The long noncoding RNA, TINCR, functions as a competing endogenous RNA to regulate PDK1 expression by sponging miR-375 in gastric cancer Zhaoliang Chen,1 Hong Liu,1 Huili Yang,1 Yukai Gao,1 Gongwen Zhang,1 Jiaojiao Hu2 1Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong, 2Department of Hematology, Zhongda Hospital, Southeast University, Nanjing, China Background: Accumulating evidence indicates that the long noncoding RNA, TINCR, plays a critical role in cancer progression and metastasis. However, the overall biological role and mechanisms of TINCR that were involved in human gastric cancer (GC) progression remain largely unknown.Methods: TINCR expression was measured in 56 paired tumor and adjacent nontumor tissue samples by real-time polymerase chain reaction (PCR). Insights of the mechanism of competitive endogenous RNAs (ceRNAs) were gained from bioinformatic analysis, luciferase assays. The effects of TINCR and miR-375 on GC cell apoptosis and proliferation were studied by RNA
Several years ago, I posted a blog about long noncoding RNAs (lncRNAs), which are defined as non-protein coding transcripts in the range of ~200 nt to ~100 kb long. Interest in lncRNA is driven in large part by a collective scientific desire to uncover and understand the existence and function of all forms of "RNA dark matter," so named by analogy to "dark energy" in cosmology. The lncRNA component of RNA dark matter is certainly generated from transcription of noncoding (formerly "junk") DNA, but much has yet to be elucidated about function.. Following are tag lines from my Jan 23, 2018 blog titled Long Noncoding RNA (lncRNA) Revisted, which provides some updates on lncRNA dark matter.. ...
Long noncoding RNA NEAT1 promotes cell proliferation and invasion by regulating hnRNP A2 expression in hepatocellular carcinoma cells Yuanyi Mang, Li Li, Jianghua Ran, Shengning Zhang, Jing Liu, Laibang Li, Yiming Chen, Jian Liu, Yang Gao, Gang Ren Department of Hepato-Biliary-Pancreatic Surgery, The Calmette Affiliated Hospital of Kunming Medical University, The First Hospital of Kunming, Kunming, Yunnan, People’s Republic of China Abstract: Growing evidence demonstrates that long noncoding RNAs (lncRNAs) are involved in the progression of various cancers, including hepatocellular carcinoma (HCC). The role of nuclear-enriched abundant transcript 1 (NEAT1), an essential lncRNA for the formation of nuclear body paraspeckles, has not been fully explored in HCC. We aimed to determine the expression, roles and functional mechanisms of NEAT1 in the proliferation and invasion of HCC. Based on real-time polymerase chain reaction data, we suggest that NEAT1 is upregulated in HCC tissues compared with
Cardiogenesis processes in human and animals have differential dynamics, suggesting the existence of species-specific regulators during heart development. However, it remains a challenge to discover the human-specific cardiac regulatory genes, given that most coding genes are conserved. Here, researchers at the University of Pittsburgh School of Medicine report the identification of a human-specific long noncoding RNA, Heart Brake LncRNA 1 (HBL1), which regulates cardiomyocyte development from human induced pluripotent stem cells (hiPSCs). Overexpression of HBL1 repressed, whereas knockdown and knockout of HBL1 increased, cardiomyocyte differentiation from hiPSCs. HBL1 physically interacted with MIR1 in an AGO2 complex. Disruption of MIR1 binding sites in HBL1 showed an effect similar to that of HBL1 knockout. SOX2 bound to HBL1 promoter and activated its transcription. Knockdown of SOX2 in hiPSCs led to decreased HBL1 expression and increased cardiomyocyte differentiation efficiency. Thus, HBL1 ...
Zhang, Liu, Gao, Zhang, Zhang (2019) Long noncoding RNA XIST acts as a competing endogenous RNA to promote malignant melanoma growth and metastasis by sponging miR-217 Panminerva medica ...
Expression of the long noncoding RNA (lncRNA) SPRY4-IT1 is low in normal human melanocytes but high in melanoma cells. siRNA knockdown of SPRY4-IT1 blocks melanoma cell invasion and proliferation, and increases apoptosis. To investigate its function further, we affinity purified SPRY4-IT1 from melanoma cells and used mass spectrometry to identify the protein lipin 2, an enzyme that converts phosphatidate to diacylglycerol (DAG), as a major binding partner. SPRY4-IT1 knockdown increases the accumulation of lipin2 protein and upregulate the expression of diacylglycerol O-acyltransferase 2 (DGAT2) an enzyme involved in the conversion of DAG to triacylglycerol (TAG). When SPRY4-IT1 knockdown and control melanoma cells were subjected to shotgun lipidomics, an MS-based assay that permits the quantification of changes in the cellular lipid profile, we found that SPRY4-IT1 knockdown induced significant changes in a number of lipid species, including increased acyl carnitine, fatty acyl chains, and
Long noncoding RNA LINC00978 has been reported to regulate the progression of several human types of cancer, including gastric and breast cancer. However, knowledge on LINC00978 in non‑small cell lung cancer (NSCLC) is limited. In the present study, it was demonstrated that LINC00978 expression was significantly upregulated in NSCLC tissues compared with the adjacent normal tissues. Furthermore, LINC00978 expression was positively correlated with the tumor, node and metastasis stage, and lymph node metastasis in NSCLC patients. Additionally, LINC00978 knockdown significantly inhibited the proliferation, migration and invasion of NSCLC cells while promoting cell apoptosis. In terms of the underlying mechanism, it was demonstrated that LINC00978 served as a competing endogenous RNA sponge for microRNA (miR)‑6754‑5p, which was downregulated in NSCLC tissues. The present study demonstrated that there was a negative correlation between LINC00978 and miR‑6754‑5p expression levels in NSCLC ...
Staphylococcus aureus is a human pathogen causing a variety of diseases by versatile expression of a large set of virulence factors that most prominently features the cytotoxic and hemolytic pore-forming alpha-toxin. Expression of alpha-toxin is regulated by an intricate network of transcription factors. These include two-component systems sensing quorum and environmental signals as well as regulators reacting to the nutritional status of the pathogen. We previously identified the repressor of surface proteins (Rsp) as a virulence regulator. Acute cytotoxicity and hemolysis are strongly decreased in rsp mutants, which are characterized by decreased transcription of toxin genes as well as loss of transcription of a 1,232- nucleotide (nt)-long noncoding RNA (ncRNA), SSR42. Here, we show that SSR42 is the effector of Rsp in transcription regulation of the alpha-toxin gene, hla. SSR42 transcription is enhanced after exposure of S. aureus to subinhibitory concentrations of oxacillin which thus leads ...
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Transcriptomic analyses have identified tens of thousands of intergenic, intronic, and cis-antisense long noncoding RNAs (lncRNAs) that are expressed from mammalian genomes. Despite progress in functional characterization, little is known about the post-transcriptional regulation of lncRNAs and their half-lives. Although many are easily detectable by a variety of techniques, it has been assumed that lncRNAs are generally unstable, but this has not been examined genome-wide. Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs in the mouse Neuro-2a cell line. We find only a minority of lncRNAs are unstable. LncRNA half-lives vary over a wide range, comparable to, although on average less than, that of mRNAs, suggestive of complex metabolism and widespread functionality. Combining half-lives with comprehensive lncRNA annotations identified hundreds of unstable (half-life | 2 h) intergenic, cis-antisense, and intronic lncRNAs, as well as lncRNAs showing
TY - JOUR. T1 - Long non-coding RNA (lncRNA) transcriptional landscape in breast cancer identifies LINC01614 as non-favorable prognostic biomarker regulated by TGFβ and focal adhesion kinase (FAK) signaling. AU - Vishnubalaji, Radhakrishnan. AU - Shaath, Hibah. AU - Elkord, Eyad. AU - Alajez, Nehad M.. PY - 2019/12/1. Y1 - 2019/12/1. N2 - Long non-coding RNAs (lncRNAs) represent a class of epigenetic regulators implicated in a number of physiological and pathological conditions. Herein, we characterized the lncRNA expression portrait from 837 patients with invasive breast cancer and 105 normals from the cancer genome atlas (TCGA), which revealed eighteen upregulated and forty-six downregulated lncRNAs. Clustering analysis revealed distinct lncRNA profile for the triple negative breast cancer (TNBC) and normal breast tissue, while less separation was observed among the HER2+HR+, HER2+HR−, HER2−HR+ molecular subtypes. LINC01614, and LINC01235 correlated with worse disease-free survival (DFS), ...
The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important.
To evaluate the relevance of our chicken lncRNA set, we analyzed the gene expression profiles of the three classes "putative lncRNA transcripts", "new mRNAs" and "ambiguous RNAs" and also compared the structural features of our lncRNAs with those of the mouse and human lncRNAs. As expected, the 2193 putative lncRNA genes are on average tenfold less expressed than the known or new protein-coding genes, and the ambiguous RNAs have an intermediate expression (Fig. 1b). This is in accordance with previous findings in mammals that showed that lncRNAs are far less expressed than protein-coding genes [6, 29-31]. Then, we characterized the structural features of these chicken putative lncRNA transcripts in comparison to the human and mouse lncRNAs available in Ensembl and compared them with the protein-coding RNAs available in Ensembl for these three species. Overall, the features observed for the chicken lncRNAs are consistent with those observed in mammals in the human and mouse ENCODE projects [6] ...
Long non-coding RNA HOTAIR exerts regulatory functions in various biological processes in cancer cells, such as proliferation, apoptosis, mobility, and invasion. We previously found that HOX transcript antisense RNA (HOTAIR) is a negative prognostic factor and exhibits oncogenic activity in hepatocellular carcinoma (HCC). In this study, we aimed to investigate the role and molecular mechanism of HOTAIR in promoting HCC cell migration and invasion. Firstly, we profiled its gene expression pattern by microarray analysis of HOTAIR loss in Bel-7402 HCC cell line. The results showed that 129 genes were significantly down-regulated, while 167 genes were significantly up-regulated (fold change |2, p | 0.05). Bioinformatics analysis indicated that RNA binding proteins were involved in this biological process. HOTAIR suppression using RNAi strategy with HepG2 and Bel-7402 cells increased the mRNA and protein expression levels of RNA binding motif protein 38 (RBM38). Moreover, the expression levels of RBM38 in
LncRNAs are among the least well-understood of non-protein-coding RNAs. They were previously considered merely transcriptional "noise" [11] but have increasingly garnered attention in recent years. Newer studies have shown that lncRNAs are involved in EMT. For example, several lncRNAs can be involved in the regulation or activation of the WNT signaling pathway in the Twist-induced EMT process [20]. H19 can promote pancreatic cancer metastasis by derepressing let-7s suppression on its target HMGA2-mediated EMT [21]. However, to our knowledge, no previous study has focused on the microarray expression profile of lncRNAs in LECs during EMT. Thus, we conducted the current study to assess the role of lncRNAs in the development and progression of EMT in LECs from the perspective of lncRNA.. In this study, we chose the HLE B-3 cell line. It is a primary cell line of LECs that is immortalized via infection with an adenovirus 12-SV40 virus, and can be used to investigate HLE physiology and cataracts ...
Accumulating evidence indicates that lncRNAs may have potential as new biomarkers to predict prognosis of different human cancers. HOTAIR lncRNA, transcribed from the human HOX locus, has been suggested to regulate gene expression of important target genes and up-regulation has been noted in malignancies. The role of HOX transcript antisense RNA in acute myeloid leukemia (AML) was investigated in the present case control study. HOTAIR expression was evaluated in blood samples of twenty five de novo AML patients and fifty healthy controls using real-time quantitative reverse transcription-PCR (qRT-PCR). Our results demonstrated no significant differences in HOTAIR lncRNA expression level between AML patients and healthy individuals. The obtained data indicate that HOTAIR is not an informative and reliable biomarker for AML diagnosis, although our results should be confirmed in further studies.
The role of long noncoding RNAs (lncRNAs) in acute myeloid leukemia (AML) is becoming increasingly concerned. Previous studies have reported that the lncRNA small nucleolar RNA host gene 1 (SNHG1) is involved in multiple human malignant tumors, while its expression and role in AML is still unexplored. Here, we show that SNHG1 is highly expressed in AML specimens from non-M3 patients, as well as AML cell lines. Meanwhile, upregulation of SNHG1 is correlated with poor prognosis. Notably, SNHG1 facilitates the proliferation and inhibits the apoptosis of AML cells in vitro. Consistent with these findings, knockdown of SNHG1 significantly inhibits AML progression in an immunodeficient mouse model. Mechanistically, we found that an anti-tumor microRNA-101 (miR-101) is upregulated and its target genes are downregulated in AML cells after SNHG1 knockdown. Further investigations display that SNHG1 can serve as a competing endogenous RNA (ceRNA) to inhibit miR-101. In conclusion, our data indicate that ...
Long noncoding RNAs (lncRNAs) have emerged as important regulators in the development and progression of gastric cancer (GC). ARHGAP27P1 is a pseudogene-derived lncRNA, and it has been found to be associated with GC in our preliminary study, but this association has not been studied further. Herein, we confirmed that ARHGAP27P1 was significantly downregulated in GC tissues, plasma and cells. Low expression of ARHGAP27P1 was closely associated with advanced TNM stage, increased invasion depth and lymphatic metastasis. Low ARHGAP27P1 expression also predicted a poor prognosis in GC patients. Functionally, overexpression of ARHGAP27P1 inhibited proliferation, invasion, and migration in GC cells, while silencing of ARHGAP27P1 showed the opposite effects. Mechanistic investigations showed that ARHGAP27P1 had a key role in G0/G1 arrest. We further demonstrated that ARHGAP27P1 was associated with Jumonji-domain containing 3 (JMJD3) and that this association was required for the demethylation of H3K27me3,
Full Text - Transforming growth factor-β1 (TGFβ1)-induced differentiation into and the activation of myofibroblasts have been regarded as critical events in benign prostatic hyperplasia (BPH); however, the underlying mechanisms of BPH pathogenesis remain unclear. Microarray profiling, STRING analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, and Gene Ontology (GO) enrichment analysis were performed to confirm the candidate genes and long non-coding RNA (lncRNAs) related to BPH. Collagen Type III (COL3A1) was significantly upregulated by TGFβ1 in prostate stromal cells (PrSCs) and might be involved in DNM3OS function in myofibroblasts upon TGFβ1 stimulation. Upon TGFβ1 stimulation, COL3A1 protein was decreased by DNM3OS silencing. miR-29a and miR-29b could directly bind to the DNM3OS and COL3A1 3' untranslated region (UTR)s to negatively regulate their expression, and by serving as a competing endogenous RNAs (ceRNA), DNM3OS competed with
The human genome encodes thousands of long non-coding RNAs (lncRNAs), the majority of which are poorly conserved and uncharacterized. Here we identify a primate-specific lncRNA (CHROME), elevated in the plasma and atherosclerotic plaques of individuals with coronary artery disease, that regulates cellular andsystemic cholesterol homeostasis. LncRNA CHROME expression is influenced by dietary and cellular cholesterol via the sterol-activated liver X receptor transcription factors, which control genes mediating responses to cholesterol overload. Using gain- and loss-of-function approaches, we show that CHROME promotes cholesterol efflux and HDL biogenesis by curbing the actions of a set of functionally related microRNAs that repress genes in those pathways. CHROME knockdown in human hepatocytes and macrophages increases levels of miR-27b, miR-33a, miR-33b and miR-128, thereby reducing expression of their overlapping target gene networks and associated biologic functions. In particular, cells lacking CHROME
The noncoding form of the steroid receptor RNA activator (SRA, AF092038, http://annolnc.cbi.pku.edu.cn/cases/SRA) has been reported to function as a noncoding RNA by Lanz et al. [41] and is the first lncRNA that has experimentally derived secondary structure, which was derived by Novikova et al. [42]. In the interactive secondary structure plot with vertebrate phyloP score as color overlay, it is easy to identify two conserved regions. One is a hairpin region from base 30 to 72 (Fig. 3a). With approximately 75% of bases colored red, this conserved sub-structure is clearly distinguishable from others. In fact, this region corresponds to the most conserved H2 sub-structure highlighted by Novikova et al. [42]. Site-directed mutagenesis of this region reduced the co-activation performance of SRA by 40% [43], suggesting the importance of lncRNA secondary structure on its function [44]. The other distinct region is a three-way junction hairpin sub-structure from base 506 to 555 with 78% colored red ...
Colorectal cancer (CRC) is one of the most common types of cancer worldwide. However, the molecular mechanisms involved in CRC initiation and progression is remained to be unknown. It seems that lncRNAs, as the main and lengthy functional transcripts of the genome, have important roles in different cancers such as CRC. CRC-related lncRNAs are reported to be involved in diverse molecular processes such as metastasis, invasion, cell proliferation, and apoptosis. This study was aimed to analyse the expression level of lncRNA SNHG1 in colorectal adenocarcinoma and normal tissues. We performed an in silico analysis on a large cohort and confirmed the results by experimental analysis of clinical samples through real-time PCR. Our findings demonstrated that that SNHG1 is potentially overexpressed in tumor tissues compared with adjacent normal tissues. The expression level of SNHG1 was shown to be potentially associated with clinicopathological features of tumors. The current study suggests the potential role
Researchers have found a set of long non-coding RNAs (lncRNAs) - RNA molecules with no protein-coding capacity - that participate in the metastatic process of ovarian cancer cells.. Inhibiting one of these molecules, called DNM3OS, reduced migration and invasion, suggesting that targeting lncRNAs might be a viable approach for treating ovarian cancer.. The study, "Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition," was published in the journal Nature Communications.. Metastasis, which refers to the spread of cancer cells, is a common occurrence in patients with ovarian cancer and occurs in as many as 80 percent of patients. Metastasis is dependent on the ability of cancer cells to undergo a process called epithelial-to-mesenchymal transition (EMT), which allows cells to detach from other cancer cells and enter circulation.. Recent studies have suggested that lncRNAs are involved in the metastatic process. These molecules are known to regulate gene ...
Hepatocellular carcinoma (HCC) is a common malignant tumor with high fatality rate. Recent studies reported that up-regulation of long non-coding RNA antisense non-coding RNA in the INK4 locus (lncRNA ANRIL) was found in HCC tissues, and which could affect HCC cells biological processes. However, the potential molecular mechanism of ANRIL in HCC is still unclear. The study aimed to uncover the effect of ANRIL on HepG2 cells growth, migration and invasion. The knockdown expression vectors of ANRIL were transfected into HepG2 cells, and qRT-PCR, CCK-8, flow cytometry, Transwell and western blot assays were performed to analyze the effect of ANRIL on cell proliferation, apoptosis, migration and invasion. The relative expression of miR-191 was then examined in ANRIL knockdown vector transfected cells. These experiments were repeated again for exploring the effect of miR-191 on HepG2 cells. NF-κB and Wnt/β-catenin signaling pathways were examined by using western blot assay. Knockdown of ANRIL inhibited
The steroid receptor RNA activator gene (SRA1) generates two distinct entities. SRA RNA coactivates several NRs whereas SRA protein (SRAP) is suspected to regulate the activity of several transcription factors, including estrogen receptors (ER). Splicing of SRA intron-1 is the major event defining SRAP coding frame. Fully spliced, coding SRA and intron-1 retained, non-coding SRA coexist in breast cancer cells. The relative proportion between the two types of SRA RNA maintains a balance between two genetically linked entities, SRA and SRAP. In this study, a minigene model was used to demonstrate that the primary sequence of SRA exon-1-intron-1-exon-2 is sufficient for alternative splicing of SRA intron-1. In addition, a modified oligoribonucleotidic construct promotes SRA intron-1 retention in breast cancer cells. This oligoribonucleotide differentially alters estradiol-induced transcription of ER regulated genes. Together, results presented herein demonstrate that the SRA-SRAP balance, which can ...
Long non-coding RNAs (lncRNAs), representing a large proportion of non-coding transcripts across the human genome, are evolutionally conserved and biologically functional. At least one-third of the phenotype-related loci identified by genome-wide association studies (GWAS) are mapped to non-coding intervals. However, the relationships between phenotype-related loci and lncRNAs are largely unknown. Utilizing the 1000 Genomes data, we compared single-nucleotide polymorphisms (SNPs) within the sequences of lncRNA and protein-coding genes as defined in the Ensembl database. We further annotated the phenotype-related SNPs reported by GWAS at lncRNA intervals. Because prostate cancer (PCa) risk-related loci were enriched in lncRNAs, we then performed meta-analysis of two existing GWAS for discovery and an additional sample set for replication, revealing PCa risk-related loci at lncRNA regions. The SNP density in regions of lncRNA was similar to that in protein-coding regions, but they were less ...
Trisomy 21, also known as Down Syndrome (DS), is the most common chromosome abnormality and causes intellectual disability. Long non-coding RNA (lncRNA) growth arrest-specific 5 (GAS5), whose differential expression has recently been reported in patients with Klinefelter syndrome, has been addressed to play a role in the development of inflammatory and autoimmune diseases, vascular endothelial cells apoptosis and atherosclerosis, all being common features in patients with DS. Therefore, the aim of this study was to assess the lncRNA GAS5 expression profile in DS patients and in controls. lncRNA GAS5 levels were evaluated by qRT-PCR assay in 23 patients with DS and 23 age-matched controls. A significant lncRNA GAS5 down-regulation was observed in patients with DS by RT-PCR analysis, The RNA sequencing experiments confirmed the qRT-PCR data. LncRNA GAS5 down-expression may play a role in the development of some typical features of the patients with DS and, particularly, in inflammatory and ...
TY - JOUR. T1 - Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. AU - Goff, Loyal A.. AU - Groff, Abigail F.. AU - Sauvageau, Martin. AU - Trayes-Gibson, Zachary. AU - Sanchez-Gomez, Diana B.. AU - Morse, Michael. AU - Martin, Ryan D.. AU - Elcavage, Lara E.. AU - Liapis, Stephen C.. AU - Gonzalez-Celeiro, Meryem. AU - Plana, Olivia. AU - Li, Eric. AU - Gerhardinger, Chiara. AU - Tomassy, Giulio S.. AU - Arlotta, Paola. AU - Rinn, John L.. PY - 2015/6/2. Y1 - 2015/6/2. N2 - Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNA-null mutant mouse models to investigate the spatiotemporal expression of lncRNAs in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncRNA loci. We show that ...
Approach and Results-Aortic and coronary VSMCs were cultured on hydrogel substrates mimicking physiological and pathological extracellular matrix stiffness. Total RNAseq was performed to compare the SS transcriptome profiles of aortic and coronary VSMCs. We identified 3098 genes (2842 protein coding and 157 lncRNA) that were stiffness sensitive in both aortic and coronary VSMCs (false discovery rate ,1%). Hierarchical clustering revealed that aortic and coronary VSMCs grouped by stiffness rather than cell origin. Conservation analyses also revealed that SS genes were more conserved than stiffness-insensitive genes. These VSMC SS genes were less tissue-type specific and expressed in more tissues than stiffness-insensitive genes. Using unbiased systems analyses, we identified MALAT1 as an SS lncRNA that regulates stiffness-dependent VSMC proliferation and migration in vitro and in vivo. ...
Heart development is a dynamic process that involves transcriptome expression changes and cis (enhancer and promoter activities) and trans (transcription factor binding) regulation. Much previous work has established the regulatory mechanisms in this process.1-3 As the importance of noncoding RNAs in regulating expression and epigenetic modifications is gaining recognition in heart development, researchers have discovered long noncoding RNA (lncRNA) that directly regulate heart development and disease.4,5 For example, the lncRNA Fendrr binds to the PRC2 and TrxG/MLL complex and acts as a modulator of chromatin signatures to regulate gene activity in mouse heart.6 The lncRNA Braveheart also interacts with a component of the PRC2 complex during cardiac commitment.7 Interestingly, lncRNAs have been implicated in common cardiac congenital abnormalities, such as ventricular septal defects.8 They have also been implicated in aberrant chromatin conformations in the region of enhancer, silencer, and ...
Despite increasing evidence to indicate that long non-coding RNAs (lncRNAs) are novel regulators of immunity, there has been no systematic attempt to identify and characterise the lncRNAs whose expression are changed following the induction of the innate immune response. To address this issue, we have employed next generation sequencing data to determine the changes in the lncRNA profile in 4 human (monocytes, macrophages, epithelium and chondrocytes) and 4 mouse cells types (RAW 264.7 macrophages, bone marrow derived macrophages, peritoneal macrophages and splenic dendritic cells) following exposure to the pro-inflammatory mediators, lipopolysaccharide (LPS) or interleukin-1. We show differential expression of 204 human and 210 mouse lncRNAs, with positional analysis demonstrating correlation with immune related genes. These lncRNAs are predominantly cell-type specific, composed of large regions of repeat sequences and show poor evolutionary conservation. Comparison within the human and mouse
Until now, lots of works indicate that lncRNAs play vital regulatory roles in tumorigenesis and tumor progression and act as potential oncogenes or tumor suppressor genes [19, 20]. Recently, several lncRNAs have been found to play an emerging role in various cancers, contributing to tumor proliferation, apoptosis, and survival, such as PANDAR [18], MEG3 [21].. BANCR, firstly found by Flockhart RJ et al. [22], has been discovered to be up-regulated in some kinds of tumors, including retinoblastoma, melanoma, papillary thyroid carcinoma, gastric cancer and hepatocellular carcinoma. In contrast, decreased expression of BANCR has been found in both colorectal and lung cancers. BANCR promotes cell proliferation by regulating MAPK pathway activation in both malignant melanoma and lung carcinoma [14, 23]. Besides, downregulation of BANCR promotes colorectal cancer cell proliferation through decreasing expression of p21 protein [10]. Furthermore, BANCR expression promoted non-small cell lung cancer cell ...
Hui Cao, Department of General Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 1630, Dongfang Road, Shanghai 200127, P.R. China. Phone: 86-021-68383711; Fax: 86-021-68383731; E-mail: huicaorj{at}126.com; and Jia Xu, E-mail: xujia1976{at}126.com ...
1. WahleE (1991) A novel poly(A)-binding protein acts as a specificity factor in the second phase of messenger RNA polyadenylation. Cell 66: 759-768.. 2. KuhnU, NemethA, MeyerS, WahleE (2003) The RNA binding domains of the nuclear poly(A)-binding protein. J Biol Chem 278: 16916-16925.. 3. KerwitzY, KuhnU, LilieH, KnothA, ScheuermannT, et al. (2003) Stimulation of poly(A) polymerase through a direct interaction with the nuclear poly(A) binding protein allosterically regulated by RNA. Embo J 22: 3705-3714.. 4. KuhnU, GundelM, KnothA, KerwitzY, RudelS, et al. (2009) Poly(A) tail length is controlled by the nuclear poly(A)-binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor. J Biol Chem 284: 22803-22814.. 5. KuhnU, WahleE (2004) Structure and function of poly(A) binding proteins. Biochim Biophys Acta 1678: 67-84.. 6. ApponiLH, LeungSW, WilliamsKR, ValentiniSR, CorbettAH, et al. (2010) Loss of nuclear poly(A)-binding protein 1 ...
Sigma-Aldrich offers abstracts and full-text articles by [Zhang, DD; Wang, WT; Xiong, J; Xie, XM; Cui, SS; Zhao, ZG; Li, MJ; Zhang, ZQ; Hao et al.].
Long stretches of DNA once considered inert "dark matter" of the genome - the over 98% of DNA that doesnt code for proteins - appear to be uniquely active in a part of the brain known to control the bodys 24-hour cycle, according to researchers at the National Institutes of Health. The findings appear in the August 14th edition of the journal Proceedings of the National Academy of Sciences [1].. ...
CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Cell and Molecular Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science & Technology of China, Hefei, Anhui, ChinaTranslational Research Institute, School of Medicine, Henan Provincial Peoples Hospital, Henan University, Zhengzhou, China ...
BioMed Research International is a peer-reviewed, Open Access journal that publishes original research articles, review articles, and clinical studies covering a wide range of subjects in life sciences and medicine. The journal is divided into 55 subject-specific sections.
BioMed Research International is a peer-reviewed, Open Access journal that publishes original research articles, review articles, and clinical studies covering a wide range of subjects in life sciences and medicine. The journal is divided into 55 subject-specific sections.
Sigma-Aldrich offers abstracts and full-text articles by [Laetitia Francelle, Laurie Galvan, Marie-Claude Gaillard, Fanny Petit, Benoît Bernay, Martine Guillermier, Gilles Bonvento, Noëlle Dufour, Jean-Marc Elalouf, Philippe Hantraye, Nicole Déglon, Michel de Chaldée, Emmanuel Brouillet].
Keywords: lengthy non-coding RNA (lncRNA) immunoprecipitation MS2 coat-binding proteins ribonucleoprotein complicated (RNP) RT-PCR biochemistry 1 Intro Recently it is becoming clear RGS12 a significant part of the transcriptome encodes gene items that tend unable to WP1130 become translated into protein. Such transcripts higher than ~200-nt in length are termed long non-coding RNAs (lncRNAs) and they may either lie in intergenic regions (lincRNAs) or overlap with protein-coding genes. That the number of lncRNAs encoded by the human genome likely far outstrips the number of protein-coding mRNAs [1] indicates that lncRNAs generally are the products of an impressive level of faulty transcription or alternatively serve yet-to-be-discovered cellular functions. Differentiating between these two possibilities requires the careful application of biochemical techniques. For those few lncRNAs that have an ascribed function [2] a combination of genetic and biochemical experiments has moved the field ...
Recent studies show that only a small part of the human transcriptome is involved in the protein-coding process [1]. Long non-coding RNAs (lncRNAs) comprise the majority of transcripts; however, little is known about the function of lncRNAs [2]. The GENCODE project discovered more than 14,000 lncRNA transcripts from approximately 9,000 gene loci [3]. The lncRNA database collected a few hundred of high-confidence, experimentally validated lncRNAs [4]. For example, the Xist RNA of humans is a large RNA sequence (19 kb) that has remained untranslated [5]. Xist RNA has been proven to have an important function in regulating X-inactivation [6, 7]. Although an increasing list of evidence demonstrates that lncRNAs may be involved in multiple biological processes, including epigenetic regulation, chromatin remodeling, and cell proliferation and differentiation, the molecular mechanisms underlying the functions of lncRNAs still remain largely elusive.. In general, lncRNAs function with their binding ...
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. LncRNAs have been recently recognized as the hallmark features in various diseases. In hematopoiesis, they regulate development at almost every stage of cell lineage differentiation; therefore, abnormal expression of lncRNAs may lead to different hematopoietic disorders. Until now there has been almost no information available about lncRNA deregulation and role in myelodysplastic syndromes (MDS).. We perform genome-wide screening of lncRNA levels in MDS patients and compare expression profiles between various risk groups of patients and healthy subjects, to find lncRNAs with altered levels in MDS. This knowledge will help us to better understand the pathogenesis of MDS and identify lncRNAs that may represent candidate diagnostic and prognostic molecular markers of the disease.. ...
Functional Integration of Large ncRNAs in the Molecular Circuitry Controlling Cell State. Mitchell Guttman. Graduate Fellow. Broad Institute of MIT and Harvard. Massachusetts Institute of Technology Monday, February 27, 2012. 4 p.m, Caspary Auditorium. Refreshments 3:45 p.m.. Recommended Readings:. Yang, LG; Lin CR; Rosebfeld MG. 2011. A lincRNA switch for embryonic stem cell fate. Cell Research 21(12):1646-1648. DOI:10.1038/cr.2011.166. Guttman M; Donachey J; Carey BW; et al. 2011. lincRNAs act in the circuitry controlling pluripotency and differentiation. NATURE. 477(7364):295-U60. DOI:10.1038/nature10398. Loewer S; Cabili MN; Guttman M: et al. 2010. Large intergenic non-coding RNA-RoR modeulates reprogramming of human induced pluripotent stem cells. NATURE Genetics. 42(12):1113- DOI: 10.1038/ng.710. Huarte M; Guttman M; Feldser D; et al. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in thep53 response. Cell. 142(3):409-419. ...
Background Long non-coding RNAs (lncRNAs) have been studied extensively over the past few years. Large numbers of lncRNAs have been identified in mouse, rat, and human, and some of them have been shown to play important roles in muscle development and myogenesis. However, there are few reports on the characterization of lncRNAs covering all the development stages of skeletal muscle in livestock. Results RNA libraries constructed from developing longissimus dorsi muscle of fetal (45, 60, and 105 days of gestation) and postnatal (3 days after birth) goat (Capra hircus) were sequenced. A total of 1,034,049,894 clean reads were generated. Among them, 3981 lncRNA transcripts corresponding to 2739 lncRNA genes were identified, including 3515 intergenic lncRNAs and 466 anti-sense lncRNAs. Notably, in pairwise comparisons between the libraries of skeletal muscle at the different development stages, a total of 577 transcripts were differentially expressed (P | 0.05) which
Long non-coding RNAs (lncRNA) are classified as a kind of RNA, which are longer than 200 nucleotides in length and cannot be translated into proteins. Multiple studies have demonstrated that lncRNAs are involved in various cellular processes, including proliferation, differentiation, cell death, and metastasis. In addition, aberrant expression of lncRNAs has been discovered in human tumors, where they function as either oncogenes or tumor suppressor genes. Among numerous lncRNAs, we focus on ZNFX1 antisense RNA 1 (ZFAS1), a well-known lncRNA that is aberrant overexpression in various tumors, including melanoma, esophageal squamous cell carcinoma, non-small cell lung cancer, gastric cancer, colon cancer, and Hepatocellular carcinoma, in which it functions as oncogene. In contrast, ZFAS1 is downregulated in breast cancer, which may function as tumor suppressor gene. In this review, we provide an overview of current evidence concerning the role and potential clinical utilities of ZFAS1 in human cancers.
Additional file 7: of Long non-coding RNA NEAT1-modulated abnormal lipolysis via ATGL drives hepatocellular carcinoma proliferation
Search "+Long non-coding RNA +hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples -kallisto +Landscape of somatic mutations in 560 breast cancer whole-genome sequences ...
The article "Effects of long non-coding RNA URHC on proliferation, apoptosis and invasion of colorectal cancer cells, by Z.-G. Gu, G.-H. Shen, J.-H. Lang, W.-X. Huang, Z.-H. Qian, J. Qiu, published in Eur Rev Med Pharmacol Sci 2018; 22 (6): 1658-1664-DOI: 10.26355/eurrev_201803_14577-PMID: 29630109" has been withdrawn from the authors. The Publisher apologizes for any inconvenience this may cause. httpss://www.europeanreview.org/article/14577. ...
PubMed journal article Long Non-Coding RNA Uc.187 Is Upregulated in Preeclampsia and Modulates Proliferation, Apoptosis, and Invasion of HTR-8/SVneo Trophoblast Cell were found in PRIME PubMed. Download Prime PubMed App to iPhone, iPad, or Android