Long Non-coding RNA Structure and Function: Is There a Link?

Zampetaki, Anna; Albrecht, Andreas; Steinhöfel, Kathleen

doi:10.3389/fphys.2018.01201

Cited by 191 publications

(132 citation statements)

References 92 publications

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“…In addition, a statistical significance was found for the differentially expressed lncRNAs, mRNAs, and target genes. Most lncRNAs act as cis-regulatory factors owing to the significant association between their expression and their adjacent protein-coding genes [18]. erefore, to derive the role of differentially expressed lncRNAs in the pathogenesis of T2DM and LADA, we screened related genes according to the regulatory relationship between lncRNAs and mRNAs.…”

Section: Analysis Of the Experimental Resultsmentioning

confidence: 99%

The Differential Expression of Long Noncoding RNAs in Type 2 Diabetes Mellitus and Latent Autoimmune Diabetes in Adults

Zhang

Yan

et al. 2020

International Journal of Endocrinology

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Background. Long noncoding RNAs (lncRNAs) were previously found to be closely related to the pathogenesis of diabetes. Objectives. To reveal the differentially expressed lncRNAs and messenger RNAs (mRNAs) involved in type 2 diabetes mellitus (T2DM) and latent autoimmune diabetes in adults (LADA) and predict the lncRNA target genes to derive their expression profiles for the diagnosis of T2DM and LADA and their differential diagnosis. Methods. Twelve venous blood samples were collected from T2DM patients, LADA patients, and nondiseased subjects to obtain total RNAs. After removing rRNA from total RNAs to establish the desired library for sequencing, quality control and quantification analyses were carried out. The fragments per kilobase of exon model per million reads mapped (FPKM) of lncRNAs were calculated to construct the gene expression profiles of lncRNAs and mRNAs. Fold changes (fold change: 2.0) and p values (p value: 0.05, FPKM ≥ 0.1) were calculated, and then differentially expressed lncRNAs and mRNAs were screened. To obtain the significantly coexpressed lncRNA-mRNA pairs, the lncRNA target genes were deduced according to the association between adjacent sites. Results. Compared to nondiseased controls, 68,763 versus 28,523 lncRNAs and 133 versus 1035 mRNAs were significantly upregulated and significantly downregulated, respectively, in T2DM patients. For LADA patients, 68,748 versus 28,538 lncRNAs and 219 versus 805 mRNAs were significantly upregulated and significantly downregulated, respectively, relative to nondiseased controls. Compared to T2DM patients, 74,207 versus 23,079 lncRNAs and 349 versus 137 mRNAs were significantly upregulated and significantly downregulated, respectively, in LADA patients. Based on the correlation analysis, seven lncRNA-mRNA pairs (BTG2, A2M, HECTD4, MBTPS1, DBH, FLVCR1, and NCBP2) were significantly coexpressed, and two lncRNAs (ENST00000608916 and ENST00000436373) were newly discovered. Conclusion. Significant differences in lncRNA expression were discovered among the three groups. Furthermore, after predicting lncRNA expression profiles, GO/KEGG pathway analysis could deduce the target gene function.

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Section: Analysis Of the Experimental Resultsmentioning

confidence: 99%

The Differential Expression of Long Noncoding RNAs in Type 2 Diabetes Mellitus and Latent Autoimmune Diabetes in Adults

Zhang

Yan

et al. 2020

International Journal of Endocrinology

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“…Noncoding RNAs are often subdivided into long and small RNAs around a cut‐off of 200 nucleotides. The long noncoding RNAs over 200 nucleotides are mostly generated from intergenic regions (Brosnan & Voinnet, ; Dhanoa, Sethi, Verma, Arora, & Mukhopadhyay, ; Zampetaki, Albrecht, & Steinhofel, ). However, the small noncoding RNAs are a disparate and heterogeneous group of distinct RNA families.…”

Section: Introductionmentioning

confidence: 99%

“…Finally, we provide a portrait of the challenges facing their detection and annotation in databases. (Brosnan & Voinnet, 2009;Dhanoa, Sethi, Verma, Arora, & Mukhopadhyay, 2018;Zampetaki, Albrecht, & Steinhofel, 2018). However, the small noncoding RNAs are a disparate and heterogeneous group of distinct RNA families.…”

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confidence: 99%

The cellular landscape of mid‐size noncoding RNA

et al. 2019

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Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid‐size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA‐binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution

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“…Long non-coding RNAs (lncRNAs) are a subclass of nontranslated RNA-sequences defined by an arbitrary length of more than 200 base pairs. These structurally complex RNA molecules interact directly with both DNA, RNA, and proteins affecting various cellular processes including genomic imprinting, gene transcription, mRNA splicing and protein activity (19)(20)(21). We are only beginning to understand how these molecules regulate cellular function, and how dysregulation can lead to malignant transformation.…”

Section: Lncrnas In Cancermentioning

confidence: 99%

Long Non-coding RNAs Involved in Resistance to Chemotherapy in Ovarian Cancer

et al. 2020

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Ovarian cancer (OC) accounts for more than 150,000 deaths worldwide every year. Patients are often diagnosed at an advanced stage with metastatic dissemination. Although platinum-and taxane-based chemotherapies are effective treatment options, they are rarely curative and eventually, the disease will progress due to acquired resistance. Emerging evidence suggests a crucial role of long non-coding RNAs (lncRNAs) in the response to therapy in OC. Transcriptome profiling studies using high throughput approaches have identified differential expression patterns of lncRNAs associated with disease recurrence. Furthermore, several aberrantly expressed lncRNAs in resistant OC cells have been related to increased cell division, improved DNA repair, up-regulation of drug transporters or reduced susceptibility to apoptotic stimuli, supporting their involvement in acquired resistance. In this review, we will discuss the key aspects of lncRNAs associated with the development of resistance to platinum-and taxane-based chemotherapy in OC. The molecular landscape of OC will be introduced, to provide a background for understanding the role of lncRNAs in the acquisition of malignant properties. We will focus on the interplay between lncRNAs and molecular pathways affecting drug response to evaluate their impact on treatment resistance. Additionally, we will discuss the prospects of using lncRNAs as biomarkers or targets for precision medicine in OC. Although there is still plenty to learn about lncRNAs and technical challenges to be solved, the evidence of their involvement in OC and the development of acquired resistance are compelling and warrant further investigation for clinical applications.

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Long Non-coding RNA Structure and Function: Is There a Link?

Cited by 191 publications

References 92 publications

The Differential Expression of Long Noncoding RNAs in Type 2 Diabetes Mellitus and Latent Autoimmune Diabetes in Adults

The Differential Expression of Long Noncoding RNAs in Type 2 Diabetes Mellitus and Latent Autoimmune Diabetes in Adults

The cellular landscape of mid‐size noncoding RNA

Long Non-coding RNAs Involved in Resistance to Chemotherapy in Ovarian Cancer

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