scholarly journals Bioinformatics Analysis of Long Non-coding RNA and Related Diseases: An Overview

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuxin Gong ◽  
Wen Zhu ◽  
Meili Sun ◽  
Lei Shi
Keyword(s):  
Small Rnas ◽  
Bioinformatics Analysis ◽  
Regulation Of Gene Expression ◽  
Research Progress ◽  
Biological Processes ◽  
Existing Problems ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Cancer Côlon ◽  
Long Non Coding Rna

Long non-coding RNAs (lncRNAs) are usually located in the nucleus and cytoplasm of cells. The transcripts of lncRNAs are >200 nucleotides in length and do not encode proteins. Compared with small RNAs, lncRNAs have longer sequences, more complex spatial structures, and more diverse and complex mechanisms involved in the regulation of gene expression. LncRNAs are widely involved in the biological processes of cells, and in the occurrence and development of many human diseases. Many studies have shown that lncRNAs can induce the occurrence of diseases, and some lncRNAs undergo specific changes in tumor cells. Research into the roles of lncRNAs has covered the diagnosis of, for example, cardiovascular, cerebrovascular, and central nervous system diseases. The bioinformatics of lncRNAs has gradually become a research hotspot and has led to the discovery of a large number of lncRNAs and associated biological functions, and lncRNA databases and recognition models have been developed. In this review, the research progress of lncRNAs is discussed, and lncRNA-related databases and the mechanisms and modes of action of lncRNAs are described. In addition, disease-related lncRNA methods and the relationships between lncRNAs and human lung adenocarcinoma, rectal cancer, colon cancer, heart disease, and diabetes are discussed. Finally, the significance and existing problems of lncRNA research are considered.

CASC15：A tumor-associated long non-coding RNA

2020 ◽  
Vol 26 ◽  
Author(s):  
Bei Wang ◽  
Wen Xu ◽  
Yuxuan Cai ◽  
Chong Guo ◽  
Gang Zhou ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Therapeutic Target ◽  
Cancer Colorectal ◽  
Tumor Development ◽  
Pathophysiological Mechanism ◽  
Biological Processes ◽  
Non Coding Rna ◽  
Cancer Côlon ◽  
The Relationship ◽  
Long Non Coding Rna

Background: CASC15, one of long non-coding RNA, is involved in the regulation of many tumor biological processes, and is expected to become a new biological therapeutic target. This paper aims to elucidate the pathophysiological function of CASC15 in various tumors. Methods: The relationship between CASC15 and tumors was analyzed by searching references, and summarizes the specific pathophysiological mechanism of CASC15. Results: LncRNA CASC15 is closely related to tumor development, and has been shown to be abnormally high expressed in all kinds of tumors, including breast cancer, cervical cancer, lung cancer, hepatocellular carcinoma, gastric cancer, bladder cancer, colon cancer, colorectal cancer, cardiac hypertrophy, intrahepatic cholangiocarcinoma, leukemia, melanoma, tongue squamous cell carcinoma, nasopharyngeal carcinoma. However, CASC15 has been found to be downexpressed abnormally in ovarian cancer, glioma and neuroblastoma. Besides, it is identified that CASC15 can affect the proliferation, invasion and apoptosis of tumors. Conclusion: LncRNA CASC15 has the potential to become a new therapeutic target or marker for a variety of tumors.

scholarly journals Long Non-Coding RNAs in Multiple Myeloma

2019 ◽  
Vol 5 (1) ◽  
pp. 13 ◽  
Author(s):  
Romana Butova ◽  
Petra Vychytilova-Faltejskova ◽  
Adela Souckova ◽  
Sabina Sevcikova ◽  
Roman Hajek
Keyword(s):  
Multiple Myeloma ◽  
Plasma Cells ◽  
Current Knowledge ◽  
Biological Processes ◽  
Cell Distribution ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
New Treatment ◽  
Long Non Coding Rna

Multiple myeloma (MM) is the second most common hematooncological disease of malignant plasma cells in the bone marrow. While new treatment brought unprecedented increase of survival of patients, MM pathogenesis is yet to be clarified. Increasing evidence of expression of long non-coding RNA molecules (lncRNA) linked to development and progression of many tumors suggested their important role in tumorigenesis. To date, over 15,000 lncRNA molecules characterized by diversity of function and specificity of cell distribution were identified in the human genome. Due to their involvement in proliferation, apoptosis, metabolism, and differentiation, they have a key role in the biological processes and pathogenesis of many diseases, including MM. This review summarizes current knowledge of non-coding RNAs (ncRNA), especially lncRNAs, and their role in MM pathogenesis. Undeniable involvement of lncRNAs in MM development suggests their potential as biomarkers.

scholarly journals Regulatory Non-coding RNAs for Death Associated Protein Kinase Family

2021 ◽  
Vol 8 ◽  
Author(s):  
Qingshui Wang ◽  
Youyu Lin ◽  
Wenting Zhong ◽  
Yu Jiang ◽  
Yao Lin
Keyword(s):  
Gene Expression ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Tumor Development ◽  
Invasion And Metastasis ◽  
Calcium Dependent ◽  
Non Coding Rna ◽  
Death Associated Protein Kinase ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

The death associated protein kinases (DAPKs) are a family of calcium dependent serine/threonine kinases initially identified in the regulation of apoptosis. Previous studies showed that DAPK family members, including DAPK1, DAPK2 and DAPK3 play a crucial regulatory role in malignant tumor development, in terms of cell apoptosis, proliferation, invasion and metastasis. Accumulating evidence has demonstrated that non-coding RNAs, including microRNA (miRNA), long non-coding RNA (lncRNA) and circRNA, are involved in the regulation of gene expression and tumorigenesis. Recent studies indicated that non-coding RNAs participate in the regulation of DAPKs. In this review, we summarized the current knowledge of non-coding RNAs, as well as the potential miRNAs, lncRNAs and circRNAs, that are involved in the regulation of DAPKs.

Research progress in the estimation of postmortem interval (PMI) using non-coding RNA (ncRNA) markers

2021 ◽  
pp. 002580242110644
Author(s):  
Ye-Hui Lv ◽  
Zhuo-Qun Wang ◽  
Qiang Lei ◽  
Jiu-Hong Zhao ◽  
Zhi-Fang Yang
Keyword(s):  
Forensic Pathology ◽  
Postmortem Interval ◽  
Research Progress ◽  
Development Trends ◽  
Rna Molecules ◽  
Existing Problems ◽  
Challenging Issue ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Pmi Estimation

Postmortem interval (PMI) estimation has always been a crucial focus and challenging issue in forensic pathology. In recent years, specific RNA molecules and their variation have been used worldwide to estimate PMI. In this review, we summarize the methods used to detect non-coding RNAs (ncRNAs) for PMI estimation based on the literature, show the existing problems and development trends, and provide technical references for relevant studies and estimation practices.

scholarly journals Identification and Functional Prediction of Drought-Responsive Long Non-Coding RNA in Tomato

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 629 ◽  
Author(s):  
Seung Hee Eom ◽  
Hee Ju Lee ◽  
Jin Hyoung Lee ◽  
Seung Hwan Wi ◽  
Sung Kyeom Kim ◽  
...  
Keyword(s):  
Higher Plants ◽  
Biological Processes ◽  
Mrna Targets ◽  
Non Coding Rna ◽  
Starting Point ◽  
Antisense Lncrnas ◽  
Non Coding Rnas ◽  
Mirnas Expression ◽  
Long Non Coding Rna

In higher plants, several lines of evidence suggest that long non-coding RNAs (lncRNAs) may play important roles in the regulation of various biological processes by regulating gene expression. In this study, we identified a total of 521 lncRNAs, classified as intergenic, intronic, sense, and natural antisense lncRNAs, from RNA-seq data of drought-exposed tomato leaves. A further 244 drought-responsive tomato lncRNAs were predicted to be putative targets of 92 tomato miRNAs. Expression pattern and preliminary functional analysis of potential mRNA targets suggested that drought-responsive tomato lncRNAs play important roles in a variety of biological processes via lncRNA–mRNA co-expression. Taken together, these data present a comprehensive view of drought-responsive tomato lncRNAs that serve as a starting point for understanding the role of long intergenic non-coding RNAs in the regulatory mechanisms underlying drought responses in crops.

scholarly journals Non-Coding RNAs in Glioma

Cancers ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 17 ◽  
Author(s):  
Ryte Rynkeviciene ◽  
Julija Simiene ◽  
Egle Strainiene ◽  
Vaidotas Stankevicius ◽  
Jurgita Usinskiene ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
High Grade Glioma ◽  
Biological Processes ◽  
Glioma Tissue ◽  
Tissue Samples ◽  
Non Coding Rna ◽  
The Central Nervous System ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Glioma is the most aggressive brain tumor of the central nervous system. The ability of glioma cells to migrate, rapidly diffuse and invade normal adjacent tissue, their sustained proliferation, and heterogeneity contribute to an overall survival of approximately 15 months for most patients with high grade glioma. Numerous studies indicate that non-coding RNA species have critical functions across biological processes that regulate glioma initiation and progression. Recently, new data emerged, which shows that the cross-regulation between long non-coding RNAs and small non-coding RNAs contribute to phenotypic diversity of glioblastoma subclasses. In this paper, we review data of long non-coding RNA expression, which was evaluated in human glioma tissue samples during a five-year period. Thus, this review summarizes the following: (I) the role of non-coding RNAs in glioblastoma pathogenesis, (II) the potential application of non-coding RNA species in glioma-grading, (III) crosstalk between lncRNAs and miRNAs (IV) future perspectives of non-coding RNAs as biomarkers for glioma.

scholarly journals Long Non-coding RNAs in Pathogenesis of Neurodegenerative Diseases

2021 ◽  
Vol 9 ◽  
Author(s):  
Shiyue Zhou ◽  
Xiao Yu ◽  
Min Wang ◽  
Yujie Meng ◽  
Dandan Song ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Chromatin Remodeling ◽  
Mrna Stability ◽  
Neurological Disorders ◽  
Regulation Of Gene Expression ◽  
Tau Phosphorylation ◽  
Research Progress ◽  
Biological Processes ◽  
Non Coding Rnas ◽  
Lateral Sclerosis

Emerging evidence addresses the link between the aberrant epigenetic regulation of gene expression and numerous diseases including neurological disorders, such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and Huntington’s disease (HD). LncRNAs, a class of ncRNAs, have length of 200 nt or more, some of which crucially regulate a variety of biological processes such as epigenetic-mediated chromatin remodeling, mRNA stability, X-chromosome inactivation and imprinting. Aberrant regulation of the lncRNAs contributes to pathogenesis of many diseases, such as the neurological disorders at the transcriptional and post-transcriptional levels. In this review, we highlight the latest research progress on the contributions of some lncRNAs to the pathogenesis of neurodegenerative diseases via varied mechanisms, such as autophagy regulation, Aβ deposition, neuroinflammation, Tau phosphorylation and α-synuclein aggregation. Meanwhile, we also address the potential challenges on the lncRNAs-mediated epigenetic study to further understand the molecular mechanism of the neurodegenerative diseases.

scholarly journals Long Non-Coding RNA H19 Promotes Porcine Satellite Cell Differentiation by Interacting with TDP43

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 259
Author(s):  
Jingxuan Li ◽  
Wenjuan Zhao ◽  
Qianqian Li ◽  
Ziying Huang ◽  
Gaoli Shi ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Biological Processes ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Functional Analyses ◽  
Long Non Coding Rna

Long non-coding RNAs (lncRNAs) have been implicated in fundamental and diverse biological processes, including myogenesis. However, the molecular mechanisms involved in this process remain largely unexplored. This study found that H19 affected the differentiation of porcine satellite cells (PSCs) by directly binding to the DNA/RNA-binding protein TDP43. Functional analyses showed that TDP43 knockdown decreased PSC differentiation, whereas TDP43 overexpression exerted opposite effects in vitro. Furthermore, rescue experiments demonstrated that TDP43 can rescue the decrease in PSC differentiation caused by H19 knockdown. Mechanistically, H19 may act as a scaffold to recruit TDP43 to the promoters of MYOD and thereby activate the transcription of MYOD, leading to PSC differentiation. In summary, we elucidate the molecular mechanism by which H19 and TDP43 regulate myogenesis.

An updated review on the therapeutic, diagnostic, and prognostic value of long non-coding RNAs in gastric cancer

2021 ◽  
Vol 28 ◽  
Author(s):  
Alemeh Mohammadzadeh ◽  
Narges Dastmalchi ◽  
Bashdar Mahmud Hussen ◽  
Mahdi Abdoli Shadbad ◽  
Reza Safaralizadeh
Keyword(s):  
Gastric Cancer ◽  
Prognostic Value ◽  
Prognostic Biomarker ◽  
Clinicopathological Features ◽  
Biological Processes ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Future Direction ◽  
Long Non Coding Rna ◽  
Diagnostic And Prognostic Value

: As a novel group of non-coding RNAs, long non-coding RNA (lncRNAs) can substantially regulate various biological processes. Downregulated tumor-suppressive lncRNAs and upregulated oncogenic lncRNAs (onco-lncRNAs) have been implicated in gastric cancer (GC) development. These dysregulations have been associated with decreased chemosensitivity, inhibited apoptosis, and increased tumor migration in GC. Besides, growing evidence indicates that lncRNAs can be a valuable diagnostic and prognostic biomarker, and their expression levels are substantially associated with the clinicopathological features of affected patients. The current study aims to review the recent findings of the tumor-suppressive lncRNAs and onco-lncRNAs in GC development and highlight their therapeutic, diagnostic, and prognostic values in treating GC cells. Besides, it intends to highlight the future direction of lncRNAs in treating GC.

scholarly journals Long Non-coding RNA FEZF1-AS1 Promotes Growth and Reduces Apoptosis Through Regulation of miR-363-3p/PAX6 Axis in Retinoblastoma

2021 ◽  
Author(s):  
Xiuming Liu ◽  
Xiaofeng Li ◽  
Jianchang Li
Keyword(s):  
Cell Viability ◽  
Antisense Rna ◽  
Tumor Formation ◽  
Retinoblastoma Cell ◽  
Non Coding Rna ◽  
High Incidence ◽  
Non Coding Rnas ◽  
Long Non Coding Rna ◽  
Common Malignancy

AbstractRetinoblastoma is the most common malignancy in children's eyes with high incidence. Long non-coding RNAs (lncRNAs) play important roles in the progression of retinoblastoma. LncRNA FEZF1 antisense RNA 1 (FEZF1-AS1) has been found to stimulate retinoblastoma. However, the mechanism of FEZF1-AS1 underlying progression of retinoblastoma is still unclear. In current study, FEZF1-AS1 was up-regulated in retinoblastoma tissues and cells. FEZF1-AS1 overexpression enhanced retinoblastoma cell viability, promoted cell cycle, and inhibited apoptosis. Conversely, FEZF1-AS1 knockdown reduced cell viability, cycle, and elevated apoptosis. The interaction between FEZF1-AS1 and microRNA-363-3p (miR-363-3p) was confirmed. FEZF1-AS1 down-regulated miR-363-3p and up-regulated PAX6. PAX6 was a target gene of miR-363-3p. EZF1-AS1 promoted retinoblastoma cell viability and suppressed apoptosis via PAX6. Further, we demonstrated that FEZF1-AS1 contribute to tumor formation in vivo. In conclusion, FEZF1-AS1 elevated growth and inhibited apoptosis by regulating miR-363-3p/PAX6 in retinoblastoma, which provide a new target for retinoblastoma treatment.

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