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Journal articles on the topic 'Long noncoding RNA (lncRNA)'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

Kazimierczyk, Kasprowicz, Kasprzyk, and Wrzesinski. "Human Long Noncoding RNA Interactome: Detection, Characterization and Function." International Journal of Molecular Sciences 21, no. 3 (2020): 1027. http://dx.doi.org/10.3390/ijms21031027.

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The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter” belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information abou

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Tani, Hidenori. "Biomolecules Interacting with Long Noncoding RNAs." Biology 14, no. 4 (2025): 442. https://doi.org/10.3390/biology14040442.

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This review explores the complex interactions between long noncoding RNAs (lncRNAs) and other biomolecules, highlighting their pivotal roles in gene regulation and cellular function. LncRNAs, defined as RNA transcripts exceeding 200 nucleotides without encoding proteins, are involved in diverse biological processes, from embryogenesis to pathogenesis. They interact with DNA through mechanisms like triplex structure formation, influencing chromatin organization and gene expression. LncRNAs also modulate RNA-mediated processes, including mRNA stability, translational control, and splicing regula

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Rinn, John L., and Howard Y. Chang. "Long Noncoding RNAs: Molecular Modalities to Organismal Functions." Annual Review of Biochemistry 89, no. 1 (2020): 283–308. http://dx.doi.org/10.1146/annurev-biochem-062917-012708.

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We have known for decades that long noncoding RNAs (lncRNAs) can play essential functions across most forms of life. The maintenance of chromosome length requires an lncRNA (e.g., hTERC) and two lncRNAs in the ribosome that are required for protein synthesis. Thus, lncRNAs can represent powerful RNA machines. More recently, it has become clear that mammalian genomes encode thousands more lncRNAs. Thus, we raise the question: Which, if any, of these lncRNAs could also represent RNA-based machines? Here we synthesize studies that are beginning to address this question by investigating fundamenta

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Morelli, Eugenio, Anil Aktas-Samur, Domenico Maisano, et al. "Isoform-Level Long Noncoding RNA Dependencies in Multiple Myeloma." Blood 144, Supplement 1 (2024): 4130. https://doi.org/10.1182/blood-2024-209546.

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Introduction Long noncoding RNAs (lncRNAs) are a diverse group of genomic elements that, despite not encoding proteins, play crucial roles in regulating cellular processes. In multiple myeloma (MM), lncRNAs have emerged as significant factors, functioning as clinical biomarkers, tumor drivers, and potential therapeutic targets. The study of lncRNAs is particularly challenging due to their complex genomic organization, frequent overlap with protein coding genes, and the generation of multiple isoforms through extensive splicing. Moreover, lncRNAs can act as DNA regulatory elements, influencing

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Jiang, Shuai, Si-Jin Cheng, Li-Chen Ren, et al. "An expanded landscape of human long noncoding RNA." Nucleic Acids Research 47, no. 15 (2019): 7842–56. http://dx.doi.org/10.1093/nar/gkz621.

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Abstract Long noncoding RNAs (lncRNAs) are emerging as key regulators of multiple essential biological processes involved in physiology and pathology. By analyzing the largest compendium of 14,166 samples from normal and tumor tissues, we significantly expand the landscape of human long noncoding RNA with a high-quality atlas: RefLnc (Reference catalog of LncRNA). Powered by comprehensive annotation across multiple sources, RefLnc helps to pinpoint 275 novel intergenic lncRNAs correlated with sex, age or race as well as 369 novel ones associated with patient survival, clinical stage, tumor met

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Li, Ao, Mengqu Ge, Yao Zhang, Chen Peng, and Minghui Wang. "Predicting Long Noncoding RNA and Protein Interactions Using Heterogeneous Network Model." BioMed Research International 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/671950.

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Recent study shows that long noncoding RNAs (lncRNAs) are participating in diverse biological processes and complex diseases. However, at present the functions of lncRNAs are still rarely known. In this study, we propose a network-based computational method, which is called lncRNA-protein interaction prediction based on Heterogeneous Network Model (LPIHN), to predict the potential lncRNA-protein interactions. First, we construct a heterogeneous network by integrating the lncRNA-lncRNA similarity network, lncRNA-protein interaction network, and protein-protein interaction (PPI) network. Then, a

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Yang, Weili, Yixiang Lyu, Rui Xiang, and Jichun Yang. "Long Noncoding RNAs in the Pathogenesis of Insulin Resistance." International Journal of Molecular Sciences 23, no. 24 (2022): 16054. http://dx.doi.org/10.3390/ijms232416054.

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Insulin resistance (IR), designated as the blunted response of insulin target tissues to physiological level of insulin, plays crucial roles in the development and progression of diabetes, nonalcoholic fatty liver disease (NAFLD) and other diseases. So far, the distinct mechanism(s) of IR still needs further exploration. Long non-coding RNA (lncRNA) is a class of non-protein coding RNA molecules with a length greater than 200 nucleotides. LncRNAs are widely involved in many biological processes including cell differentiation, proliferation, apoptosis and metabolism. More recently, there has be

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Li, Weilong, Jan Baumbach, Martin J. Larsen, et al. "Differential long noncoding RNA profiling of BMI in twins." Epigenomics 12, no. 17 (2020): 1531–41. http://dx.doi.org/10.2217/epi-2020-0033.

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Aim: Many efforts have been deployed to identify genetic variants associated with BMI. Alternatively, we explore epigenetic contribution to BMI variation by focusing on long noncoding RNAs (lncRNAs) which represents a key layer of epigenetic control. Materials & methods: We analyzed lncRNA expression in whole blood of 229 monozygotic twin pairs in association with BMI using generalized estimating equations. Results & conclusion: Six lncRNA probes were identified as significant (false discovery rate <0.05), with BMI showing causal effects on the expression of the significant lncRNAs.

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Luo, Jianjun, and Runsheng Chen. "Genetic variations associated with long noncoding RNAs." Essays in Biochemistry 64, no. 6 (2020): 867–73. http://dx.doi.org/10.1042/ebc20200033.

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Abstract Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including the long noncoding RNA (lncRNA) regions. The changes at locus might produce numerous effects in a variety of aspects. Multiple bioinformatics resources and tools were also developed for systematically dealing with genetic variations associated with lncRNAs. Moreover, correlation of the genetic variations in lncRNAs with immune disease, cancers, and other disease as well as development process were all included for discussion. In this essay, we

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Jin, Jingjing, Peng Lu, Yalong Xu, et al. "PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs." Nucleic Acids Research 49, no. D1 (2020): D1489—D1495. http://dx.doi.org/10.1093/nar/gkaa910.

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Abstract Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Lon

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Bo, Hao, Zhizhong Liu, Fang Zhu, et al. "Long noncoding RNAs expression profile and long noncoding RNA-mediated competing endogenous RNA network in nonobstructive azoospermia patients." Epigenomics 12, no. 8 (2020): 673–84. http://dx.doi.org/10.2217/epi-2020-0008.

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Aim: To analyze the expression profile and competing endogenous RNA (ceRNA) network of long noncoding RNAs (lncRNAs) in nonobstructive azoospermia (NOA). Materials & methods: The lncRNA expression profile in NOA was determined by microarray reanalysis. Differential expression analysis was performed by R software. The ceRNA network was constructed using correlation analysis and gene target miRNA prediction. Metascape was used for enrichment analysis. Again ceRNA network was validated by quantitative real-time PCR. Results: Many lncRNAs are differently expressed in NOA. LncRNAs might partici

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Arza-Apalategi, Saioa, Daan Gilissen, Anne van der Grinten, et al. "Genetic Classification of Acute Myeloid Leukemia By Differential Long Noncoding RNA Expression." Blood 144, Supplement 1 (2024): 2933. https://doi.org/10.1182/blood-2024-201431.

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Long noncoding RNAs (lncRNAs) are &gt;200 nucleotides in size, lack protein coding potential, and together represent ~2% of the human genome. LncRNAs control important biological processes like cell division, - differentiation and apoptosis. They do this by binding chromatin, RNA, and proteins to control gene expression, protein synthesis, mRNA splicing, and so on. Changes in lncRNA expression have been clearly implicated in malignant cell transformation including acute myeloid leukemia (AML). As changes in protein coding gene expression are key to AML development we determined whether sim

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Liu, Fen, Yang Yang, Tong Liu, et al. "Analysis of Differentially Expressed Long Noncoding RNA in Renal Ischemia-Reperfusion Injury." Kidney and Blood Pressure Research 45, no. 5 (2020): 686–701. http://dx.doi.org/10.1159/000508217.

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Background: Renal ischemia-reperfusion (IR) injury is one of the major causes of acute renal failure which seriously endangers the health and life of patients. Currently, there is still lack of comprehensive knowledge of the molecular mechanism of renal IR injury, and the regulatory role of long noncoding RNA (lncRNA) in renal IR damage remains poorly understood. Aim: The aim of this study was to analyze the expression spectrum of lncRNA in renal IR damage in mice and to explore specific lncRNA that may be involved in regulating the development of human renal IR injury. Methods: RNA-Seq was us

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Kazimierczyk, Marek, and Jan Wrzesinski. "Long Non-Coding RNA Epigenetics." International Journal of Molecular Sciences 22, no. 11 (2021): 6166. http://dx.doi.org/10.3390/ijms22116166.

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Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to underst

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Cagle, Patrice, Qi Qi, Suryakant Niture, and Deepak Kumar. "KCNQ1OT1: An Oncogenic Long Noncoding RNA." Biomolecules 11, no. 11 (2021): 1602. http://dx.doi.org/10.3390/biom11111602.

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Long noncoding RNAs (lncRNAs) are transcripts greater than 200 nucleotides that do not code for proteins but regulate gene expression. Recent studies indicate that lncRNAs are involved in the modulation of biological functions in human disease. KCNQ1 Opposite Strand/Antisense Transcript 1 (KCNQ1OT1) encodes a lncRNA from the opposite strand of KCNQ1 in the CDKN1C/KCNQ1OT1 cluster that is reported to play a vital role in the development and progression of cancer. KCNQ1OT1 regulates cancer cell proliferation, cell cycle, migration and invasion, metastasis, glucose metabolism, and immune evasion.

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Qian, Yanxia, Mingming Zhang, Ningtian Zhou, et al. "A long noncoding RNA CHAIR protects the heart from pathological stress." Clinical Science 134, no. 13 (2020): 1843–57. http://dx.doi.org/10.1042/cs20200149.

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Abstract Mammalian genomes have been found to be extensively transcribed. In addition to classic protein coding genes, a large numbers of long noncoding genes (lncRNAs) have been identified, while their functions, especially in heart diseases, remain to be established. We hypothesized that heart failure progression is controlled by tissue-specific lncRNAs. In the present study, we found that the cardiac-enriched lncRNA 4632428C04Rik, named as cardiomyocyte hypertrophic associated inhibitory RNA (CHAIR), is dynamically regulated during heart development, is expressed at low levels in embryonic

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Alvarez-Dominguez, Juan R., and Harvey F. Lodish. "Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis." Blood 130, no. 18 (2017): 1965–75. http://dx.doi.org/10.1182/blood-2017-06-788695.

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Abstract Long noncoding RNAs (lncRNAs) are increasingly recognized as vital components of gene programs controlling cell differentiation and function. Central to their functions is an ability to act as scaffolds or as decoys that recruit or sequester effector proteins from their DNA, RNA, or protein targets. lncRNA-modulated effectors include regulators of transcription, chromatin organization, RNA processing, and translation, such that lncRNAs can influence gene expression at multiple levels. Here we review the current understanding of how lncRNAs help coordinate gene expression to modulate c

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Sun, Zhenqiang, Jinbo Liu, Chen Chen, et al. "The Biological Effect and Clinical Application of Long Noncoding RNAs in Colorectal Cancer." Cellular Physiology and Biochemistry 46, no. 2 (2018): 431–41. http://dx.doi.org/10.1159/000488610.

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Colorectal cancer (CRC) is one of the most common malignancies in the world. Easier recurrence and metastasis is the main cause of mortality in CRC patients, and the markers applied for diagnosis and treatment of CRC is still urgently needed to early diagnose and evaluate therapeutic effect. Long noncoding RNA (lncRNA) is a class of noncoding RNA that the length is more than 200 nucleotides. With the development of sequencing technique about transcriptome, increasing lncRNAs are focused on their function and mechanism related to the nosogenesis and pathology of CRC. Recent studies report that

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Glover, A. R., J. T. Zhao, J. C. Ip, et al. "Long noncoding RNA profiles of adrenocortical cancer can be used to predict recurrence." Endocrine-Related Cancer 22, no. 1 (2015): 99–109. http://dx.doi.org/10.1530/erc-14-0457.

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Adrenocortical carcinoma (ACC) is an aggressive malignancy with high rates of recurrence following surgical resection. Long noncoding RNAs (lncRNAs) play an important role in cancer development. Pathogenesis of adrenal tumours have been characterised by mRNA, microRNA and methylation expression signatures, but it is unknown if this extends to lncRNAs. This study describes lncRNA expression signatures in ACC, adrenal cortical adenoma (ACA) and normal adrenal cortex (NAC) and presents lncRNAs associated with ACC recurrence to identify novel prognostic and therapeutic targets. RNA was extracted f

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Liu, Bin, Chun-Feng Pan, Zhi-Cheng He, et al. "Long Noncoding RNA-LET Suppresses Tumor Growth and EMT in Lung Adenocarcinoma." BioMed Research International 2016 (2016): 1–9. http://dx.doi.org/10.1155/2016/4693471.

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Recently, many studies showed that long noncoding RNAs (lncRNAs) are involved in tumor progression. It is reported that lncRNA-LET is downregulated and has antitumor effect on several types of cancer. This study focuses on the role of lncRNA-LET on lung adenocarcinoma (LAC) progression. RT-PCR results indicated that frequent downregulation of lncRNA-LET in LAC tissues was related to clinicopathologic factors. lncRNA-LET knockdown significantly promoted LAC cell proliferation, invasion, and migration while lncRNA-LET overexpression obviously inhibited LAC cell proliferation, invasion, and migra

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Choi, Jae-Young, KyeongHye Won, Seungwoo Son, Donghyun Shin, and Jae-Don Oh. "Comparison of characteristics of long noncoding RNA in Hanwoo according to sex." Asian-Australasian Journal of Animal Sciences 33, no. 5 (2020): 696–703. http://dx.doi.org/10.5713/ajas.18.0533.

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Objective: Cattle were some of the first animals domesticated by humans for the production of milk, meat, etc. Long noncoding RNA (lncRNA) is defined as longer than 200 bp in non-protein coding transcripts. lncRNA is known to function in regulating gene expression and is currently being studied in a variety of livestock including cattle. The purpose of this study is to analyze the characteristics of lncRNA according to sex in Hanwoo cattle.Methods: This study was conducted using the skeletal muscles of 9 Hanwoo cattle include bulls, steers and cows. RNA was extracted from skeletal muscle of Ha

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Yu, Xiaoqing, Jingsong Zhang, Rui Yang, and Chun Li. "Identification of Long Noncoding RNA Biomarkers for Hepatocellular Carcinoma Using Single-Sample Networks." BioMed Research International 2020 (November 14, 2020): 1–12. http://dx.doi.org/10.1155/2020/8579651.

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Objective. Many studies have found that long noncoding RNAs (lncRNAs) are differentially expressed in hepatocellular carcinoma (HCC) and closely associated with the occurrence and prognosis of HCC. Since patients with HCC are usually diagnosed in late stages, more effective biomarkers for early diagnosis and prognostic prediction are in urgent need. Methods. The RNA-seq data of liver hepatocellular carcinoma (LIHC) were downloaded from The Cancer Genome Atlas (TCGA). Differentially expressed lncRNAs and mRNAs were obtained using the edgeR package. The single-sample networks of the 371 tumor sa

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Liu, Zhihong, Zhimei Zhang, Guangyao Song, Xing Wang, Hanying Xing, and Chao Wang. "Resveratrol Alleviates Skeletal Muscle Insulin Resistance by Downregulating Long Noncoding RNA." International Journal of Endocrinology 2022 (January 19, 2022): 1–16. http://dx.doi.org/10.1155/2022/2539519.

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Long noncoding RNA (lncRNA) is a crucial factor in the progression of insulin resistance (IR). Resveratrol (RSV) exhibits promising therapeutic potential for IR. However, there are few studies on whether RSV improves IR through lncRNA. This study aimed to determine whether RSV could influence the expression of lncRNA and to elucidate the underlying mechanism. Mice were divided into three groups: control group, high-fat diet (HFD) group, and HFD + RSV group. We conducted a high-throughput sequencing analysis to detect lncRNA and mRNA expression signatures and the ceRNA-network in the skeletal m

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Yu, Qun, Jiangong Lin, Qiqi Ma, et al. "Long Noncoding RNA ENSG00000254693 Promotes Diabetic Kidney Disease via Interacting with HuR." Journal of Diabetes Research 2022 (April 19, 2022): 1–13. http://dx.doi.org/10.1155/2022/8679548.

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Diabetic kidney disease (DKD) is one of the most common complications of diabetes mellitus (DM), without suitable therapies, causing end-stage renal diseases (ESRDs) ultimately. Moreover, there is increasing evidence demonstrating that long noncoding RNAs (lncRNAs) play crucial roles in the development of DKD. Our RNA sequencing data revealed a large group of differentially expressed lncRNAs in renal tissues of DKD, of which lncRNA ENSG00000254693 (lncRNA 254693 for short) changed drastically. In this study, we found that the expression of lncRNA 254693 was increased in both DKD patients and h

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Nishitsuji, Hironori, Saneyuki Ujino, Sachiyo Yoshio, et al. "Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression." Proceedings of the National Academy of Sciences 113, no. 37 (2016): 10388–93. http://dx.doi.org/10.1073/pnas.1525022113.

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Despite the breadth of knowledge that exists regarding the function of long noncoding RNAs (lncRNAs) in biological phenomena, the role of lncRNAs in host antiviral responses is poorly understood. Here, we report that lncRNA#32 is associated with type I IFN signaling. The silencing of lncRNA#32 dramatically reduced the level of IFN-stimulated gene (ISG) expression, resulting in sensitivity to encephalomyocarditis virus (EMCV) infection. In contrast, the ectopic expression of lncRNA#32 significantly suppressed EMCV replication, suggesting that lncRNA#32 positively regulates the host antiviral re

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Ahmad, Imran, Araceli Valverde, Fayek Ahmad, and Afsar Raza Naqvi. "Long Noncoding RNA in Myeloid and Lymphoid Cell Differentiation, Polarization and Function." Cells 9, no. 2 (2020): 269. http://dx.doi.org/10.3390/cells9020269.

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Long noncoding RNA (lncRNA) are a class of endogenous, non-protein coding RNAs that are increasingly being associated with various cellular functions and diseases. Yet, despite their ubiquity and abundance, only a minute fraction of these molecules has an assigned function. LncRNAs show tissue-, cell-, and developmental stage-specific expression, and are differentially expressed under physiological or pathological conditions. The role of lncRNAs in the lineage commitment of immune cells and shaping immune responses is becoming evident. Myeloid cells and lymphoid cells are two major classes of

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Chen, Junhao, Yi Pan, Yunhui Lu, et al. "The Function and Mechanism of Long Noncoding RNAs in Adipogenic Differentiation." Genes 15, no. 7 (2024): 875. http://dx.doi.org/10.3390/genes15070875.

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Adipocytes are crucial for maintaining energy balance. Adipocyte differentiation involves distinct stages, including the orientation stage, clone amplification stage, clone amplification termination stage, and terminal differentiation stage. Understanding the regulatory mechanisms governing adipogenic differentiation is essential for comprehending the physiological processes and identifying potential biomarkers and therapeutic targets for metabolic diseases, ultimately improving glucose and fat metabolism. Adipogenic differentiation is influenced not only by key factors such as hormones, the p

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Gong, Chengwu, Xueliang Zhou, Songqing Lai, Lijun Wang, and Jichun Liu. "Long Noncoding RNA/Circular RNA-miRNA-mRNA Axes in Ischemia-Reperfusion Injury." BioMed Research International 2020 (November 25, 2020): 1–33. http://dx.doi.org/10.1155/2020/8838524.

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Ischemia-reperfusion injury (IRI) elicits tissue injury involved in a wide range of pathologies. Multiple studies have demonstrated that noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), participate in the pathological development of IRI, and they may act as biomarkers, therapeutic targets, or prognostic indicators. Nonetheless, the specific molecular mechanisms of ncRNAs in IRI have not been completely elucidated. Regulatory networks among lncRNAs/circRNAs, miRNAs, and mRNAs have been the focus of attention in recent years. Stu

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Zhou, Min, Wen-Jin Ding, Ying-Wei Chen, et al. "Expression Changes of Long Noncoding RNA in the Process of Endothelial Cell Activation." Cellular Physiology and Biochemistry 41, no. 1 (2017): 115–23. http://dx.doi.org/10.1159/000455980.

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Background: Endothelial cells have been shown to be in response to a variety of local and systemic stimuli, and are able to transition between quiescent and activated states. Endothelial cell activation is critical for the pathogenesis of various cardiovascular diseases. However, the expression changes of long non-coding RNAs (lncRNAs) are still unknown in the process of endothelial cell activation. Thus, this study was aimed to investigate expression changes of lncRNA before and after endothelial cell activation. Materials and Methods: In an experimental model of peripheral venous congestion,

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Qu, Yidi, Hor-Yue Tan, Yau-Tuen Chan, Hongbo Jiang, Ning Wang, and Di Wang. "The functional role of long noncoding RNA in resistance to anticancer treatment." Therapeutic Advances in Medical Oncology 12 (January 2020): 175883592092785. http://dx.doi.org/10.1177/1758835920927850.

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Chemotherapy is one of the fundamental methods of cancer treatment. However, drug resistance remains the main cause of clinical treatment failure. We comprehensively review the newly identified roles of long noncoding RNAs (lncRNAs) in oncobiology that are associated with drug resistance. The expression of lncRNAs is tissue-specific and often dysregulated in human cancers. Accumulating evidence suggests that lncRNAs are involved in chemoresistance of cancer cells. The main lncRNA-driven mechanisms of chemoresistance include regulation of drug efflux, DNA damage repair, cell cycle, apoptosis, e

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Hansmeier, Nils R., Pia J. M. Widdershooven, Sajjad Khani, and Jan-Wilhelm Kornfeld. "Rapid Generation of Long Noncoding RNA Knockout Mice Using CRISPR/Cas9 Technology." Non-Coding RNA 5, no. 1 (2019): 12. http://dx.doi.org/10.3390/ncrna5010012.

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In recent years, long noncoding RNAs (lncRNAs) have emerged as multifaceted regulators of gene expression, controlling key developmental and disease pathogenesis processes. However, due to the paucity of lncRNA loss-of-function mouse models, key questions regarding the involvement of lncRNAs in organism homeostasis and (patho)-physiology remain difficult to address experimentally in vivo. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 platform provides a powerful genome-editing tool and has been successfully applied across model organisms to facilitate targeted gen

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Zhao, Yang, Hongqi Teng, Fan Yao, Shannon Yap, Yutong Sun, and Li Ma. "Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs." Cancers 12, no. 6 (2020): 1458. http://dx.doi.org/10.3390/cancers12061458.

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Long noncoding RNAs (lncRNAs) are involved in many physiological and pathological processes, such as development, aging, immunity, and cancer. Mechanistically, lncRNAs exert their functions through interaction with proteins, genomic DNA, and other RNA, leading to transcriptional and post-transcriptional regulation of gene expression, either in cis or in trans; it is often difficult to distinguish between these two regulatory mechanisms. A variety of approaches, including RNA interference, antisense oligonucleotides, CRISPR-based methods, and genetically engineered mouse models, have yielded ab

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Zhang, Zhan, Ping Wang, Linlin Zhang, et al. "Identification of Key Genes and Long Noncoding RNA-Associated Competing Endogenous RNA (ceRNA) Networks in Early-Onset Preeclampsia." BioMed Research International 2020 (June 5, 2020): 1–9. http://dx.doi.org/10.1155/2020/1673486.

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Background. Preeclampsia (PE) is a pregnancy-specific hypertension syndrome and is one of the leading causes of maternal and perinatal morbidity and mortality. Long noncoding RNAs (lncRNAs) have been reported to be abnormally expressed in many diseases, including preeclampsia. The present study is aimed at identifying the key genes and lncRNA-associated competing endogenous RNA (ceRNA) networks in early-onset preeclampsia (EOPE). Methods. We investigated expression profiles of differentially expressed lncRNAs (DElncRNAs) and genes (DEGs) in placental tissues of EOPE and healthy controls with H

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Tsung, Kathleen, Jane Han, Kristie Liu, Eddie Loh, and Frank Attenello. "CNSC-31. CRISPR FUNCTIONAL SCREEN IDENTIFIES A NOVEL LONG NONCODING RNA MODULATING GLIOBLASTOMA INVASION." Neuro-Oncology 24, Supplement_7 (2022): vii29. http://dx.doi.org/10.1093/neuonc/noac209.112.

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Abstract INTRODUCTION Glioblastoma(GBM) invasion studies traditionally target coding genes. Long noncoding RNAs (lncRNAs), are transcripts without coding potential, with limited data regarding function. We leveraged CRISPR-interference, repressing lncRNA transcription via Cas9-KRAB, to evaluate invasive function of GBM-associated lncRNAs in a CRISPRi functional screen. METHODS 2,307 candidate lncRNAs were assembled from GBM differential gene expression. Guide RNAs targeting candidates were lentivirally incorporated into GBM screening populations. Screen populations were evaluated via Matrigel

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Bogu, Gireesh K., Pedro Vizán, Lawrence W. Stanton, Miguel Beato, Luciano Di Croce, and Marc A. Marti-Renom. "Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse." Molecular and Cellular Biology 36, no. 5 (2015): 809–19. http://dx.doi.org/10.1128/mcb.00955-15.

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Discovering and classifying long noncoding RNAs (lncRNAs) across all mammalian tissues and cell lines remains a major challenge. Previously, mouse lncRNAs were identified using transcriptome sequencing (RNA-seq) data from a limited number of tissues or cell lines. Additionally, associating a few hundred lncRNA promoters with chromatin states in a single mouse cell line has identified two classes of chromatin-associated lncRNA. However, the discovery and classification of lncRNAs is still pending in many other tissues in mouse. To address this, we built a comprehensive catalog of lncRNAs by com

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Xi, Tianyi, Yuying Zhou, Sai Ma, et al. "Construction of a potential long noncoding RNA prognostic model involved competitive endogenous RNA for patients with gastric cancer." Medicine 103, no. 24 (2024): e38458. http://dx.doi.org/10.1097/md.0000000000038458.

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Increasing evidence has underscored the role of long noncoding RNAs (lncRNAs) make up the major proportion of the competing endogenous RNAs (ceRNAs) network and can regulate gene expression by competitively binding to miRNAs in the development and progression of tumors. Nevertheless, the role of lncRNA-mediated ceRNAs in gastric cancer (GC) and their regulatory mechanisms have not been elucidated to some extent. This study is aimed at constructing a prognostic risk model for GC based on lncRNAs. A TCGA (The Cancer Genome Atlas) dataset was analyzed using edgeR to identify differentially expres

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Mishra, Kankadeb, and Chandrasekhar Kanduri. "Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far." Non-Coding RNA 5, no. 4 (2019): 54. http://dx.doi.org/10.3390/ncrna5040054.

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With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence from these new technologies emphasize that chromatin targeting of lncRNAs is a prominent mechanism and that these chromatin targeted lncRNAs exert their functionality by fine tuning chromatin architecture resulting in an altered transcriptional readout. Currently, there are no

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Kong, Yiwei, Zeyuan Lu, Pengyuan Liu, et al. "Long Noncoding RNA: Genomics and Relevance to Physiology." Comprehensive Physiology 9, no. 3 (2019): 933–46. https://doi.org/10.1002/j.2040-4603.2019.tb00085.x.

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ABSTRACTThe mammalian cell expresses thousands of long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides but do not encode any protein. lncRNAs can change the expression of protein‐coding genes through both cis and trans mechanisms, including imprinting and other types of transcriptional regulation, and posttranscriptional regulation including serving as molecular sponges. Deep sequencing, coupled with analysis of sequence characteristics, is the primary method used to identify lncRNAs. Physiological roles of specific lncRNAs can be examined using genetic targeting or knockdown wit

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Huang, Diyu, Jie Fang, and Gaojian Luo. "Roles of long noncoding RNAs in Hepatocellular Carcinoma." Open Life Sciences 11, no. 1 (2016): 91–97. http://dx.doi.org/10.1515/biol-2016-0012.

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AbstractLong noncoding RNAs (lncRNAs) are nonprotein coding transcripts longer than 200 nucleotides. Aberrant expression of lncRNAs has been found to be associated with hepatocellular carcinoma, one of the most malignant tumors. In this paper, we give a systematic and comprehensive review of existing literature about the involvement of lncRNAs in hepatocellular carcinoma. To date, evidence suggests that a number of lncRNAs, including HEIH, H19, HOTAIR, MALAT1, and PVT1, may regulate the transcription of target genes by recruiting histone-modifying complexes. Under certain circumstances, lncRNA

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Song, Chaoying, Jiali Zhang, Zongyao Zhao, et al. "DLEU1: A Functional Long Noncoding RNA in Tumorigenesis." Current Pharmaceutical Design 26, no. 15 (2020): 1742–48. http://dx.doi.org/10.2174/1381612826666200122145305.

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Background: LncRNA DLEU1 participates in various biological processes, playing an indispensable role in the pathophysiology of human diseases, especially in tumorigenesis and other processes. Besides, it may represent a promising target for biotherapy in numerous tumors. The aim of this review was to reveal the pathophysiological functions and mechanisms of lncRNA DLEU1 in different types of cancer. Methods: LncRNA DLEU1 participates in various biological processes, playing an indispensable role in the pathophysiology of human diseases, especially in tumorigenesis and other processes. Besides,

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Han, Siyu, Yanchun Liang, Ying Li, and Wei Du. "Long Noncoding RNA Identification: Comparing Machine Learning Based Tools for Long Noncoding Transcripts Discrimination." BioMed Research International 2016 (2016): 1–14. http://dx.doi.org/10.1155/2016/8496165.

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Long noncoding RNA (lncRNA) is a kind of noncoding RNA with length more than 200 nucleotides, which aroused interest of people in recent years. Lots of studies have confirmed that human genome contains many thousands of lncRNAs which exert great influence over some critical regulators of cellular process. With the advent of high-throughput sequencing technologies, a great quantity of sequences is waiting for exploitation. Thus, many programs are developed to distinguish differences between coding and long noncoding transcripts. Different programs are generally designed to be utilised under dif

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Paralkar, Vikram R., Tejaswini Mishra, Jing Luan, et al. "Long Noncoding RNAs in Erythropoiesis and Megakaryopoiesis." Blood 120, no. 21 (2012): 2331. http://dx.doi.org/10.1182/blood.v120.21.2331.2331.

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Abstract Abstract 2331 Lnc (long noncoding) RNAs are RNA transcripts greater than 200nt that regulate gene expression independent of protein coding potential. It is estimated that thousands of lncRNAs play vital roles in diverse cellular processes and are involved in numerous diseases, including cancer. We hypothesize that multiple lncRNAs regulate erythrocyte and megakaryocyte formation by modulating gene expression. To identify lncRNAs in erythro-megakaryopoiesis, we purified two biological replicates each of murine Ter119+ erythroblasts, CD41+ megakaryocytes and bipotential megakaryocyte-er

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Xiao, Yun, Yanling Lv, Hongying Zhao, et al. "Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network." BioMed Research International 2015 (2015): 1–14. http://dx.doi.org/10.1155/2015/839590.

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Long noncoding RNAs (lncRNAs) have been shown to play key roles in various biological processes. However, functions of most lncRNAs are poorly characterized. Here, we represent a framework to predict functions of lncRNAs through construction of a regulatory network between lncRNAs and protein-coding genes. Using RNA-seq data, the transcript profiles of lncRNAs and protein-coding genes are constructed. Using the Bayesian network method, a regulatory network, which implies dependency relations between lncRNAs and protein-coding genes, was built. In combining protein interaction network, highly c

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Guo, Wen, Haitao Jiang, Haijun Li, et al. "LncRNA-SRA1 Suppresses Osteosarcoma Cell Proliferation While Promoting Cell Apoptosis." Technology in Cancer Research & Treatment 18 (January 1, 2019): 153303381984143. http://dx.doi.org/10.1177/1533033819841438.

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Objective: Osteosarcoma is a common malignant bone tumor that is frequently found in the long bones of children and adolescents. The aim of this study is to examine long noncoding RNA-steroid receptor RNA activator 1 expression in osteosarcoma to explore the biological function of long noncoding RNA steroid receptor RNA activator 1 on proliferation, migration, and invasion along with apoptosis and its regulatory mechanism, which would facilitate the early diagnosis and targeted therapy of osteosarcoma. Methods: First, microarray analysis was applied to determine the expression of long noncodin

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Xie, Jiaogui, Ying Jiang, Yichao Wang, and Dalin He. "Crucial Biological Roles of Long Noncoding RNA-Mediated Pyroptosis in Urological Tumors." Journal of Biomedical Nanotechnology 19, no. 8 (2023): 1309–20. http://dx.doi.org/10.1166/jbn.2023.3637.

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Urologic neoplasm is one of the most general neoplasms, including bladder neoplam, prostate neoplasm and renal neoplasm. Researches have shown that tumor formation is a very complicated process, and it is the result of cell proliferation that is seriously out of control. Long noncoding RNA (lncRNA) and pyroptosis act separately or together on the tumorigenesis, growth and metastasis of urinary tumors, and are related to their treatment and prognosis. In this review, we summarized existing studies and found that lncRNA-mediated pyroptosis can promote or inhibit the development of urinary tumors

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Liu, Hao, Yiping Huang, Yingying Zhang, et al. "Long noncoding RNA expression profile of mouse cementoblasts under compressive force." Angle Orthodontist 89, no. 3 (2019): 455–63. http://dx.doi.org/10.2319/061118-438.1.

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ABSTRACT Objectives: To investigate the long noncoding RNA (lncRNA) expression profile of cementoblasts under compressive force. Materials and Methods: Mouse cementoblasts were exposed to compression (1.5 g/cm2) for 8 hours. RNA sequencing (RNA-seq) was performed to compare the transcriptomes of the compressed and control cells. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate five of the differentially expressed lncRNAs of interest. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also performed. R

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Bai, Youhuang, Xiaozhuan Dai, Tiantian Ye, et al. "PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions." Current Bioinformatics 14, no. 7 (2019): 621–27. http://dx.doi.org/10.2174/1574893614666190131161002.

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Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts. Results: More than five thousand lncRNAs are collected from four plant species (Arabi

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Wang, Lian, Ruifeng Lu, Yujia Wang, et al. "Identification of Long Noncoding RNA Associated ceRNA Networks in Rosacea." BioMed Research International 2020 (February 24, 2020): 1–13. http://dx.doi.org/10.1155/2020/9705950.

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Rosacea is a chronic and relapsing inflammatory cutaneous disorder with highly variable prevalence worldwide that adversely affects the health of patients and their quality of life. However, the molecular characterization of each rosacea subtype is still unclear. Furthermore, little is known about the role of long noncoding RNAs (lncRNAs) in the pathogenesis or regulatory processes of this disorder. In the current study, we established lncRNA-mRNA coexpression networks for three rosacea subtypes (erythematotelangiectatic, papulopustular, and phymatous) and performed their functional enrichment

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Hanjin, Cui, Liu Tao, Li Pengfei, et al. "Altered Long Noncoding RNA and Messenger RNA Expression in Experimental Intracerebral Hemorrhage - a Preliminary Study." Cellular Physiology and Biochemistry 45, no. 3 (2018): 1284–301. http://dx.doi.org/10.1159/000487464.

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Background/Aims: Functional recovery in the chronic phase is a difficult problem in intracerebral hemorrhage (ICH) treatment. Long noncoding RNAs (lncRNAs) are demonstrated to be involved in central nervous system (CNS) disorders. However, the roles of lncRNAs in post-ICH injury and repair are poorly understood, especially those that may be attributed to long-term neurological deficit. The present study depicted the lncRNA and messenger RNA (mRNA) profile by microarray at late stage after an experimental ICH. Methods: LncRNA and mRNA microarray was used to first identify differentially express

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Douka, Katerina, Isabel Birds, Dapeng Wang, et al. "Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation." RNA 27, no. 9 (2021): 1082–101. http://dx.doi.org/10.1261/rna.078782.121.

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The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SY5Y cells. We discovered 237 cytoplasmic lncRNAs up-regulated during early neuronal differentiation, 58%–70% of which are associated with polysome translation complexes. Among these polysome-associated lncRNAs, we f

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