Article
Biochemistry & Molecular Biology
Dingfeng Li, Ran Cao, Qiaodan Li, Yang Yang, Aihui Tang, Juan Zhang, Qiang Liu
Summary: In this study, the authors demonstrate that the lncRNA LoNA plays a role in connecting nucleolar structure with epigenetic reprogramming and zygotic genome activation. Loss of LoNA leads to developmental arrest at the two-cell stage by affecting nucleolar assembly and repression of 2C gene transcription. The findings suggest that lncRNA is essential for establishing nucleolar structure and has an impact on early embryonic development via transcriptional activation of 2C genes.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Xiaojiao Zhao, Hongliang Zeng, Li Lei, Xiaoliang Tong, Lun Yang, Yan Yang, Si Li, Ying Zhou, Liping Luo, Jinhua Huang, Rong Xiao, Jing Chen, Qinghai Zeng
Summary: Tight junction (TJ) is a zipping up junction structure located at the uppermost portion of adjacent epithelial/endothelial cells in organs and tissues, maintaining the stability of intracellular substances and functions. TJs are widely present in various organs and tissues, dysfunction of which can lead to various diseases, and they are also regulated by non-coding RNAs.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
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.
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)
Article
Immunology
Dongjie Shi, Wenjie Zhong, Dan Liu, Xiaochuan Sun, Shilei Hao, Yaying Yang, Lei Ao, Junjie Zhou, Yongzhi Xia, Yudong Zhou, Hua Yu, Haijian Xia
Summary: This study developed a computational framework based on immune score to identify immune-related long noncoding RNAs (IRLncSig) in human glioblastoma multiforme (GBM). The IRLncSig was found to have significant clinical value in predicting prognosis and immune landscape of GBM.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hsiao-Fan Chen, Chia-Ting Chang, Kai-Wen Hsu, Pei-Hua Peng, Joseph Chieh-Yu Lai, Mien-Chie Hung, Kou-Juey Wu
Summary: This study identifies the epigenetic regulatory mechanisms, including BRD4 and lncRNA LIBR, that control asymmetric cell division (ACD). The findings suggest limitations in using BRD4 inhibitors for cancer treatment due to their potential to promote symmetric cell division.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Xiaomin Zheng, Yanjun Chen, Yifan Zhou, Keke Shi, Xiao Hu, Danyang Li, Hanzhe Ye, Yu Zhou, Kun Wang
Summary: The study integrated multiple RNA sequencing technologies to identify 9,240 lncRNAs in the diploid cotton Gossypium arboreum. It revealed the widespread alternative usage of transcription start and termination sites in lncRNAs during plant growth, and discovered that many lncRNAs act in cis to regulate adjacent protein-coding genes.
Review
Cell Biology
Manjima Chatterjee, Pragasam Viswanathan
Summary: Long noncoding RNAs (lncRNAs) play significant roles in human malignancies, regulating cell survival or apoptosis and interacting closely with the p53 network and apoptosis pathways. They may serve as potential therapeutic targets or diagnostic/prognostic markers.
CELL BIOLOGY INTERNATIONAL
(2021)
Review
Biochemistry & Molecular Biology
Weijin Xu, Jeetayu Biswas, Robert H. Singer, Michael Rosbash
Summary: RNA binding proteins (RBPs) regulate post-transcriptional processes in cells, and it is crucial to identify their in vivo targets for understanding their function. Standard techniques for profiling RBP targets have limitations in certain situations, but new genetic approaches have been developed for such circumstances. These approaches, including TRIBE, RNA tagging, and STAMP, provide useful tools for studying post-transcriptional regulation and RBP identification, with potential therapeutic implications.
Article
Biochemistry & Molecular Biology
Adam Frankish, Silvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet, Daniel Cerdan-Velez, Fiona Cunningham, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos Garcia Giron, Jose Manuel Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike Kay, Julien Lagarde, Fergal J. Martin, Laura Martinez Gomez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew Yates, Zahoor Zafrulla, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigo, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek
Summary: GENCODE provides high quality gene and transcript annotation for the human and mouse genomes, supported by experimental data, serving as a reference for genome biology and clinical genomics. The consortium generates data, develops tools and carries out analyses to support the identification and annotation of transcript structures and their function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Endocrinology & Metabolism
Zhihuai Wang, Peng Gao, Weijun Sun, Adeel Ur Rehman, Jiakai Jiang, Suobao Xu, Cailin Xue, Chunfu Zhu, Xihu Qin
Summary: This study investigated the diagnostic value of long noncoding RNA (lncRNA) lnc-MyD88 as a plasma biomarker in hepatocellular carcinoma (HCC). The results showed that lnc-MyD88 was highly expressed in the plasma samples of HCC patients and HBV-associated HCC patients. Compared to alpha-fetoprotein (AFP), lnc-MyD88 had better diagnostic value in HCC patients, especially in HBV-associated HCC and AFP-negative HCC. Therefore, lnc-MyD88 may be a potential diagnostic biomarker for HCC.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Genetics & Heredity
Xue-Cang Li, Zhi-Dong Tang, Li Peng, Yan-Yu Li, Feng-Cui Qian, Jian-Mei Zhao, Ling-Wen Ding, Xiao-Juan Du, Meng Li, Jian Zhang, Xue-Feng Bai, Jiang Zhu, Chen-Chen Feng, Qiu-Yu Wang, Jian Pan, Chun-Quan Li
Summary: This study identified a distinct group of circRNAs (TAH-circRNAs) with epigenomically unique features, independently transcribed via enhancers and super-enhancers by TFs and playing roles in cancer biology.
FRONTIERS IN GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Tim Y. Hou, W. Lee Kraus
Summary: Recent studies have shown that enhancer RNAs (eRNAs) play functional roles in activating gene expression, rather than just being non-functional byproducts of nearby transcription machinery. Challenges in elucidating the functions of eRNAs lie in their unstable nature and limitations of knockdown approaches.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Buze Chen, Xiaoyuan Lu, Qingmei Zhou, Qing Chen, Siyan Zhu, Guilin Li, Hui Liu
Summary: It was found that the long non-coding RNA PAXIP1-AS1 promoted various functions in ovarian cancer cells, while its relationship with clinical characteristics, prognosis, and immune infiltration in OC patients and its regulatory network were unclear. Through various tests and analyses, it was discovered that low PAXIP1-AS1 expression was associated with poor survival and immune infiltration in OC patients. The study suggested that PAXIP1-AS1 could potentially serve as a biomarker for prognosis and response to immunotherapy in OC.
Review
Medicine, Research & Experimental
Chunjie Huang, Paniz Azizi, Masoud Vazirzadeh, Seyed Mohsen Aghaei-Zarch, Fatemehsadat Aghaei-Zarch, Jalaledin Ghanavi, Poopak Farnia
Summary: Cancer is a complex disease with diverse factors. DNA methylation and dysregulation of non-coding RNAs play critical roles in cancer progression. Understanding the interplay between DNMT3B and ncRNAs provides insights into tumorigenesis and potential therapeutic interventions.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Oncology
Fritz F. Parl, Philip S. Crooke, W. Dale Plummer, William D. Dupont
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2018)
Article
Immunology
Maxwell J. Heinrich, Caroline A. Purcell, Andrea J. Pruijssers, Yang Zhao, Charles F. Spurlock, Subramaniam Sriram, Kristen M. Ogden, Terence S. Dermody, Matthew B. Scholz, Philip S. Crooke, John Karijolich, Thomas M. Aune
JOURNAL OF AUTOIMMUNITY
(2019)
Article
Medicine, Research & Experimental
Ryo Hatano, Takumi Itoh, Haruna Otsuka, Sayo Okamoto, Eriko Komiya, Satoshi Iwata, Thomas M. Aune, Nam H. Dang, Kyoko Kuwahara-Arai, Kei Ohnuma, Chikao Morimoto
Review
Rheumatology
Bruce N. Cronstein, Thomas M. Aune
NATURE REVIEWS RHEUMATOLOGY
(2020)
Article
Biochemical Research Methods
John T. Tossberg, Tashawna M. Esmond, Thomas M. Aune
Article
Immunology
John T. Tossberg, Rachel M. Heinrich, Virginia M. Farley, Philip S. Crooke, Thomas M. Aune
JOURNAL OF IMMUNOLOGY
(2020)
Article
Immunology
Philip S. Crooke, John T. Tossberg, Krislyn P. Porter, Thomas M. Aune
Summary: Decreased A-to-I editing of Alu dsRNAs is associated with increased inflammatory responses in patients with severe COVID-19 disease.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Rheumatology
Anna E. Patrick, Wei Wang, Elly Brokamp, Thomas Brent Graham, Thomas M. Aune, Jessica B. Duis
ARTHRITIS RESEARCH & THERAPY
(2019)
Article
Oncology
Fritz F. Parl, William D. Dupont, Philip S. Crooke
CANCER INFORMATICS
(2019)
Meeting Abstract
Gastroenterology & Hepatology
Charles Spurlock, Tossberg John, Shaginurova Guzel, Harmata Andrew, Philip Crooke, Aune Thomas
AMERICAN JOURNAL OF GASTROENTEROLOGY
(2018)
Meeting Abstract
Clinical Neurology
C. F. Spurlock, J. T. Tossberg, G. Shaginurova, S. Sriram, J. Wingstrom, P. S. Crooke, T. M. Aune
MULTIPLE SCLEROSIS JOURNAL
(2017)
Meeting Abstract
Clinical Neurology
Charles Spurlock, John Tossberg, Subramaniam Sriram, Phillip Crooke, Thomas Aune
Meeting Abstract
Clinical Neurology
Charles F. Spurlock, John T. Tossberg, Subramaniam Sriram, Philip S. Crooke, Thomas M. Aune
MULTIPLE SCLEROSIS JOURNAL
(2017)