu, Yongsheng Li
Summary: TransLnc is a database that provides experimentally supported and predicted lncRNA peptides in multiple species, with hundreds of thousands of peptides recorded. Various types of evidence supporting the coding potential of lncRNAs are integrated, and users can access lncRNA peptides in 34 tissues and predicted tumor neoantigens.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Dimitrios Tsitsipatis, Jennifer L. L. Martindale, Krystyna Mazan-Mamczarz, Allison B. B. Herman, Yulan Piao, Nirad Banskota, Jen-Hao Yang, Linna Cui, Carlos Anerillas, Ming-Wen Chang, Mary Kaileh, Rachel Munk, Xiaoling Yang, Ceereena Ubaida-Mohien, Chee W. W. Chia, Ajoy C. C. Karikkineth, Linda Zukley, Jarod D'Agostino, Kotb Abdelmohsen, Nathan Basisty, Supriyo De, Luigi Ferrucci, Myriam Gorospe
Summary: We identified age-associated changes in the transcriptome, including coding and noncoding RNAs, of healthy human skin fibroblasts from 82 individuals across a wide age range. The differential abundance of 1437 coding and 1177 long noncoding RNAs was observed as a function of age. Transcription factors and RNA-binding proteins were implicated in regulating the expression of differentially abundant mRNAs and age-associated lncRNAs. These findings suggest that the identified transcripts may have potential as biomarkers and therapeutic targets for aging skin.
Editorial Material
Genetics & Heredity
Claire Wilson, Aditi Kanhere
Summary: This study speculates on the potential role of variants of lncRNAs in cancer development by drawing upon emerging research findings.
TRENDS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Qing Xia, Qibin Yan, Zehua Wang, Qinyuan Huang, Xinying Zheng, Jinze Shen, Lihua Du, Hanbing Li, Shiwei Duan
Summary: This study aimed to construct a prediction model for breast cancer subtypes based on disulfidptosis-related lncRNAs. The random forest algorithm was used to select important lncRNAs, and a prediction model was successfully established. The study also revealed that key lncRNAs were closely related to RNA methylation modification, angiogenesis, and immune infiltrating cells.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Jingxuan Li, Xueyan Zhao, Yanping Wang, Jiying Wang
Summary: This study sequenced the expression profiles of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in the longissimus dorsi (LD) muscle of Laiwu pigs to understand their role in the regulation of intramuscular fat (IMF) deposition. The results identified differentially expressed protein-coding genes and noncoding RNAs related to adipogenesis, suggesting their important roles in regulating IMF deposition. A connective network was also constructed, revealing miRNAs that may affect lipid metabolism or adipogenesis. This work provides valuable information for further research on the functions of lncRNAs and circRNAs in IMF deposition.
Article
Multidisciplinary Sciences
Razia Khalid, Hammad Naveed, Zoya Khalid
Summary: Long non-coding RNAs (lncRNAs) have emerged as important players in regulating biological processes and their mutations are associated with complex diseases. In this study, we developed a machine learning model that combines sequence and structure-based features to predict disease-related lncRNAs. Our model outperformed existing methods and achieved the highest F1 score of 76% on the SVM classifier. We also addressed limitations in previous methods by incorporating redundancy checking and oversampling techniques. Combining multiple features, particularly lncRNA sequence mutations, significantly contributed to the prediction of disease-related lncRNAs.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Xiaoying Jiang, Ronghui Lei
Summary: Exosomes are membrane-surrounded extracellular vesicles that mediate intercellular communication by delivering bioactive molecules. Long noncoding RNAs (lncRNAs), a class of non-protein-coding RNAs, play important roles in the development of cardiovascular diseases (CVDs). In this article, we review the current studies on exosomal lncRNAs secreted and absorbed by cardiomyocytes and their functional roles in CVDs, aiming to deepen our understanding of the pathological mechanisms of CVDs and their potential for clinical diagnosis and therapy.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Zhongli Wang, Chao Liu
Summary: The study revealed downregulation of hsa_circRNA_100269 in GC tissues, with a negative correlation to elevated levels of PI3K. Overexpression of hsa_circRNA_100269 inhibited GC cell proliferation, migration, invasion, and EMT, while promoting cell cycle arrest and apoptosis. The PI3K/Akt signaling pathway was implicated in hsa_circRNA_100269-regulated functions of GC cells.
Article
Reproductive Biology
Bei-Bei Zhang, Meng-Xiao Li, Hong-Na Wang, Chao Liu, Yan-Yan Sun, Teng-He Ma
Summary: In this study, the expression of lncRNAs and mRNAs associated with ovarian follicle development in Taihang chickens was analyzed at the genome-wide level. The findings identified key pathways and regulatory factors related to follicle selection, providing a new foundation for future research on reproductive physiology in Taihang chickens and offering new opportunities to improve their laying performance.
Review
Biochemistry & Molecular Biology
Igor Petrone, Everton Cruz dos Santos, Renata Binato, Eliana Abdelhay
Summary: Long noncoding RNAs (lncRNAs) are noncoding transcripts encoded by the mammalian genome, functioning as decoys, scaffolds, and enhancer RNAs. They play a vital role in regulating other molecules, including microRNAs. Abnormal expression of lncRNAs has been implicated in breast cancer (BC) initiation and progression, highlighting the need for a better understanding of lncRNA regulatory mechanisms. Specifically, this review focuses on the role of lncRNAs in ductal carcinoma in situ (DCIS) and their potential contribution to the progression of DCIS to invasive BC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Xi-Wen Wang, Chu-Xiao Liu, Ling-Ling Chen, Qiangfeng Cliff Zhang
Summary: RNA molecules fold into complex structures to perform diverse functions in cells, and recent advancements in RNA structural probing have led to profound discoveries linking RNA regulation and biological processes. Understanding how long noncoding RNAs form unique secondary structures is crucial for studying their interactions with proteins and regulating RNA functions. These dynamic structures play a key role in mediating RNA regulatory functions and future developments aim to improve sensitivity and resolution for more physiologically relevant studies.
NATURE CHEMICAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Man Wu, Liang-Zhong Yang, Ling-Ling Chen
Summary: Despite being expressed at low levels, long noncoding RNAs (lncRNAs) play crucial roles in gene regulation by interacting with proteins. Understanding the mechanisms of these interactions, even at low stoichiometric concentrations, is important for comprehending the functions of lncRNAs.
Article
Cell Biology
Jiaquan Liu, Liang-Zhong Yang, Ling-Ling Chen
Summary: This mini-review outlines molecular methods for identifying lncRNA-protein interactions, including large-scale and individual level approaches, as well as imaging and single-molecule methods. Despite some limitations, these methods enable quantification and comprehensive analysis of RNA-protein interactions.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Chu-Xiao Liu, Si-Kun Guo, Fang Nan, Yi-Feng Xu, Li Yang, Ling-Ling Chen
Summary: Exon back-splicing-generated circular RNAs can suppress PKR in cells. We synthesized immunogenicity-free RNA circles containing short dsRNA and found that they induce an immune response. Directly ligated circular RNAs efficiently suppress PKR activation.
Review
Cell Biology
Li Yang, Jeremy E. Wilusz, Ling-Ling Chen
Summary: Covalently closed, single-stranded circular RNAs can be produced from viral RNA genomes as well as from the processing of cellular RNAs. Recent studies have revealed that many protein-coding genes can undergo backsplicing, leading to widespread expression of circular RNAs (circRNAs) in eukaryotic cells. circRNAs play various roles in gene regulation, acting as noncoding RNAs or encoding functional peptides. They are involved in physiological processes including early development, immune responses, neurogenesis, and tumorigenesis.
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Chu-Xiao Liu, Ling-Ling Chen
Summary: In this review, we discuss the methods used in circular RNA studies and the current understanding of their regulatory roles and potential applications. Circular RNAs can modulate transcription and splicing, regulate the stability and translation of mRNAs, interfere with signaling pathways, and play important roles in cellular processes and immune responses.
Article
Biochemistry & Molecular Biology
Takaaki Yasuhara, Yu-Hang Xing, Nicholas C. Bauer, Lukuo Lee, Rui Dong, Tribhuwan Yadav, Roy J. Soberman, Miguel N. Rivera, Lee Zou
Summary: The proper function of the genome relies on the spatial organization of DNA, RNA, and proteins. Research shows that transcription inhibition leads to the formation of condensates (CITIs) that drastically alter the genome's spatial organization. Additionally, proper transcription and RNA processing prevent the generation of gene fusions caused by DNA double-strand breaks (DSBs).
Article
Multidisciplinary Sciences
Emely Moeller, Viviane Praz, Sanalkumar Rajendran, Rui Dong, Alexandra Cauderay, Yu-Hang Xing, Lukuo Lee, Carlo Fusco, Liliane C. Broye, Luisa Cironi, Sowmya Iyer, Shruthi Rengarajan, Mary E. Awad, Beverly Naigles, Igor Letovanec, Nicola Ormas, Giovanna Finzi, Stefano La Rosa, Fausto Sessa, Ivan Chebib, G. Petur Nielsen, Antonia Digklia, Dimitrios Spentzos, Gregory M. Cote, Edwin Choy, Martin Aryee, Ivan Stamenkovic, Gaylor Boulay, Miguel N. Rivera, Nicolo Riggi
Summary: This study investigated the gene regulation networks of the EWSR1-ATF1 fusion gene in Clear Cell Sarcoma, revealing its mechanisms in chromatin activation and establishment of 3D networks. It also suggested precursor cells in the neural crest lineage as potential cells of origin for these tumors.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Siqi Li, Hao Wu, Ling-Ling Chen
Summary: This study presents a detailed protocol based on the RfxCas13d/BSJ-gRNA system for large-scale functional circRNA screening in human cell lines. The protocol allows for the differentiation between circRNAs and mRNAs and the identification of highly expressed circRNAs affecting cell growth.
Editorial Material
Biochemical Research Methods
Ling-Ling Chen
Summary: This article highlights the recent progress and technological advances in understanding lncRNA biogenesis, modes of action, and cellular phenotypes, and discusses the challenges and opportunities for higher-resolution and in vivo studies in this field.
Editorial Material
Cell Biology
Ling-Ling Chen, Albrecht Bindereif, Irene Bozzoni, Howard Y. Y. Chang, A. Gregory Matera, Myriam Gorospe, Thomas B. B. Hansen, Jorgen Kjems, Xu-Kai Ma, Jun Wei Pek, Nikolaus Rajewsky, Julia Salzman, Jeremy E. E. Wilusz, Li Yang, Fangqing Zhao
Summary: This Comment calls for a common nomenclature for naming circRNAs to ensure clarity and reproducibility in studies.
NATURE CELL BIOLOGY
(2023)
Review
Cell Biology
John S. S. Mattick, Paulo P. P. Amaral, Piero Carninci, Susan Carpenter, Howard Y. Y. Chang, Ling-Ling Chen, Runsheng Chen, Caroline Dean, Marcel E. E. Dinger, Katherine A. A. Fitzgerald, Thomas R. R. Gingeras, Mitchell Guttman, Tetsuro Hirose, Maite Huarte, Rory Johnson, Chandrasekhar Kanduri, Philipp Kapranov, Jeanne B. B. Lawrence, Jeannie T. T. Lee, Joshua T. T. Mendell, Timothy R. R. Mercer, Kathryn J. J. Moore, Shinichi Nakagawa, John L. L. Rinn, David L. L. Spector, Igor Ulitsky, Yue Wan, Jeremy E. E. Wilusz, Mian Wu
Summary: Genes encoding lncRNAs are abundant in complex organisms and are transcribed by RNA polymerase I, II, and III, as well as processed introns. The classification and annotation of lncRNAs are challenging due to their various functions, isoforms, and interactions with other genes. These lncRNAs evolve rapidly, are cell type-specific, and regulate multiple cellular processes, including gene expression and translation control.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lin Shan, Guang Xu, Run-Wen Yao, Peng-Fei Luan, Youkui Huang, Pei-Hong Zhang, Yu-Hang Pan, Lin Zhang, Xiang Gao, Ying Li, Shi-Meng Cao, Shuai-Xin Gao, Zheng-Hu Yang, Siqi Li, Liang-Zhong Yang, Ying Wang, Catharine C. L. Wong, Li Yu, Jinsong Li, Li Yang, Ling-Ling Chen
Summary: The nucleolus, composed of hundreds of proteins, plays a crucial role in ribosomal RNA transcription and processing. Through screening and imaging studies, researchers identified a static protein, URB1, enriched in the periphery of the dense fibrillar component of nucleolus. URB1 is responsible for proper pre-rRNA anchoring and folding, and its depletion disrupts nucleolar organization and leads to aberrant pre-rRNA intermediates, resulting in decreased rRNA production and developmental defects.
Article
Biotechnology & Applied Microbiology
Yu-Hang Xing, Rui Dong, Lukuo Lee, Shruthi Rengarajan, Nicolo Riggi, Gaylor Boulay, Miguel N. Rivera
Summary: DisP-seq is an antibody-independent chemical precipitation assay that can map endogenous DNA-associated disordered proteins genome-wide. The profiles generated by DisP-seq are composed of thousands of peaks associated with diverse chromatin states, enriched for disordered transcription factors, and arranged in large clusters with high local concentrations of disordered proteins and different combinations of histone modifications. DisP-seq analysis of cancer cells reveals the role of disordered protein-associated islands in controlling the binding and function of disordered transcription factors, including oncogene-dependent sequestration and reactivation of differentiation pathways upon loss of oncogenic stimuli in Ewing sarcoma.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Rajendran Sanalkumar, Rui Dong, Lukuo Lee, Yu -Hang Xing, Sowmya Iyer, Igor Letovanec, Stefano La Rosa, Giovanna Finzi, Elettra Musolino, Roberto Papait, Ivan Chebib, G. Petur Nielsen, Raffaele Renella, Gregory M. Cote, Edwin Choy, Martin Aryee, Kimberly Stegmaier, Ivan Stamenkovic, Miguel N. Rivera, Nicole Riggi
Summary: Cell fate transitions in pediatric cancer Ewing sarcoma involve changes in genomic organization, with chromatin interactions controlled by the oncogenic fusion protein EWS-FLI1. Depletion of EWS-FLI1 leads to disassembly of looping networks and reestablishment of nuclear organization resembling mesenchymal stem cells, suggesting a progenitor role for Ewing sarcoma. These findings emphasize the reversibility of major nuclear architectural features in cancer cells.
