Article
Biochemistry & Molecular Biology
Tamer Ali, Sandra Rogala, Nina M. Krause, Jasleen Kaur Bains, Maria-Theodora Melissari, Sandra Waehrisch, Harald Schwalbe, Bernhard G. Herrmann, Phillip Grote
Summary: Long non-coding RNAs can regulate cell function and other genes on the transcriptional level through mechanisms such as direct interaction with DNA and formation of RNA:dsDNA triplexes. In this study, we genetically deleted the triplex forming sequence from the lncRNA Fendrr in mice and found its partial requirement for Fendrr function in vivo. Loss of the triplex forming site in developing lungs led to dysregulation of gene programs associated with lung fibrosis, with some genes containing a triplex site directly at their promoter. We confirmed the formation of an RNA:dsDNA triplex with target promoters in vitro and implicated the synergistic role of Fendrr and the Wnt signaling pathway in lung fibrosis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Tianyuan Liu, Bohao Zou, Manman He, Yongfei Hu, Yiying Dou, Tianyu Cui, Puwen Tan, Shaobin Li, Shuan Rao, Yan Huang, Sixi Liu, Kaican Cai, Dong Wang
Summary: This study developed a deep-learning model called LncReader, which uses a multi-head self-attention mechanism to identify dual functional lncRNAs. By comparing it with various machine learning methods, it was demonstrated that LncReader has advantages in predicting dual functional lncRNAs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Tianyuan Liu, Bohao Zou, Manman He, Yongfei Hu, Yiying Dou, Tianyu Cui, Puwen Tan, Shaobin Li, Shuan Rao, Yan Huang, Sixi Liu, Kaican Cai, Dong Wang
Summary: Recently, we developed a deep-learning model called LncReader with a multi-head self-attention mechanism to identify dual functional long noncoding ribonucleic acids (lncRNAs). Our data showed that LncReader exhibited several advantages over various classical machine learning methods using benchmark datasets. Additionally, independent in-house datasets generated through mass spectrometry proteomics combined with RNA-seq and Ribo-seq confirmed that LncReader achieved the best performance compared to other tools. Therefore, LncReader provides an accurate and practical tool for fast identification of dual functional lncRNAs.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Yu Zhang, Cangzhi Jia, Melissa Jane Fullwood, Chee Keong Kwoh
Summary: The development of deep sequencing technologies has led to the discovery of novel transcripts. Many methods have been developed for assessing the coding potential of these transcripts, with DeepCPP being a deep learning method that outperforms other state-of-the-art methods, especially on sORF type data. The use of discontinuous k-mer, nucleotide bias, and minimal distribution similarity feature selection methods proved crucial in improving the accuracy of coding potential prediction for RNA.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Christopher A. Ryan, Md Motiar Rahman, Vipin Kumar, Eriks Rozners
Summary: RNA folding is influenced by the presence of bulges consisting of unpaired nucleotides, which play a significant role in stabilizing various interactions involving RNA. This study demonstrates that triplex-forming peptide nucleic acids (PNAs) have a high affinity for single-purine-nucleotide bulges in double-helical RNA. The formation of the RNA-PNA triplex alters the equilibrium between looped out and stacked-in conformations, potentially providing a valuable tool for studying RNA structure-function relationships and developing therapeutic strategies targeting disease-related RNAs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Yu-Jian Kang, Jing-Yi Li, Lan Ke, Shuai Jiang, De-Chang Yang, Mei Hou, Ge Gao
Summary: This study introduces the ribosome calculator, which quantitatively models the coding ability of RNAs in the human genome, and successfully predicts transcripts with different coding abilities in various cell types. This suggests that the coding ability of transcripts should be modeled as a continuous spectrum with context-dependent nature.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Wentao Ma, Weihong Zhang, Bing Cui, Jing Gao, Qiuhong Liu, Mengying Yao, Hanbing Ning, Lihua Xing
Summary: This study reveals that EPCs derived EVs transmit TUG1 to alleviate sepsis by promoting macrophage M2 polarization. Additionally, TUG1 can competitively bind to miR-9-5p to upregulate SIRT1 expression, leading to the inhibition of miR-9-5p-mediated SIRT1 inhibition, which contributes to a more comprehensive understanding of the pathogenesis of sepsis.
CELL DEATH & DISEASE
(2021)
Article
Biotechnology & Applied Microbiology
Benjamin Soibam, Ayzhamal Zhamangaraeva
Summary: This study reveals that long noncoding RNAs (lncRNAs) with triplex-forming sites are enriched in topologically associated domains (TADs) and can be used as predictors to discriminate TADs from other genomic regions. These observations suggest that lncRNA:DNA triplex formation may be a common mechanism for chromatin organization beyond direct gene regulation.
Review
Biochemistry & Molecular Biology
Yuai Xiao, Yu Xia, Yuchong Wang, Chunyu Xue
Summary: Melanoma, a dangerous type of cutaneous neoplasm, has been extensively studied to improve diagnostic and treatment options. Long noncoding RNAs (lncRNAs) have been discovered and found to play significant roles in the occurrence and progression of melanoma. Researchers have categorized melanoma-associated lncRNAs based on their cellular functions, gene expression, and signaling pathways, and discussed the possibility of lncRNA-targeted treatments and the application of liquid biopsies for lncRNA detection in melanoma diagnosis and prognosis.
Review
Biochemistry & Molecular Biology
Hailong Chen, Mengwen Zhang, Yongchuan Deng
Summary: Breast cancer is a common and deadly disease among women. Chemotherapy, particularly taxanes, has greatly improved the prognosis of breast cancer patients. However, taxane resistance caused by various factors remains a challenge. Long noncoding RNAs (lncRNAs) have been found to play a significant role in taxane resistance. This review systematically summarizes the mechanisms of taxane resistance in breast cancer and the functions of lncRNAs in this resistance. The findings suggest that lncRNAs may serve as therapeutic targets to prevent or reverse taxane resistance in breast cancer patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Bin Zhang, Tongbing Su, Peirong Li, Xiaoyun Xin, Yunyun Cao, Weihong Wang, Xiuyun Zhao, Deshuang Zhang, Yangjun Yu, Dayong Li, Shuancang Yu, Fenglan Zhang
Summary: This study analyzed the mRNAs and long noncoding RNAs involved in resistance to Brassica downy mildew in Chinese cabbage through high-throughput RNA sequencing. Different expression patterns and proposed functions of long noncoding RNAs were identified among resistant and susceptible lines, indicating distinct disease response mechanisms. A candidate resistance-related long noncoding RNA was identified, which played a role in the defense response against pathogens.
HORTICULTURE RESEARCH
(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.
Review
Endocrinology & Metabolism
Susanne N. Wijesinghe, Thomas Nicholson, Kostas Tsintzas, Simon W. Jones
Summary: Obesity is associated with chronic low-grade inflammation and long noncoding RNAs have been identified as key regulators of inflammatory pathways. Some lncRNAs are differentially expressed in obesity and related conditions like insulin resistance, type 2 diabetes, sarcopenia, osteoarthritis, and rheumatoid arthritis. Understanding the role of lncRNAs in mediating obesity-associated inflammation may lead to new therapeutic targets.
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)
Review
Cell Biology
Elahe Soltani-Fard, Marzieh Asadi, Sina Taghvimi, Asma Vafadar, Parisa Vosough, Amir Tajbakhsh, Amir Savardashtaki
Summary: Endometriosis is a gynecological disorder characterized by the growth of endometrial-like cells outside the uterus. It is difficult to diagnose noninvasively, leading to delays in treatment and increased burden on patients. Exosomes, which transport bioactive molecules, including microRNAs and long noncoding RNAs, have been found to play a significant role in endometriosis development. This review focuses on the potential functions of exosomal noncoding RNAs in the therapy and diagnosis of endometriosis.
CELL AND TISSUE RESEARCH
(2023)
Article
Cell Biology
Nicolas Valenzuela, Benjamin Soibam, Lerong Li, Jing Wang, Lauren A. Byers, Yu Liu, Robert J. Schwartz, M. David Stewart
JOURNAL OF CELL SCIENCE
(2017)
Article
Multidisciplinary Sciences
Xiaopeng Shen, Wenjing Bao, Wei Yu, Rui Liang, Bao Nguyen, Yu Liu
Article
Biotechnology & Applied Microbiology
Fan Wang, Zachariah Dohogne, Jin Yang, Yu Liu, Benjamin Soibam
Article
Cell Biology
Zhe-Ling Chen, Jiao Yang, Yan-Wei Shen, Shu-Ting Li, Xin Wang, Meng Lv, Bi-Yuan Wang, Pan Li, Wen Zhao, Rui-Yue Qiu, Yu Liu, Pei-Jun Liu, Jin Yang
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2018)
Meeting Abstract
Oncology
Neha Tandon, Benjamin Soibam, Robert Schwartz, Yu Liu
Article
Biochemistry & Molecular Biology
Fan Wang, Rui Liang, Benjamin Soibam, Jin Yang, Yu Liu
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2019)
Review
Biochemistry & Molecular Biology
Fan Wang, Rui Liang, Neha Tandon, Elizabeth R. Matthews, Shreesti Shrestha, Jiao Yang, Benjamin Soibam, Jin Yang, Yu Liu
CELLULAR AND MOLECULAR LIFE SCIENCES
(2019)
Article
Cell & Tissue Engineering
Rui Liang, Yu Liu
STEM CELL RESEARCH & THERAPY
(2018)
Article
Cell Biology
Jiao Yang, Xiaoman Zhang, Zheling Chen, Yanwei Shen, Fan Wang, Yaochun Wang, Yu Liu, Peijun Liu, Jin Yang
CELL DEATH & DISEASE
(2019)
Article
Biochemistry & Molecular Biology
John Henderson, Vi Ly, Shawn Olichwier, Pranik Chainani, Yu Liu, Benjamin Soibam
NUCLEIC ACIDS RESEARCH
(2019)
Article
Medicine, General & Internal
Neha Tandon, Kristina Goller, Fan Wang, Benjamin Soibam, Mihai Gagea, Abhinav K. Jain, Robert J. Schwartz, Yu Liu
Article
Biology
Xiaopeng Shen, Feng Xu, Shen Wu, Meng Li, Jingyi Zhang, Rui Liang, Yu Liu
Article
Biology
Neha Tandon, Kaushik N. Thakkar, Edward L. LaGory, Yu Liu, Amato J. Giaccia
Review
Biochemistry & Molecular Biology
Yu Liu
CELLULAR AND MOLECULAR LIFE SCIENCES
(2017)