Review
Genetics & Heredity
Rujuan Dai, Zhuang Wang, S. Ansar Ahmed
Summary: Systemic lupus erythematosus (SLE) is a complex autoimmune disease affecting multiple organs, with DNA methylation and miRNAs playing key roles in its pathogenesis. The interaction between DNA methylation and miRNAs regulation impacts the expression of lupus-related miRNAs and DNA methylation status.
Review
Oncology
Fatemeh Sadoughi, Seyyed Mehdi Mirhashemi, Zatollah Asemi
Summary: Recent investigations have shown the important role of small non-coding RNAs, with a focus on piRNAs and their potential relationship to colorectal cancer (CRC). CRC, a common gastrointestinal malignancy, is believed to be linked to genetic and epigenetic alterations.
CANCER CELL INTERNATIONAL
(2021)
Article
Genetics & Heredity
Chuang Yin, Chuandong Wang, Chen Wang
Summary: This study examines the differential expression of small noncoding RNAs in keloid skin tissue (KST) and reveals potential targets for the development of new treatment for keloids.
FRONTIERS IN GENETICS
(2022)
Review
Cell Biology
Jacek Kabzinski, Aleksandra Kucharska-Lusina, Ireneusz Majsterek
Summary: Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Liquid biopsy, a non-invasive diagnostic approach, holds great promise for the early detection, prognosis, and personalized treatment of HNC. Various types of RNA have been explored as potential biomarkers in HNC liquid-based diagnostics, and their roles in diagnosis, metastasis, tumor resistance, and overall prognosis are discussed.
Article
Immunology
Ding Ma, Xing Zhou, Yu Wang, Liming Dai, Jie Yuan, Jianping Peng, Xiaoling Zhang, Chuandong Wang
Summary: In this study, we investigated the expression changes of small noncoding RNAs during macrophage polarization using high-throughput sequencing analysis and qPCR. Our results showed that miRNAs, piRNAs, snoRNAs, snRNAs, and repeat RNAs exhibited altered expression patterns during different polarization states, suggesting their potential roles in regulating macrophage function.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Oncology
Shokooh Salimimoghadam, Sina Taefehshokr, Reid Loveless, Yong Teng, Gloria Bertoli, Nima Taefehshokr, Fatemeh Musaviaroo, Khalil Hajiasgharzadeh, Behzad Baradaran
Summary: This review discusses the tumor suppressing roles of non-coding RNAs in breast cancer, and the mechanisms by which these RNAs target tumor hallmarks, including apoptosis, proliferation, invasion, metastasis, epithelial-mesenchymal transition, angiogenesis, and cell cycle progression.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
Article
Orthopedics
Hui Wang, Guiquan Cai, Fengbin Yu, De Li, Chenglong Wang, Ding Ma, Xiuguo Han, Jiajia Chen, Chuandong Wang, Jiye He
Summary: Osteosarcoma, the most common malignant bone tumor, primarily affects adolescents and the elderly. Bone marrow mesenchymal stem cells (BMSCs) are believed to be a potential source of osteosarcoma cells. Understanding the gene expression differences between BMSCs and osteosarcoma cells, specifically in small noncoding RNAs, provides valuable insights into the pathogenesis and early diagnosis and treatment of osteosarcoma.
JOURNAL OF ORTHOPAEDIC SURGERY AND RESEARCH
(2023)
Article
Endocrinology & Metabolism
Fei Xiao, Jianping Peng, Yang Li, Xing Zhou, Ding Ma, Liming Dai, Jie Yuan, Xiaodong Chen, Chuandong Wang
Summary: This study investigated the cellular senescence mechanism of BMSCs and identified the expression changes of small noncoding RNAs during the senescence process, providing potential clues for developing new targeting senescence strategies.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Oncology
David A. Skaar, Eric C. Dietze, Jackelyn A. Alva-Ornelas, David Ann, Dustin E. Schones, Terry Hyslop, Christopher Sistrunk, Carola Zalles, Adrian Ambrose, Kendall Kennedy, Ombeni Idassi, Gustavo Miranda Carboni, Michael N. Gould, Randy L. Jirtle, Victoria L. Seewaldt
Summary: Genomic imprinting is a specific form of epigenetic regulation that is influenced by poor prenatal nutrition and environmental toxins. KCNK9, a gene associated with breast cancer, was found to be imprinted in breast tissue and hypomethylation at its differentially methylated region was significantly associated with triple-negative breast cancer, particularly in African-American women. The study suggests that hypomethylation of the KCNK9 DMR may serve as a marker of risk and a potential target for prevention of TNBC.
Article
Multidisciplinary Sciences
Tianxiong Yu, Kaili Fan, Deniz M. Ozata, Gen Zhang, Yu Fu, William E. Theurkauf, Phillip D. Zamore, Zhiping Weng
Summary: An unusually long first exon or a long, unspliced transcript is associated with germline-specific transcription and piRNA production in pachytene piRNA clusters. Additionally, a highly methylated promoter containing a low or intermediate level of CG dinucleotides correlates with germline expression and somatic silencing of pachytene piRNA clusters. Furthermore, pachytene piRNA precursor transcripts bind THOC1 and THOC2, contributing to the production of piRNAs.
NATURE COMMUNICATIONS
(2021)
Article
Cardiac & Cardiovascular Systems
Yu Wang, Tianhua Liu, Wenying Xiao, Yanyan Bai, Dandan Yue, Liuliu Feng
Summary: Atherosclerosis (AS) is a common cardiovascular disease characterized by endothelial cell injury and dysfunction. Oxidative low-density lipoprotein (Ox-LDL) is a key risk factor for AS development. This study identified the expression changes of small non-coding RNAs (sncRNAs) in Ox-LDL-treated endothelial cells, providing new markers for the diagnosis and treatment of endothelial cell injury.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Review
Biochemistry & Molecular Biology
Alexander Bishop Coley, Jeffrey David DeMeis, Neil Yash Chaudhary, Glen Mark Borchert
Summary: In the past decade, sdRNAs derived from snoRNAs have emerged as important regulators in cancer gene expression. They possess miRNA-like functions and can act as oncogenic or tumor-suppressing RNAs depending on the tissue context. Despite being frequently overlooked in non-coding RNA analyses, sdRNAs represent a subclass of miRNAs that deserve further study to uncover their underlying biology and identify potential biomarkers and therapeutic targets for various human cancers.
Review
Biochemistry & Molecular Biology
Nicole R. DeSouza, Danielle Quaranto, Michelle Carnazza, Tara Jarboe, Raj K. Tiwari, Jan Geliebter
Summary: RNA biology has gained recognition in the past two decades through the discovery of novel transcriptomic elements and functions. Differential gene expression patterns of wild-type loci have contributed to the understanding of molecular mechanisms driving carcinogenic transformation. Non-coding RNA molecules, particularly long non-coding RNA expression, play a role in cellular activity and pathological cell transformation, expanding cancer studies and molecular targeting.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Alexander B. Coley, Ashlyn N. Stahly, Mohan Kasukurthi, Addison A. Barchie, Sam B. Hutcheson, Dominika Houserova, Yulong Huang, Brianna C. Watters, Valeria M. King, Meghan A. Dean, Justin T. Roberts, Jeffrey D. DeMeis, Krisha Amin, Cameron H. McInnis, Noel L. Godang, Ryan M. Wright, David F. Haider, Neha B. Piracha, Cana L. Brown, Zohaib M. Ijaz, Shengyu Li, Yaguang Xi, Oliver G. McDonald, Jingshan Huang, Glen M. Borchert
Summary: This study identified differentially expressed snoRNA fragments in prostate cancer patients and found that two specific fragments, sdRNA-D19b and -A24, play important roles in promoting proliferation, migration, and chemotherapeutic resistance in prostate cancer. The targets of sdRNA-D19b and sdRNA-A24 were identified as tumor suppressor genes CD44 and CDK12, respectively.
Article
Multidisciplinary Sciences
Brittany L. Carpenter, Tanaka K. Remba, Stacey L. Thomas, Zachary Madaj, Lucy Brink, Rochelle L. Tiedemann, Hein J. Odendaal, Peter A. Jones
Summary: Genomic imprinting occurs before fertilization, impacts every cell of the developing child, and may be sensitive to environmental perturbations. The nc886 gene is the only known example of a human gene imprinted by DNA methylation, showing consistent imprinting across different tissues. The imprint frequency in newborns is influenced by maternal age and alcohol consumption before conception, while smoking does not seem to have a significant relationship with imprinting frequency. This suggests an epigenetic change during oocyte maturation that can be affected by environmental factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Jade Hebras, Nicolai Krogh, Virginie Marty, Henrik Nielsen, Jerome Cavaille
Article
Instruments & Instrumentation
Gildas Diguet, Gael Sebald, Masami Nakano, Mickael Lallart, Jean-Yves Cavaille
SMART MATERIALS AND STRUCTURES
(2020)
Article
Polymer Science
Vladislav Egorov, Hiroshi Koibuchi, Chrystelle Bernard, Jean-Marc Chenal, Gildas Diguet, Gael Sebald, Jean-Yves Cavaille, Toshiyuki Takagi, Laurent Chazeau
Article
Biology
Jade Hebras, Virginie Marty, Jean Personnaz, Pascale Mercier, Nicolai Krogh, Henrik Nielsen, Marion Aguirrebengoa, Herve Seitz, Jean-Phillipe Pradere, Bruno P. Guiard, Jerome Cavaille
Editorial Material
Genetics & Heredity
Yui Imaizumi, Robert Feil
Article
Materials Science, Multidisciplinary
Gildas Diguet, Jean-Yves Cavaille, Gael Sebald, Toshiyuki Takagi, Hiroshi Yabu, Ai Suzuki, Ryuji Miura
Summary: The study investigates the electrostrictive response of soft elastomers and reveals its strong dependence on their chemical nature and multiphase microstructure. By analyzing experimental data and developing a microstructural model, the mechanism behind electrostriction in composite-like materials with phase separation is elucidated, offering valuable insights for material design and performance optimization.
COMPUTATIONAL MATERIALS SCIENCE
(2021)
Article
Physics, Multidisciplinary
V Egorov, O. Maksimova, H. Koibuchi, C. Bernard, J-M Chenal, O. Lame, G. Diguet, G. Sebald, J-Y Cavaille, T. Takagi
Summary: PVDF is a ferroelectric polymer with negative strain along the direction of the applied electric field. The Finsler geometry model is used to explain the electromechanical response of PVDF. Simulated mechanical deformation and polarization closely match experimental observations.
Review
Biochemistry & Molecular Biology
David Lleres, Yui Imaizumi, Robert Feil
Summary: Different classes of non-coding RNA have been found to impact chromatin organization, with long non-coding RNAs (lncRNAs) in imprinted gene domains showing parent-of-origin dependent expression patterns. These lncRNAs can repress nearby and distant protein-coding genes through various mechanisms, and may also influence gene expression on other chromosomes. The focal accumulation of these lncRNAs in cis facilitates the recruitment of repressive complexes and chromatin-modifying proteins, which in turn can affect the higher-order chromatin structure.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Article
Multidisciplinary Sciences
Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio
Summary: ZFP57 is crucial for maintaining germline-marked differential methylation at ICRs in mouse ESCs, and its dependency on methylation is vital for imprinted gene expression during neural differentiation. Compensatory mechanisms may exist for imprinted genes acquiring biallelic expression.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Marie-Line Bortolin-Cavaille, Quillien Aurelie, Thalalla Gamage Supuni, Justin M. Thomas, Aldema Sas-Chen, Sunny Sharma, Celia Plisson-Chastang, Laurence Vandel, Patrick Blader, Denis L. J. Lafontaine, Schraga Schwartz, Jordan L. Meier, Jerome Cavaille
Summary: This study reveals the essential role of SNORD13 in the acetylation of a specific cytidine in human and zebrafish 18S rRNA. However, this acetylation does not have a significant impact on human cell growth, ribosome biogenesis, translation, or development. The study also identifies several novel SNORD13 genes and discovers an atypical SNORD13-like RNA in Drosophila melanogaster.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Norio Kobayashi, Hiroaki Okae, Hitoshi Hiura, Naoto Kubota, Eri H. Kobayashi, Shun Shibata, Akira Oike, Takeshi Hori, Chie Kikutake, Hirotaka Hamada, Hirokazu Kaji, Mikita Suyama, Marie-Line Bortolin-Cavaille, Jerome Cavaille, Takahiro Arima
Summary: Activation of miRNA cluster C19MC in human embryonic stem cells confers differentiation potential into trophoblast lineages. The cluster is active in naive hES cells but silenced in primed ones. Genome and epigenome editing experiments demonstrate the essential role of C19MC in trophoblast stem cell maintenance and its reactivation in primed hES cells can give rise to trophoblast stem cells.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Supuni Thalalla Gamage, Marie-Line Bortolin-Cavaille, Courtney Link, Keri Bryson, Aldema Sas-Chen, Schraga Schwartz, Jerome Cavaille, Jordan L. Meier
Summary: There are two methods for studying RNA-guided cytidine acetylation in human cells: rescuing h45 in a SNORD13 knockout cell line by ectopically expressing SNORD13, and defining the structure and sequence elements critical for SNORD13 function by using mutant snoRNAs in combination with nucleotide resolution ac(4)C sequencing. Additionally, the substrate specificity of endogenous NAT10-SNORD13 can be studied through mutational analysis of an ectopically expressed pre-rRNA substrate.
Article
Instruments & Instrumentation
G. Coativy, K. Yuse, G. Diguet, V Perrin, L. Seveyrat, F. Dalmas, S. Livi, J. Courbon, H. Takana, J. Y. Cavaille
Summary: This study investigates the electromechanical deformation of segmented polyurethane (PUs) thin films over a long time period. Experimental and simulation results reveal that the accumulation of electric charges near the electrodes leads to local stretching, and the different migration velocities of negative and positive carriers result in distinct macroscopic effects. The simulation supports the experimental observations.
SMART MATERIALS AND STRUCTURES
(2022)
Article
Biochemistry & Molecular Biology
Claire Dupont, Dhanvantri Chahar, Antonio Trullo, Thierry Gostan, Caroline Surcis, Charlotte Grimaud, Daniel Fisher, Robert Feil, David Lleres
Summary: Contrary to expectations, heterochromatin is not highly compacted at the nanoscale but resides in a dynamic low nanocompaction state. This state is influenced by H4K20me2/3, the balance between HP1 isoforms, and the cellular proliferation marker Ki-67.
Review
Biochemistry & Molecular Biology
Flavio Di Michele, Isabel Chillon, Robert Feil
Summary: Imprinted genes have diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express long non-coding RNAs (lncRNAs), which control the expression of protein-coding genes. The aberrant regulation of imprinted gene expression, including imprinted lncRNAs, can have long-lasting phenotypic consequences and is associated with human disease syndromes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
