• HOTAIR (for HOX transcript antisense RNA) is a human gene located between HOXC11 and HOXC12 on chromosome 12. (wikipedia.org)
  • In particular, the FANTOM (Functional Annotation of the Mammalian Genome) consortium pioneered the discovery of the noncoding RNA world by providing, through Cap Analysis of Gene Expression (CAGE-Seq), the first evidence that large portions of our genome are transcribed, producing a multitude of sense and antisense transcripts 12 . (nature.com)
  • Some lncRNAs (referred to as long intergenic non-coding RNAs, lincRNAs) are transcribed from separate loci, whereas others are transcribed divergently from promoters of protein-coding genes or in antisense direction to these. (biomedcentral.com)
  • This lncRNA is an antisense of intron 1 of unc-5 netrin receptor B (UNC5B) gene. (jcancer.org)
  • Interestingly, the enhancing rim fraction score was found to become correlated with a known predictor of tumor metastasis, HOTAIR (homeobox transcript antisense intergenic RNA). (calcium-channel.com)
  • Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
  • Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
  • More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
  • presents an opportunity to manipulate gene expression within the cells to treat various diseases, and acts as a powerful tool for studying gene function utilizing antisense agents to manage the diseases by regulating the expression of the specific factor that actually causes the particular disease. (genomicglossaries.com)
  • Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message. (genomicglossaries.com)
  • HOX transcript antisense intergenic RNA (HOTAIR) is a long non-coding RNA (lncRNA) discovered at 2007. (biomedcentral.com)
  • SNHG3 was identified as a competitive endogenous RNA molecule to promote the malignant progression of colorectal cancer [ 8 ]. (hindawi.com)
  • Emerging evidence suggests that competing endogenous RNA (ceRNA) plays a role in the molecular biological mechanisms related to the occurrence and development of cancer. (bvsalud.org)
  • Mechanistically, PTTG3P upregulated the expression of miR-383 targets Cyclin D1 (CCND1) and poly ADP-ribose polymerase 2 (PARP2) by sponging miR-383, acting as a competing endogenous RNA (ceRNA). (biomedcentral.com)
  • A series of studies indicate that lncRNAs serve as competing endogenous RNAs (ceRNA) by sponging miRNAs, and modulate the targets of miRNAs [ 15 , 16 ]. (biomedcentral.com)
  • Deep RNA-DNA, RNA-protein interaction studies, and phenotype rescue analyses reveal that LETR1 is a nuclear trans-acting lncRNA modulating, via key epigenetic factors, the expression of essential target genes, including KLF4 and SEMA3C , governing the growth and migratory ability of LECs. (nature.com)
  • CASC9 expression discriminated tumors from normal tissues with even higher specificity than HOTAIR, a lncRNA previously suggested as an HNSCC biomarker. (biomedcentral.com)
  • For instance, H19 is the first lncRNA transcribed by RNA polymerase II and is expressed mainly in human embryonic cells. (jcancer.org)
  • The function and possible mechanism of lncRNA Small Nucleolar RNA Host Gene 3 (SNHG3) in GC have not been fully studied. (hindawi.com)
  • Luciferase reporter gene analysis and RNA immunoprecipitation (RIP) analysis confirmed the interaction between lncRNA SNHG3, miR-326, and TWIST. (hindawi.com)
  • Long noncoding RNA (lncRNA) is more than 200 nucleotides in length without significant protein-coding potential [ 5 ]. (hindawi.com)
  • In this study, we globally assessed the transcriptomic differences of lncRNAs in gastric cancer using publicly available microarray data from Gene Expression Omnibus (GEO) and identified an oncogenetic lncRNA ZFAS1, which may promote gastric tumorigenesis. (oncotarget.com)
  • qPCR and Western blot were used to analyze LncRNA PTTG3P, miR-383 and other target genes' expression. (biomedcentral.com)
  • Luciferase reporter assay and RNA pull-down assay were carried out to detect the interaction between miR-383 and LncRNA PTTG3P. (biomedcentral.com)
  • As a peripheral blood biomarker, the crucial role of long non-coding RNA (lncRNA) HOTAIR has recently been suggested in many types of disorder. (biomedcentral.com)
  • Despite the critical role of HOTAIR in the mammalians' developmental processes, overexpression of this lncRNA has been reported to coordinate in several genetic abnormalities. (biomedcentral.com)
  • Obviously, expression level analysis of this lncRNA in the breast cancer patients' peripheral blood could suggest a novel non-invasive biomarker on the basis of circulating RNA. (biomedcentral.com)
  • Here, we investigate a lncRNA-mediated targeting of DNMT1 to specific gene loci by the combined power of in silico modeling of RNA/DNA interactions and wet lab approaches, in the context of the clinically relevant use case of ephrinA5-dependent regulation of cellular motility of cerebellar granule cells. (biomedcentral.com)
  • We provide evidence that Snhg15 , a cancer-related lncRNA, recruits DNMT1 to the Ncam1 promoter through RNA/DNA triplex structure formation and the interaction with DNMT1. (biomedcentral.com)
  • The most recent equine transcriptome based on RNA-seq from several tissues was a prime opportunity to obtain a concurrent long non-coding RNA (lncRNA) database. (lncrnablog.com)
  • Researchers from the Centre for Genomic Regulation and the University of Bern have created "LncATLAS", a comprehensive resource of lncRNA localisation in human cells based on RNA-sequencing datasets. (lncrnablog.com)
  • PRC2 is dispensable for HOTAIR-mediated transcriptional silencing. (wikipedia.org)
  • Non (protein)-coding RNAs are the most abundant transcriptional products of the coding genome, and comprise several different classes of molecules with unique lengths, conformations and targets. (frontiersin.org)
  • Therefore, this complex regulatory network requires precise control of gene expression patterns at both transcriptional and post-transcriptional levels in order to ensure proper maturation, differentiation, and formation of blood and lymphatic vessels. (nature.com)
  • lncRNAs have been reported to possess multiple functions including regulation of gene expression, transcriptional activation and silencing of genes and thus play critical roles in a diversity of cellular process [ 14 , 15 ]. (researchsquare.com)
  • To date, it is well known that lncRNAs participate in chromatin modifications and transcriptional and translational regulation of protein-encoding genes or regulate protein function and activity through specific binding [ 3 - 5 ]. (jcancer.org)
  • The emergence of next-generation sequencing technologies has provided an excellent chance for increasingly rapid improvement of RNA sequencing, shedding light on novel and undiscovered transcriptional and epigenetic regulators in breast cancer. (calcium-channel.com)
  • In the post-genomic era, the cancer research is focused on the dysregulation of transcriptional dysregulation mediated by epigenetic modifications in the enhancer, SE, and gene promoter regions of key tumor suppressor and tumor-promoting genes [ 5 , 6 ]. (ijbs.com)
  • Previously, we reported ephrinA5 to trigger transcriptional changes of lncRNAs and protein-coding genes in cerebellar granule cells, a cell model for medulloblastoma. (biomedcentral.com)
  • Typically, transcriptional regulation is fine-tuned by epigenetic mechanisms, comprising histone modifications, DNA methylation, and non-coding RNAs (ncRNAs). (biomedcentral.com)
  • Gene regulatory network perturbations contribute to the development and progression of cancer, however, molecular determinants that mediate transcriptional perturbations remain a fundamental. (lncrnablog.com)
  • Despite their lack of protein-coding potential, lncRNAs and circRNAs have emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. (lncrnablog.com)
  • 87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
  • After second- strand cDNA synthesis, T7 RNA polymerase was used to generate aRNA. (genomicglossaries.com)
  • SEs are defined as large clusters of active enhancers in large clusters that are enriched with high levels of transcription factors (TFs), master co-factors, mediator complexes, RNA polymerase II (RNA pol II), and epigenetic modifications [ 5 , 7 ]. (ijbs.com)
  • Recently, noncoding RNAs (ncRNAs) have been reported to regulate protein expression, and it is definite that PTEN expression is controlled by ncRNAs epigenetically or posttranscriptionally as well. (biomedcentral.com)
  • NONCODE is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). (lncrnablog.com)
  • Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. (lncrnablog.com)
  • Long noncoding RNAs, defined as the noncoding transcript, are a important group of regulatory RNAs that have been implicated within the development of numerous forms of strong tumors. (calcium-channel.com)
  • Among these reports, few investigations have indicated overexpression of HOTAIR transcript in the breast cancer patients' peripheral blood. (biomedcentral.com)
  • Lnc2Meth, an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases. (lncrnablog.com)
  • Results In the present study, we performed a systematic transcriptome analysis based on the deep RNA sequencing of ten asthmatic children before and after desensitization treatment. (researchsquare.com)
  • A growing body of evidence indicates that epigenetic regulators rely, amongst other factors, on their interaction with untranslated RNA molecules for guidance to particular targets on DNA. (frontiersin.org)
  • Long non-coding RNAs (lncRNAs) have shown promise as biomarkers in other cancer types and in some cases functionally contribute to tumor development and progression. (biomedcentral.com)
  • New sequencing technologies have shown that a large number of aberrantly expressed lncRNAs are associated with multiple cancer types and indicated they have emerged as an important class of pervasive genes during the development and progression of cancer. (biomedcentral.com)
  • Emerging evidence indicates that Long non-coding RNAs (LncRNAs) and microRNAs (miRNAs) play crucial roles in tumor progression, including hepatocellular carcinoma (HCC). (biomedcentral.com)
  • We highlight the role of SE-driven genes, enhancer RNAs (eRNAs), lncRNAs, and miRNAs in the digestive system tumor growth and progression. (ijbs.com)
  • Aberrant changes in epigenetic mechanisms regulating DNA methylation, histone methylation and acetylation, expression of noncoding RNAs, and mRNA methylation are associated with the initiation, growth, and progression of digestive system tumors [ 2 , 4 ]. (ijbs.com)
  • Current evidences have revealed the association of HOTAIR with progression, in addition to the prediction/prognosis of many different cancer types (including glioblastoma, liver, gastric, pancreatic, colorectal and cervical malignancies). (biomedcentral.com)
  • Pseudogene, a subclass of long non-coding RNAs (lncRNAs), are considered as genomic loci that resemble real gene, but lost some functionality because they are lack of protein-coding ability because of disabling mutation, lack of transcription, or their inability to encode RNA [ 3 ]. (biomedcentral.com)
  • However, whether and how DNMT targets specific gene loci, and induces transcriptionally relevant changes in DNA methylation signatures that elicit physiological responses, is not fully understood. (biomedcentral.com)
  • In particular, there are incremental examples of the participation of the distinct class of long non-coding RNAs (lncRNAs) in AML epigenetic regulation, some of which have translational potential. (frontiersin.org)
  • We have recently aimed to investigate regulation of HOTAIR in the whole peripheral blood (including circulating as well as white blood cell RNA) of breast cancer patients compared to normal individuals. (biomedcentral.com)
  • The 5′ end of HOTAIR interacts with a Polycomb-group protein Polycomb Repressive Complex 2 (PRC2) and as a result regulates chromatin state. (wikipedia.org)
  • However, a growing body of evidence suggests that recruitment, stability, and function of epigenetic factors can be mediated by non-protein-coding RNAs. (frontiersin.org)
  • Western blotting was performed to detect the protein levels of TWIST and EMT-related genes. (hindawi.com)
  • Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
  • The Human Genome Project has revealed that protein-coding genes represent less than 2% of the total genome sequence [ 7 ], and the remaining greater portion of human genomes are regarded as "junk DNAs", for they do not encode any protein. (oncotarget.com)
  • Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. (lncrnablog.com)
  • 102) created a radiomics model with all eight minimum redundancy maximum relevance options from CT images of 170 RCC sufferers and located it to be considerably linked with VHL mutation.RNA SequencingThe Oncotype Dx Recurrence Score (ODxRS), which incorporates the mRNA expression of 21 genes, is made use of clinically to predict the prognosis of early-stage invasive breast cancer (95). (calcium-channel.com)
  • More than half of all human genes are alternatively spliced, so it is expected that alternative pre- mRNA splicing will be responsible for the identification of more than 90 percent of all human proteins. (genomicglossaries.com)
  • High- fidelity mRNA amplification for gene profiling. (genomicglossaries.com)
  • RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. (genomicglossaries.com)
  • A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
  • This is partially due to HOTAIR-mediated overexpression of the HER2 oncogene through sequestration of miR-331-3p, which is a negative regulator of HER2 expression. (wikipedia.org)
  • Taken together, our data suggest that UASR1 plays an oncogenic role in breast cancer cells through activation of the AKT/mTOR signaling pathway, being a novel RNA oncogene. (jcancer.org)
  • Conclusions Our study successfully discovered many key noncoding RNA molecules related to pathogenesis of asthma and relevant treatment, which may provide novel biomarkers and therapeutic targets for asthmatic diagnose and therapy. (researchsquare.com)
  • Recent studies have revealed the importance of long noncoding RNAs (lncRNAs) as tissue-specific regulators of gene expression. (nature.com)
  • Long non-coding RNAs (lncRNAs) have moved into the focus of cancer research as good candidates for tumor biomarkers and as regulators of various neoplastic cell properties. (biomedcentral.com)
  • Recently, long noncoding RNAs have been emerged as critical regulators of human disease and prognostic markers in several cancers, including gastric cancer. (oncotarget.com)
  • Long non-coding RNAs (lncRNAs) are emerging as important regulators in different biological processes through various ways. (lncrnablog.com)
  • cDNA was next prepared from the consistent amount of individual RNA samples, using a cDNA synthesis kit (ParsTous). (biomedcentral.com)
  • It is the first example of an RNA expressed on one chromosome that has been found to influence transcription of HOXD cluster posterior genes located on chromosome 2. (wikipedia.org)
  • While the conserved sequence paralogous with HOXD cluster is 32 nucleotide long, the HOTAIR sequence conserved from human to fish is about 200 nucleotide long and is marked by active enhancer features (bidirectional transcription, H3K4me1 and H3K27ac peaks). (wikipedia.org)
  • RF outperformed ANN in that study (95.0 vs 88.2 ) (104).Runt-Related Transcription Factor-3 MethylationThe runt-related transcription factor-3 (RUNX3) gene, a noted tumor suppressor gene, regulates gene expression in some dominant developmental pathways and has antitumor activity in several sorts of tumors (105). (calcium-channel.com)
  • Mechanistically, RNA immunoprecipitation and RNA pull-down experiment showed that ZFAS1 could simultaneously interact with EZH2 and LSD1/CoREST to repress underlying targets KLF2 and NKD2 transcription. (oncotarget.com)
  • The core transcription regulatory loop of the digestive system tumors is complex and a high density of transcription regulatory complexes in the SEs and the crosstalk between SEs and the noncoding RNAs. (ijbs.com)
  • For the individual samples, GAPDH expression level was also analysed by quantitative reverse-transcription PCR (qRT-PCR) to relatively determine HOTAIR expression level. (biomedcentral.com)
  • The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet to be characterized in the horse. (lncrnablog.com)
  • RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)
  • The aim of this mini-review is to discuss emerging epigenetic roles of long non-coding RNAs (lncRNAs) in Acute Myeloid Leukemia (AML). (frontiersin.org)
  • Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. (lncrnablog.com)
  • The 3′ end of HOTAIR interacts with the histone demethylase LSD1. (wikipedia.org)
  • Glypican 3 ( GPC3 ) is a heparan sulfate proteoglycan whose gene is located on chromosome Xq26. (biolifesas.org)
  • A subsequent study identified HOTAIR has 32 nucleotide long conserved noncoding element (CNE) that has a paralogous copy in HOXD cluster region (located between HOXD11 and HOXD12), suggesting that the HOTAIR conserved sequences predates whole genome duplication events at the root of vertebrate. (wikipedia.org)
  • In the latest genome annotation, lncRNAs, which are arbitrarily defined as noncoding RNAs longer than 200 nucleotides, constitute ~72% of the transcribed genome 13 , whereas mRNAs comprise only 19%, indicating the need for functional annotation of lncRNAs. (nature.com)
  • Concretely, genome-wide association studies have detected numerous asthma-associated gene variants, while few of them (less than 10%) can be explained to contribute to the risk of asthma [ 10 ]. (researchsquare.com)
  • In general, lncRNAs are defined as being longer than 200 nucleotides and lacking a functional open reading frame. (biomedcentral.com)
  • Studies in recent years have demonstrated that long non-coding RNAs (lncRNAs) have multiple biological functions in cell growth, differentiation and proliferation. (oncotarget.com)
  • MiR-326 plays an anticancer role in a variety of malignant tumors and targets different genes in glioma, endometrial cancer, and cervical cancer [ 11 - 14 ]. (hindawi.com)
  • Some of them are for non-coding RNA transcripts longer than 200 nucleotides, called long non-coding RNAs (lncRNAs) [ 1 , 2 ]. (jcancer.org)
  • LncRNAs, little or no coding potential, are defined as capped transcripts longer than 200 nucleotides. (biomedcentral.com)
  • The HOTAIR gene contains 6,232 bp and encodes 2.2 kb long noncoding RNA molecule, which controls gene expression. (wikipedia.org)
  • In cells, especially those that over express PRC2, the prevention of HOTAIR expression leads to a reduction in invasive potential of that cell. (wikipedia.org)
  • On the other hand, environmental factors have been reported to modulate epigenetic modifications and thereby affect gene expression and phenotype [ 11 , 12 ]. (researchsquare.com)
  • The results showed that the expression of Small Nucleolar RNA Host Gene 3 (SNHG3) was related to the malignant state, and the prognosis was relatively poor. (hindawi.com)
  • 97) performed a radiogenomics analysis to ascertain the association between the enhancing rim fraction and also the expression of 14,880 long noncoding RNAs. (calcium-channel.com)
  • Circulating long non-coding RNAs NKILA, NEAT1, MALAT1, and MIAT expression and their association in type 2 diabetes mellitus. (informaticsstudies.org)
  • A biological process that is crucial for gene expression in most animal life, including humans. (genomicglossaries.com)
  • The multistep transformation of normal cells into malignant cells involves genetic and epigenetic alterations that promote the aberrant expression of critical oncogenes and tumor suppressor genes [ 1 , 2 ]. (ijbs.com)
  • Does HOTAIR expression level in the peripheral blood have veritably predictive/prognostic impact on breast cancer patients? (biomedcentral.com)
  • In this regard, we studied the potential impact of radiotherapy on the peripheral blood HOTAIR expression of different breast cancer patients. (biomedcentral.com)
  • Curiously, no significant expression level of HOTAIR was determined in the breast cancer patients' peripheral blood, before and after radiotherapy (10 Gy exposure). (biomedcentral.com)
  • Deliberating these investigations raised some debates on the specificity of the utilized methods, the corresponding obtained findings and impact of HOTAIR expression on breast cancer predication, as a potential peripheral blood biomarker, which is discussed in this article. (biomedcentral.com)
  • Nevertheless, definitive conclusion of predictive/prognostic effect of HOTAIR expression in this type of cancer still remains challenging. (biomedcentral.com)
  • Additionally, potential effect of the radiotherapy on HOTAIR expression of these patients was evaluated, following the performance of ethic procedures. (biomedcentral.com)
  • To determine HOTAIR expression level, total RNA was isolated from the whole blood samples, according to the manufacturer's instruction (ParsTous, Iran). (biomedcentral.com)
  • Analysis of data obtained from the quantitative and qualitative PCR products showed expression level of HOTAIR in the peripheral blood of neither normal individual nor breast cancer patients before and after exposure to 10 Gy radiation (Fig. 1 ), whereas the quality of cDNA samples as well as sensitivity and specificity of the primers was appraised. (biomedcentral.com)
  • LncRNAs represent important adaptors for epigenetic writers through which they regulate gene expression. (biomedcentral.com)
  • Even though the physiological relevance of Eph/ephrin signaling has been well-proven for developmental and cancer-related processes, whether and how the ligand-mediated activation of Eph receptors triggers changes in gene expression that underlie discrete cell physiological responses is greatly unknown. (biomedcentral.com)
  • This set of HOTAIR primers is able to amplify distinctive sizes of both genomic and transcriptomic products. (biomedcentral.com)
  • Ultimately, genomic analysis was performed for some samples to validate the sensitivity and specificity of the HOTAIR primers. (biomedcentral.com)
  • Additionally, analysis of the genomic DNA validated sensitivity and specificity of the HOTAIR primers. (biomedcentral.com)
  • Long non-coding RNAs (lncRNAs) are non-coding RNAs longer than 200 nucleotides that function as regulatory factors in many human diseases, including cancer. (jcancer.org)
  • Therefore, diverse cellular compartments orchestrated by multiple environment-driving factors make the mechanisms underlying asthma extraordinary complex and unclear, particularly with respect to long noncoding RNAs (lncRNAs). (researchsquare.com)
  • Furthermore, bioinformatics approaches are employed to provide in silico evidences for the link between long noncoding RNAs and mitochondrial gene interaction in obesity. (informaticsstudies.org)
  • Sequence analysis of HOTAIR revealed that it exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. (wikipedia.org)
  • For example, misaligned lncRNAs may act as oncogenes or tumor suppressor genes in the HCC process [ 7 ]. (hindawi.com)
  • In addition to the indicated malignancies, it has also been demonstrated that HOTAIR is up-regulated in various type of breast cancer tissues and cells. (biomedcentral.com)
  • The sequence and function of HOTAIR is different in human and mouse. (wikipedia.org)
  • RNA which contains an intron sequence that has an enzyme- like catalytic activity. (genomicglossaries.com)
  • Emerging evidence indicates a putative role of long noncoding RNAs in regulating mitochondrial functions and metabolism. (informaticsstudies.org)
  • This article discusses the relationship between mitochondrial respiration and long noncoding RNAs and further outlines the implications of these interactions in obesity. (informaticsstudies.org)
  • Although there is little knowledge about lncRNAs at present, their potential implications in gene transcriptomics have aroused great interest and attention in the most recent years [ 12 ]. (oncotarget.com)
  • Finally, we discuss clinical significance of the CRISPR-Cas9 gene editing system and inhibitors of SE-related proteins such as BET and CDK7 as potential cancer therapeutics. (ijbs.com)
  • Specificity of HNSCC detection by CASC9 was further improved by combination with HOTAIR. (biomedcentral.com)