High-throughput sequencing technologies and innovative bioinformatics tools discovered that most of the genome is transcribed into RNA. However, only a fraction of the RNAs in cell translates into proteins, while the majority of them are categorized as noncoding RNAs (ncRNAs). The ncRNAs with more than 200 nt without protein-coding ability are termed long noncoding RNAs (lncRNAs). Hundreds of studies established that lncRNAs are a crucial RNA family regulating gene expression. Regulatory RNAs, including lncRNAs, modulate gene expression by interacting with RNA, DNA, and proteins. Several databases and computational tools have been developed to explore the functions of lncRNAs in cellular physiology. This chapter discusses the tools available for lncRNA functional analysis and provides a detailed workflow for the computational analysis of lncRNAs.
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Sci Rep
December 2024
School of Engineering and Technology, Sunway University, No. 5, Jalan Universiti, Bandar Sunway, Petaling Jaya, 47500, Selangor Darul Ehsan, Malaysia.
Cervical cancer is a deadly disease in women globally. There is a greater chance of getting rid of cervical cancer in case of earliest diagnosis. But for some patients, there is a chance of recurrence.
View Article and Find Full Text PDFNat Commun
December 2024
Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
Modern maize (Zea mays ssp. mays) was domesticated from Teosinte parviglumis (Zea mays ssp. parviglumis), with subsequent introgressions from Teosinte mexicana (Zea mays ssp.
View Article and Find Full Text PDFNat Commun
December 2024
Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Glioblastoma is immunologically "cold" and resistant to single-agent immune-checkpoint inhibitors (ICI). Our previous study of neoadjuvant pembrolizumab in surgically-accessible recurrent glioblastoma identified a molecular signature of response to ICI and suggested that neoadjuvant pembrolizumab may improve survival. To increase the power of this observation, we enrolled an additional 25 patients with a primary endpoint of evaluating the cell cycle gene signature associated with neoadjuvant pembrolizumab and performed bulk-RNA seq on resected tumor tissue (NCT02852655).
View Article and Find Full Text PDFFront Oncol
December 2024
Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong, China.
Background: Preoperative determination of muscular infiltration is crucial for appropriate treatment planning in patients with muscle-invasive bladder cancer (MIBC). We aimed to explore early diagnostic biomarkers in serum for MIBC in this study.
Methods: The expression profiles of long noncoding RNA (lncRNA) were initially screened by high-throughput sequencing and evaluation of potential lncRNAs were conducted by two phases of RT-qPCR assays using serum samples from 190 patients with MIBC and 190 non-muscle-invasive BC (NMIBC) patients.
Front Cell Dev Biol
December 2024
Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, Henan, China.
Pseudouridine (Ψ) is a post-transcriptional modifier of RNA, often referred to as the 'fifth nucleotide' owing to its regulatory role in various biological functions as well as because of its significant involvement in the pathogenesis of human cancer. In recent years, research has revealed various Ψ modifications in different RNA types, including messenger RNA, transfer RNA, ribosomal RNA, small nuclear RNA, and long noncoding RNA. Pseudouridylation can significantly alter RNA structure and thermodynamic stability, as the Ψ-adenine (A) base pair is more stable than the typical uridine (U)-A base pair is due to its structural similarity to adenine.
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