scholarly journals Long-non Coding RNAs Related to Fat Deposition in Pigs Included lncRNA Corresponding to Human MALAT1

2021 ◽  
Author(s):  
Katarzyna Piórkowska ◽  
Kacper Żukowski ◽  
Katarzyna Ropka-Molik ◽  
Mirosław Tyra
Keyword(s):  
Regulatory Elements ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Sequencing Method ◽  
Non Coding Rnas ◽  
Potential Interactions ◽  
Long Non Coding Rna ◽  
Generation Sequencing

Obesity is a problem in the last decades since the development of different technologies forced the submission of a faster pace of life, resulting in nutrition style changes. In turn, domestic pigs are an excellent animal model in recognition of adiposity-related processes, corresponding to the size of individual organs, the distribution of body fat in the organism, and similar metabolism. The present study applied the next-generation sequencing method to identify adipose tissue (AT) transcriptomic signals related to increased fat content by identifying differentially expressed genes (DEGs), included long-non coding RNA molecules. The Freiburg RNA tool was applied to recognise predicting hybridisation energy of RNA-RNA interactions. The results indicated several long non-coding RNAs (lncRNAs) whose expression was significantly positively or negatively associated with fat deposition. lncRNAs play an essential role in regulating gene expression by sponging miRNA, binding transcripts, facilitating translation, or coding other smaller RNA regulatory elements. In the pig fat tissue of obese group, increased expression of lncRNAs corresponding to human MALAT1 was observed that previously recognised in the obesity-related context. Moreover, hybridisation energy analyses pinpointed numerous potential interactions between identified differentially expressed lncRNAs, and obesity-related genes and miRNAs expressed in AT.

scholarly journals Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 459 ◽  
Author(s):  
Priyanka Borah ◽  
Antara Das ◽  
Matthew Milner ◽  
Arif Ali ◽  
Alison Bentley ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Next Generation Sequencing ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Endogenous Target ◽  
Long Non Coding Rna ◽  
Nutrient Homeostasis ◽  
Generation Sequencing

Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.

scholarly journals The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress

2020 ◽  
Vol 21 (8) ◽  
pp. 2659
Author(s):  
Hong Zhang ◽  
Huan Guo ◽  
Weiguo Hu ◽  
Wanquan Ji
Keyword(s):  
Stress Responses ◽  
Higher Plants ◽  
Regulatory Elements ◽  
Cellular Functions ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Resistance To Infection ◽  
Regulatory Functions ◽  
Long Non Coding Rna

Growing interest and recent evidence have identified long non-coding RNA (lncRNA) as the potential regulatory elements for eukaryotes. LncRNAs can activate various transcriptional and post-transcriptional events that impact cellular functions though multiple regulatory functions. Recently, a large number of lncRNAs have also been identified in higher plants, and an understanding of their functional role in plant resistance to infection is just emerging. Here, we focus on their identification in crop plant, and discuss their potential regulatory functions and lncRNA-miRNA-mRNA network in plant pathogen stress responses, referring to possible examples in a model plant. The knowledge gained from a deeper understanding of this colossal special group of plant lncRNAs will help in the biotechnological improvement of crops.

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 LncSEA: a platform for long non-coding RNA related sets and enrichment analysis

2020 ◽  
Vol 49 (D1) ◽  
pp. D969-D980 ◽  
Author(s):  
Jiaxin Chen ◽  
Jian Zhang ◽  
Yu Gao ◽  
Yanyu Li ◽  
Chenchen Feng ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Regulatory Elements ◽  
Biological Functions ◽  
Comprehensive Collection ◽  
Non Coding Rna ◽  
Regulatory Data ◽  
Non Coding Rnas ◽  
Dna Regulatory Elements ◽  
Long Non Coding Rna ◽  
Upstream Regulators

Abstract Long non-coding RNAs (lncRNAs) have been proven to play important roles in transcriptional processes and various biological functions. Establishing a comprehensive collection of human lncRNA sets is urgent work at present. Using reference lncRNA sets, enrichment analyses will be useful for analyzing lncRNA lists of interest submitted by users. Therefore, we developed a human lncRNA sets database, called LncSEA, which aimed to document a large number of available resources for human lncRNA sets and provide annotation and enrichment analyses for lncRNAs. LncSEA supports >40 000 lncRNA reference sets across 18 categories and 66 sub-categories, and covers over 50 000 lncRNAs. We not only collected lncRNA sets based on downstream regulatory data sources, but also identified a large number of lncRNA sets regulated by upstream transcription factors (TFs) and DNA regulatory elements by integrating TF ChIP-seq, DNase-seq, ATAC-seq and H3K27ac ChIP-seq data. Importantly, LncSEA provides annotation and enrichment analyses of lncRNA sets associated with upstream regulators and downstream targets. In summary, LncSEA is a powerful platform that provides a variety of types of lncRNA sets for users, and supports lncRNA annotations and enrichment analyses. The LncSEA database is freely accessible at http://bio.liclab.net/LncSEA/index.php.

scholarly journals Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1374
Author(s):  
Yibing Liu ◽  
Ying Yu ◽  
Hong Ao ◽  
Fengxia Zhang ◽  
Xitong Zhao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Gene Prediction ◽  
Fat Deposition ◽  
Acid Oxidation ◽  
Rna Seq ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Rate Limiting ◽  
Long Non Coding Rna

Adipose is an important body tissue in pigs, and fatty traits are critical in pig production. The function of long non-coding RNA (lncRNA) in fat deposition and metabolism has been found in previous studies. In this study, we collected the adipose tissue of six Landrace pigs with contrast backfat thickness (nhigh = 3, nlow = 3), after which we performed strand-specific RNA sequencing (RNA-seq) based on pooling and biological replicate methods. Biological replicate and pooling RNA-seq revealed 1870 and 1618 lncRNAs, respectively. Using edgeR, we determined that 1512 genes and 220 lncRNAs, 2240 genes and 127 lncRNAs were differentially expressed in biological replicate and pooling RNA-seq, respectively. After target gene prediction, we found that ACSL3 was cis-targeted by lncRNA TCONS-00052400 and could activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 cis-regulated gene ACACB regulated the rate-limiting enzyme in fatty acid oxidation. Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect backfat deposition in swine through regulation of their target genes. Our study explored the regulation of lncRNA and their target genes in porcine backfat deposition and provided new insights for further investigation of the biological functions of lncRNA.

scholarly journals Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yifang Liao ◽  
Ping Li ◽  
Yanxia Wang ◽  
Hong Chen ◽  
Shangwei Ning ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Repositioning ◽  
New Drugs ◽  
Differentially Expressed ◽  
Interaction Data ◽  
Competing Endogenous Rna ◽  
Non Coding Rna ◽  
Competing Endogenous Rna Network ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Abstract Background Asthma is a heterogeneous disease characterized by chronic airway inflammation. Long non-coding RNA can act as competing endogenous RNA to mRNA, and play significant role in many diseases. However, there is little known about the profiles of long non-coding RNA and the long non-coding RNA related competing endogenous RNA network in asthma. In current study, we aimed to explore the long non-coding RNA-microRNA-mRNA competing endogenous RNA network in asthma and their potential implications for therapy and prognosis. Methods Asthma-related gene expression profiles were downloaded from the Gene Expression Omnibus database, re-annotated with these genes and identified for asthma-associated differentially expressed mRNAs and long non-coding RNAs. The long non-coding RNA-miRNA interaction data and mRNA-miRNA interaction data were downloaded using the starBase database to construct a long non-coding RNA-miRNA-mRNA global competing endogenous RNA network and extract asthma-related differentially expressed competing endogenous RNA network. Finally, functional enrichment analysis and drug repositioning of asthma-associated differentially expressed competing endogenous RNA networks were performed to further identify key long non-coding RNAs and potential therapeutics associated with asthma. Results This study constructed an asthma-associated competing endogenous RNA network, determined 5 key long non-coding RNAs (MALAT1, MIR17HG, CASC2, MAGI2-AS3, DAPK1-IT1) and identified 8 potential new drugs (Tamoxifen, Ruxolitinib, Tretinoin, Quercetin, Dasatinib, Levocarnitine, Niflumic Acid, Glyburide). Conclusions The results suggested that long non-coding RNA played an important role in asthma, and these novel long non-coding RNAs could be potential therapeutic target and prognostic biomarkers. At the same time, potential new drugs for asthma treatment have been discovered through drug repositioning techniques, providing a new direction for the treatment of asthma.

scholarly journals Non-Coding RNA Databases in Cardiovascular Research

2020 ◽  
Vol 6 (3) ◽  
pp. 35
Author(s):  
Deepak Balamurali ◽  
Monika Stoll
Keyword(s):  
Vascular System ◽  
Cardiovascular Research ◽  
Data Repositories ◽  
Protein Coding ◽  
Rna Molecules ◽  
High Throughput Data ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Generation Sequencing

Cardiovascular diseases (CVDs) are of multifactorial origin and can be attributed to several genetic and environmental components. CVDs are the leading cause of mortality worldwide and they primarily damage the heart and the vascular system. Non-coding RNA (ncRNA) refers to functional RNA molecules, which have been transcribed into DNA but do not further get translated into proteins. Recent transcriptomic studies have identified the presence of thousands of ncRNA molecules across species. In humans, less than 2% of the total genome represents the protein-coding genes. While the role of many ncRNAs is yet to be ascertained, some long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been associated with disease progression, serving as useful diagnostic and prognostic biomarkers. A plethora of data repositories specialized in ncRNAs have been developed over the years using publicly available high-throughput data from next-generation sequencing and other approaches, that cover various facets of ncRNA research like basic and functional annotation, expressional profile, structural and molecular changes, and interaction with other biomolecules. Here, we provide a compendium of the current ncRNA databases relevant to cardiovascular research.

scholarly journals Coding and non-coding RNAs transcribed at the RORA locus (ROR𝛂) are differentially expressed in the whole blood of sepsis patients.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Expression Analysis ◽  
Whole Blood ◽  
Gene Expression Analysis ◽  
Differentially Expressed ◽  
Blood Gene Expression ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Sepsis is a leading cause of mortality (1). We mined published datasets from the whole blood of patients with sepsis to identify differentially expressed genes in the septic state (2, 3). We found changes in RORA expression as among the most significant quantitative differences in sepsis whole blood gene expression. Analysis of a separate dataset (4) demonstrated significant repression of a long non-coding RNA produced at the RORA locus in the blood of patients with sepsis.

scholarly journals Gestational Age Dependence of the Maternal Circulating Long Non-Coding RNA Transcriptome During Normal Pregnancy Highlights Antisense and Pseudogene Transcripts

2021 ◽  
Vol 12 ◽  
Author(s):  
Erica L. Kleinbrink ◽  
Nardhy Gomez-Lopez ◽  
Donghong Ju ◽  
Bogdan Done ◽  
Anton-Scott Goustin ◽  
...  
Keyword(s):  
Human Genome ◽  
Normal Pregnancy ◽  
Differentially Expressed ◽  
Cajal Body ◽  
Protein Coding ◽  
Longitudinal Changes ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Long Non Coding Rna ◽  
In Pregnancy

In the post-genomic era, our understanding of the molecular regulators of physiologic and pathologic processes in pregnancy is expanding at the whole-genome level. Longitudinal changes in the known protein-coding transcriptome during normal pregnancy, which we recently reported (Gomez-Lopez et al., 2019), have improved our definition of the major operant networks, yet pregnancy-related functions of the non-coding RNA transcriptome remain poorly understood. A key finding of the ENCODE (Encyclopedia of DNA Elements) Consortium, the successor of the Human Genome Project, was that the human genome contains approximately 60,000 genes, the majority of which do not encode proteins. The total transcriptional output of non-protein-coding RNA genes, collectively referred to as the non-coding transcriptome, is comprised mainly of long non-coding RNA (lncRNA) transcripts (Derrien et al., 2012). Although the ncRNA transcriptome eclipses its protein-coding counterpart in abundance, it has until recently lacked a comprehensive, unbiased, genome-scale characterization over the timecourse of normal human pregnancy. Here, we annotated, characterized, and selectively validated the longitudinal changes in the non-coding transcriptome of maternal whole blood during normal pregnancy to term. We identified nine long non-coding RNAs (lncRNAs), including long intergenic non-coding RNAs (lincRNAs) as well as lncRNAs antisense to or otherwise in the immediate vicinity of protein-coding genes, that were differentially expressed with advancing gestation in normal pregnancy: AL355711, BC039551 (expressed mainly in the placenta), JHDM1D-AS1, A2M-AS1, MANEA-AS1, NR_034004, LINC00649, LINC00861, and LINC01094. By cross-referencing our dataset against major public pseudogene catalogs, we also identified six transcribed pseudogenes that were differentially expressed over time during normal pregnancy in maternal blood: UBBP4, FOXO3B, two Makorin (MKRN) pseudogenes (MKRN9P and LOC441455), PSME2P2, and YBX3P1. We also identified three non-coding RNAs belonging to other classes that were modulated during gestation: the microRNA MIR4439, the small nucleolar RNA (snoRNA) SNORD41, and the small Cajal-body specific ncRNA SCARNA2. The expression profiles of most hits were broadly suggestive of functions in pregnancy. These time-dependent changes of the non-coding transcriptome during normal pregnancy, which may confer specific regulatory impacts on their protein-coding gene targets, will facilitate a deeper molecular understanding of pregnancy and lncRNA-mediated molecular pathways at the maternal-fetal interface and of how these pathways impact maternal and fetal health.

scholarly journals Long Non-Coding RNA and Breast Cancer

2019 ◽  
Vol 18 ◽  
pp. 153303381984388 ◽  
Author(s):  
Tianzhu Zhang ◽  
Hui Hu ◽  
Ge Yan ◽  
Tangwei Wu ◽  
Shuiyi Liu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Molecular Mechanisms ◽  
Biological Function ◽  
Tumor Development ◽  
Health Concern ◽  
Sequencing Technologies ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Long Non Coding Rna ◽  
Generation Sequencing

Breast cancer, one of the most common diseases among women, is regarded as a heterogeneous and complicated disease that remains a major public health concern. Recently, owing to the development of next-generation sequencing technologies, long non-coding RNAs have received extensive attention. Numerous studies reveal that long non-coding RNAs are playing important roles in tumor development. Although the biological function and molecular mechanisms of long non-coding RNAs remain enigmatic, recent researchers have demonstrated that an array of long non-coding RNAs express abnormally in cancers, including breast cancer. Herein, we summarized the latest literature about long non-coding RNAs in breast cancer, with a particular focus on the multiple molecular roles of regulatory long non-coding RNAs that regulate cell proliferation, invasion, metastasis, and apoptosis.

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