Large Intergenic Noncoding RNAs Research Articles

Differential Expression of lincRNA-ROR Spliced Transcript Variants in Breast Cancer.

We investigated the expression pattern of a human stem cell-specific, large intergenic noncoding RNA (lincRNA) regulator of reprogramming (lincRNA-ROR) and its spliced transcript variants in breast tumors. Breast cancer is the leading cause of cancer mortality in women; therefore, finding a reliable diagnostic tumor marker, based on the molecular profile of tumor cells, is warranted. qRT-PCR was used to investigate the expression alteration of a specific stem cell-related lincRNA and its spliced transcript variants in breast tumors which provided by the Iran National Tumor Bank (2014-2016). Suitability of lincRNA-ROR and expression alterations of its spliced transcript variants as breast tumor biomarkers were examined by ROC curve analysis. Expression was significantly upregulated in lincRNA-ROR variants 1 (NR-048536) and 4 (AB844432) and downregulated in variant 3 (AB844431), with expression levels failing to distinguish between breast tumor types, grades, and malignancy stages. Whereas ROC curve analysis gave good scores to the expressions of variants 1 (AUC=0.7675, P=0.003) and 3 (AUC=0.9383, P=0.00173), suggesting their suitability as potential breast tumor biomarkers, it gave an AUC score of 0.6033 for lincRNA-ROR spliced variant 4 (P=0.4118), denoting its unsuitability as a breast cancer biomarker. Aberrant expressions of lincRNA-ROR spliced transcript variants could serve as reliable biomarkers with potential usefulness in breast cancer diagnosis. However, further research should elucidate the role and tissue expression of lincRNA-ROR spliced transcript variants in various cancers.

LINC00669 promotes lung adenocarcinoma growth by stimulating the Wnt/β-catenin signaling pathway.

Lung cancer poses severe threats to human health. It is indispensable to discover more druggable molecular targets. We identified a novel dysregulated long non-coding RNA (lncRNA), LINC00669, in lung adenocarcinoma (LUAD) by analyzing the TCGA and GEO databases. Pan-cancer analysis indicated significantly upregulated LINC00669 across 33 cancer types. GSEA revealed a tight association of LINC00669 with the cell cycle. We next attempted to improve the prognostic accuracy of this lncRNA by establishing a risk signature in reliance on cell cycle genes associated with LINC00669. The resulting risk score combined with LINC00669 and stage showed an AUC of 0.746. The risk score significantly stratified LUAD patients into low- and high-risk subgroups, independently predicting prognosis. Its performance was verified by nomogram (C-index=0.736) and decision curve analysis. Gene set variation analysis disclosed the two groups' molecular characteristics. We also evaluated the tumor immune microenvironment by dissecting 28 infiltrated immune cells, 47 immune checkpoint gene expressions, and immunophenoscore within the two subgroups. Furthermore, the risk signature could predict sensitivity to immune checkpoint inhibitors and other anticancer therapies. Eventually, in vitro and in vivo experiments were conducted to validate LINC00669's function using qRT-PCR, CCK8, flow cytometry, western blot, and immunofluorescence staining. The gain- and loss-of-function study substantiated LINC00669's oncogenic effects, which stimulated non-small cell lung cancer cell proliferation but reduced apoptosis via activating the Wnt/β-catenin pathway. Its oncogenic potentials were validated in the xenograft mouse model. Overall, we identified a novel oncogenic large intergenic non-coding RNA (lincRNA), LINC00669. The resulting signature may facilitate predicting prognosis and therapy responses in LUAD.

HOTAIR interacts with PRC2 complex regulating the regional preadipocyte transcriptome and human fat distribution.

Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA HOTAIR (HOX transcript antisense RNA) is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with polycomb repressive complex 2 (PRC2) and we identify core HOTAIR-PRC2 target genes involved in adipocyte lineage determination. Repression of target genes coincides with PRC2 promoter occupancy and H3K27 trimethylation. HOTAIR is also involved in modifying the gluteal adipocyte transcriptome through alternative splicing. Gluteal-specific expression of HOTAIR is maintained by defined regions of open chromatin across the HOTAIR promoter. HOTAIR expression levels can be modified by hormonal (estrogen, glucocorticoids) and genetic variation (rs1443512 is a HOTAIR eQTL associated with reduced gynoid fat mass). These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.

Regulations of LINC0196/miR-584-5p/miR-34a-5p/TRIM59 on Progression of Pediatric Neuroblastoma.

This work was to study the regulatory mechanism of large intergenic non-coding RNA 0196 (LINC0196), miR-584-5p, miR-34a-5p, and tripartite motif 59 (TRIM59) on neuroblastoma. The interaction among the four was analyzed to provide a research basis for the clinical treatment of neuroblastoma at the molecular level. The human neuroblastoma SK-N-SH cells were collected and cultured. According to the transfection methods, the cells were divided into control group (without any treatment), si-LINC0196 group (si-LINC0196 transfection), si-LINC0196-NC group (si-LINC0196 vector transfection), miR-584-5p group (miR-584-5p mimic transfection), miR-584-5p-NC group (miR-584-5p inhibitor transfection), miR-34a-5p group (miR-34a-5p mimic transfection), and miR-34a-5p-NC group (miR-34a-5p inhibitor transfection). The proliferation, migration, and apoptosis of SK-N-SH cells in each group were compared. The effects of LINC0196, miR-584-5p, miR-34a-5p, and TRIM59 were evaluated. The expressions of LINC0196 and TRIM59 in SK-N-SH cells in si-LINC0196, miR-584-5p, and miR-34a-5p groups were up-regulated. miR-584-5p and miR-34a-5p in si-LINC0196-NC, miR-584-5p-NC, and miR-34a-5p-NC groups decreased significantly (P < 0.05). The proliferation rate, migration rate, and invasiveness of SK-N-SH cells in miR-584-5p and miR-34a-5p groups were lower than those in si-LINC0196-NC, miR-584-5p-NC, and miR-34a-5p-NC groups, while the apoptosis rate increased (P < 0.05). After miR-584-5p and miR-34a-5p transfections, the relative activities of WT-LINC0196 and WT-TRIM59 dual luciferase were greatly inhibited (P < 0.05). LINC0196 could regulate TRIM59 by regulating miR-584-5p and miR-34a-5p, thereby indirectly regulating cell proliferation, apoptosis, migration, and invasion of SK-N-SH cells.

Clinicopathological and prognostic significance of long non-coding RNA-ROR in cancer patients: A systematic review and meta-analysis.

Background:Accumulating studies have focused on the clinicopathological and prognostic roles of large intergenic noncoding RNA regulator of reprogramming (lincRNA-ROR) in cancer patients. However, the results were controversial and unconvincing. Thus, we performed a meta-analysis to assess the associations between lincRNA-ROR expression and survival and clinicopathological characteristics of cancer patients.Methods:Hazard ratios for overall survival and disease-free survival with their 95% confidence intervals were used to evaluate the role of lincRNA-ROR expression in the prognosis of cancer patients. Risk ratios with their 95% confidence intervals were applied to assess the relationship between lincRNA-ROR expression and clinicopathological parameters.Results:A total of 18 articles with 1441 patients were enrolled. Our results indicated that high lincRNA-ROR expression was significant associated with tumor size, TNM stage, clinical stage, lymph metastasis, metastasis and vessel invasion of cancer patients. There were no correlations between high lincRNA-ROR expression and age, gender, infiltration depth, differentiation, serum CA19–9 and serum CEA of cancer patients. In addition, high lincRNA-ROR expression was associated with shorter Overall survival and disease-free survival on both univariate and multivariate analyses. Meanwhile, there were no obvious publication bias in our meta-analysis.Conclusions:LincRNA-ROR expression was associated with the clinicopathological features and outcome of cancer patients, which suggested that lincRNA-ROR might serve as a potential biomarker for cancer prognosis.Ethical approval:Since this study is on the basis of published articles, ethical approval and informed consent of patients are not required.

Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms.

Long non-coding RNAs (lncRNAs) are key regulators of major biological processes and their functional modes are dictated by their subcellular localization. Relative nuclear enrichment of lncRNAs compared to mRNAs is a prevalent phenomenon but the molecular mechanisms governing their nuclear retention in cells remain largely unknown. Here in this study, we harness the recently released eCLIP data for a large number of RNA-binding proteins (RBPs) in K562 and HepG2 cells and utilize multiple bioinformatics methods to comprehensively survey the roles of RBPs in lncRNA nuclear retention. We identify an array of splicing RBPs that bind to nuclear-enriched lincRNAs (large intergenic non-coding RNAs) thus may act as trans-factors regulating their nuclear retention. Further analyses reveal that these RBPs may bind with distinct core motifs, flanking sequence compositions, or secondary structures to drive lincRNA nuclear retention. Moreover, network analyses uncover potential co-regulatory RBP clusters and the physical interaction between HNRNPU and SAFB2 proteins in K562 cells is further experimentally verified. Altogether, our analyses reveal previously unknown factors and mechanisms that govern lincRNA nuclear localization in cells.

LncRNA Pulldown Combined with Mass Spectrometry to Identify the Novel lncRNA-Associated Proteins.

Long non-coding RNAs (LncRNAs) are non-protein coding transcripts longer than 200 nucleotides. Recent studies have revealed that nearly 80% of transcripts in human cells are lncRNA species. Based on their genomic location, most lncRNAs can be characterized as large intergenic non-coding RNAs, natural antisense transcripts, pseudogenes, and long intronic ncRNAs, as well as other divergent transcripts. However, despite mounting evidence suggesting that many lncRNAs are likely to be functional, only a small proportion has been demonstrated to be biologically and physiologically relevant due to their lower expression levels and current technique limitations. Thus, there is a greater need to design and develop new assays to investigate the real function of lncRNAs in depth in various systems. Indeed, several methods such as genome-wide chromatin immunoprecipitation-sequencing (ChIP-seq) and RNA immunoprecipitation followed by sequencing (RIP-seq) have been developed to examine the genome localization of lncRNAs and their interacting proteins in cells. Here, we describe an open-ended method, LncRNA pulldown assay, which has been frequently used to identify lncRNA interacting protein partners in a cellular context. We provide a detailed protocol for this assay with hands-on tips based on our own experience working in the lncRNA field.

Rapid and Scalable Profiling of Nascent RNA with fastGRO

SUMMARYGenome-wide profiling of nascent RNA has become a fundamental tool to study transcription regulation. Unlike steady-state RNA-sequencing (RNA-seq), nascent RNA profiling mirrors real-time activity of RNA polymerases and provides an accurate readout of transcriptome-wide variations. Some species of nuclear RNAs (i.e., large intergenic noncoding RNAs [lincRNAs] and eRNAs) have a short half-life and can only be accurately gauged by nascent RNA techniques. Furthermore, nascent RNA-seq detects post-cleavage RNA at termination sites and promoter-associated antisense RNAs, providing insights into RNA polymerase II (RNAPII) dynamics and processivity. Here, we present a run-on assay with 4-thio ribonucleotide (4-S-UTP) labeling, followed by reversible biotinylation and affinity purification via streptavidin. Our protocol allows streamlined sample preparation within less than 3 days. We named the technique fastGRO (fast Global Run-On). We show that fastGRO is highly reproducible and yields a more complete and extensive coverage of nascent RNA than comparable techniques can. Importantly, we demonstrate that fastGRO is scalable and can be performed with as few as 0.5 × 106 cells.

The role of the novel LincRNA uc002jit.1 in NF-kB-mediated DNA damage repair in acute myeloid leukemia cells

The roles and therapeutic potential of long noncoding RNAs (lncRNAs) in acute myeloid leukemia (AML) have attracted increased attention. However, many lncRNAs have not been annotated in AML, and their predictive value for AML therapy remains unclear. In this study, we identified a novel large intergenic noncoding RNA uc002jit.1 (D43770) from a lncRNA microarray. We first proved uc002jit.1 is a target gene of nuclear factor kappa B/RELA, RELA regulated uc002jit.1 transcription by binding to its promoter. Additionally, uc002jit.1 knockdown impaired the stability of poly (ADP-ribose) polymerase 1 (PARP1) mRNA, and then reduced PARP1 protein content and PARylation level upon DNA damage, thus inhibiting DNA damage repair in AML cells. Moreover, uc002jit.1 knockdown significantly inhibited AML cells proliferation and increased the sensitivity to chemotherapeutic drugs in vitro as well as in a mouse model in vivo. Overall, our study indicated that uc002jit.1 may be associated with the occurrence and prognosis of AML and could be a new diagnostic/prognostic biomarker and therapeutic target for AML.

LincRNA Cox-2 Regulates Lipopolysaccharide-Induced Inflammatory Response of Human Peritoneal Mesothelial Cells via Modulating miR-21/NF-κB Axis.

Postoperative peritoneal adhesion (PPA) is a common postoperative complication caused by any peritoneal inflammatory process. This study aimed to identify the biological function of large intergenic non-coding RNAs (lincRNAs) Cox-2 in the inflammation reaction of adhesion formation. The Cox-2 expression in peritoneal adhesion tissues and normal tissues was detected. The human peritoneal mesothelium cells (HPMCs) were treated with lipopolysaccharide (LPS) to induce inflammatory injury. The effect of Cox-2 suppression on cell viability, apoptosis and inflammatory factors of LPS induced HPMCs injury were explored. The regulatory correlation between Cox-2 and miR-21, as well as the targeted genes of miR-21 were identified. Meanwhile, the regulatory mechanism of Cox-2/miR-21 axis on NF-κB pathway was explored. It indicated that Cox-2 was highly expressed in peritoneal adhesion tissues compared with that in normal tissues. Suppression of Cox-2 ameliorated LPS induced HMPCs injury as cell viability was promoted, and cell apoptosis and the production of inflammatory factors were inhibited. And suppression of Cox-2 reversed the LPS induced HPMCs injury by regulation of miR-21 negatively. miR-21 was negatively correlated with TLR4, and TLR4 was predicted as target gene of miR-21. Furthermore, the suppression of miR-21 on LPS induced HPMCs injury was reversed by knockdown of TLR4, which could inhibited the activation of NF-κB pathway axis. It suggested that the effect of Cox-2 on LPS induced HPMCs injury was achieved by negatively regulation of miR-21 and targeted TLR4 through NF-κB pathway axis. The findings may provide a new insight into preventing postoperative peritoneal adhesion.

Linc-RoR promotes proliferation, migration, and invasion via the Hippo/YAP pathway in pancreatic cancer cells.

Large intergenic noncoding RNA regulator of reprogramming (Linc-RoR) was first identified as a regulator to increase the emergence of induced pluripotent stem cells through reprogramming differentiated cells and is abnormal expression in a variety of malignant tumors. However, the function of Linc-RoR in pancreatic cancer progression needs further clarification. The data from this study demonstrated that Linc-RoR knockdown suppressed cell proliferative capacity and colony formation, while Linc-RoR overexpression promoted these behaviors. In particular, Linc-RoR overexpression promoted the level of mesenchymal markers, inhibited the expression of epithelial markers, as well as enhanced pancreatic cancer cells migration and invasion, whereas Linc-RoR knockdown inhibited the expression of mesenchymal markers, promoted the expression of epithelial markers, as well as weakened pancreatic cancer cells migration and invasion. Further study revealed that Linc-RoR knockdown brought about a significant fall in YAP phosphorylation and a rise in total YAP, while Linc-RoR overexpression produced the opposite results. Specifically, Linc-RoR promoted YAP in the cytoplasm into the nucleus. Taken together, we conjectured that Linc-RoR promoted proliferation, migration, and invasion of pancreatic cancer cells by activating the Hippo/YAP pathway. YAP might be an underlying target of Linc-RoR and mediate epithelial-mesenchymal transition (EMT) in pancreatic cancer (PC); thus, Linc-RoR might be a very meaningful biomarker for PC.

LincRNA-p21 promotes mesenchymal stem cell migration capacity and survival through hypoxic preconditioning

BackgroundMesenchymal stem cells (MSCs) derived from bone marrow have potent stabilizing effects for the treatment of acute respiratory distress syndrome (ARDS). However, low efficiency and survival in MSC homing to injured lung tissue remains to be solved. Therefore, the aim of this study was to assess whether large intergenic noncoding RNA (LincRNA)-p21 promote MSC migration and survival capacity through hypoxic preconditioning in vitro.MethodsMSCs were cultured and divided into the normoxia culture group (20% O2) and hypoxia culture group (1% O2). To determine roles and mechanisms, lentivirus vector-mediated LincRNA-p21 knockdown of MSCs and hypoxia-inducible factor (HIF-1α) inhibitor KC7F2 were introduced. Additionally, MSC migration was analyzed by scratch test and transwell migration assays. MSC proliferation was tested by cell counting kit-8 and trypan blue dye. Apoptosis was detected by Annexin V-PE/7-AAD stained flow cytometry. Moreover, LincRNA-p21 and HIF-1α mRNA was measured by reverse transcription-polymerase chain reaction, and HIF-1α and CXCR4/7 protein were assayed by western blot (WB) or enzyme-linked immunosorbent assay (ELISA). Apoptosis protein caspase-3 and cleaved-caspase-3 were investigated by WB analysis. Considering interactions between VHL and HIF-1α under LincRNA-p21 effect, co-immunoprecipitation was detected.ResultsHypoxic preconditioning MSC promoted migration capacity and MSC survival than normoxia culture group. MSCs induced by hypoxic preconditioning evoked an increase in expression of LincRNA-p21, HIF-1α, and CXCR4/7(both were chemokine stromal-derived factor-1(SDF-1) receptors). Contrarily, blockade of LincRNA-p21 by shRNA and HIF-1α inhibitor KC7F2 abrogated upregulation of hypoxic preconditioning induced CXCR4/7 in MSCs, cell migration, and survival. Furthermore, co-immunoprecipitation assay revealed that hypoxic preconditioning isolated VHL and HIF-1α protein by increasing HIF-1α expression.ConclusionsHypoxic preconditioning was identified as a promoting factor of MSC migration and survival capacity. LincRNA-p21 promotes MSC migration and survival capacity through HIF-1α/CXCR4 and CXCR7 pathway under hypoxic preconditioning in vitro.

A Linc1405/Eomes Complex Promotes Cardiac Mesoderm Specification and Cardiogenesis

Large intergenic non-coding RNAs (lincRNAs) play widespread roles in epigenetic regulation during multiple differentiation processes, but little is known about their mode of action in cardiac differentiation. Here, we identified the key roles of a lincRNA, termedlinc1405, in modulating the core network of cardiac differentiation by functionally interacting with Eomes. Chromatin- and RNA-immunoprecipitation assays showed that exon 2 of linc1405 physically mediates a complex consisting of Eomes, trithorax group (TrxG) subunit WDR5, and histone acetyltransferase GCN5 binding at the enhancer region of Mesp1 gene and activates its expression during cardiac mesoderm specification of embryonic stem cells. Importantly, linc1405 co-localizes with Eomes, WDR5, and GCN5 at the primitive streak, and linc1405 depletion impairs heart development and function invivo. In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis invitro and invivo.

An N-Ethyl-N-Nitrosourea (ENU) Mutagenized Mouse Model for Autosomal Dominant Nonsyndromic Kyphoscoliosis Due to Vertebral Fusion.

ABSTRACTKyphosis and scoliosis are common spinal disorders that occur as part of complex syndromes or as nonsyndromic, idiopathic diseases. Familial and twin studies implicate genetic involvement, although the causative genes for idiopathic kyphoscoliosis remain to be identified. To facilitate these studies, we investigated progeny of mice treated with the chemical mutagen N‐ethyl‐N‐nitrosourea (ENU) and assessed them for morphological and radiographic abnormalities. This identified a mouse with kyphoscoliosis due to fused lumbar vertebrae, which was inherited as an autosomal dominant trait; the phenotype was designated as hereditary vertebral fusion (HVF) and the locus as Hvf. Micro–computed tomography (μCT) analysis confirmed the occurrence of nonsyndromic kyphoscoliosis due to fusion of lumbar vertebrae in HVF mice, consistent with a pattern of blocked vertebrae due to failure of segmentation. μCT scans also showed the lumbar vertebral column of HVF mice to have generalized disc narrowing, displacement with compression of the neural spine, and distorted transverse processes. Histology of lumbar vertebrae revealed HVF mice to have irregularly shaped vertebral bodies and displacement of intervertebral discs and ossification centers. Genetic mapping using a panel of single nucleotide polymorphic (SNP) loci arranged in chromosome sets and DNA samples from 23 HVF (eight males and 15 females) mice, localized Hvf to chromosome 4A3 and within a 5‐megabase (Mb) region containing nine protein coding genes, two processed transcripts, three microRNAs, five small nuclear RNAs, three large intergenic noncoding RNAs, and 24 pseudogenes. However, genome sequence analysis in this interval did not identify any abnormalities in the coding exons, or exon‐intron boundaries of any of these genes. Thus, our studies have established a mouse model for a monogenic form of nonsyndromic kyphoscoliosis due to fusion of lumbar vertebrae, and further identification of the underlying genetic defect will help elucidate the molecular mechanisms involved in kyphoscoliosis. © 2018 The Authors. JBMR Plus is published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research

N6-Methyladenosine modification of lincRNA 1281 is critically required for mESC differentiation potential.

Previous studies have revealed the critical roles of N6-methyladenosine (m6A) modification of mRNA in embryonic stem cells (ESCs), but the biological function of m6A in large intergenic noncoding RNA (lincRNA) is unknown. Here, we showed that the internal m6A modification of linc1281 mediates a competing endogenous RNA (ceRNA) model to regulate mouse ESC (mESC) differentiation. We demonstrated that loss of linc1281 compromises mESC differentiation and that m6A is highly enriched within linc1281 transcripts. Linc1281 with RRACU m6A sequence motifs, but not an m6A-deficient mutant, restored the phenotype in linc1281-depleted mESCs. Mechanistic analyses revealed that linc1281 ensures mESC identity by sequestering pluripotency-related let-7 family microRNAs (miRNAs), and this RNA-RNA interaction is m6A dependent. Collectively, these findings elucidated the functional roles of linc1281 and its m6A modification in mESCs and identified a novel RNA regulatory mechanism, providing a basis for further exploration of broad RNA epigenetic regulatory patterns.

Long Non-coding RNAs, Novel Culprits, or Bodyguards in Neurodegenerative Diseases.

Long non-coding RNA (lncRNA) is a kind of non-coding RNA (ncRNA), with a length of 200 nt to 100 kb, that lacks a significant open reading frame (ORF) encoding a protein. lncRNAs are widely implicated in various physiological and pathological processes, such as epigenetic regulation, cell cycle regulation, cell differentiation regulation, cancer, and neurodegenerative diseases, through their interactions with chromatin, protein, and other RNAs. Numerous studies have suggested that lncRNAs are closely linked with the occurrence and development of a variety of diseases, especially neurodegenerative diseases, of which the etiologies are complicated and the underlying mechanisms remain elusive. Determining the roles of lncRNA in the pathogenesis of neurodegenerative diseases will not only deepen understanding of the physiological and pathological processes that occur in those diseases but also provide new ideas and solutions for their diagnosis and prevention. This review aims to highlight the progress of lncRNA research in the pathological and behavioral changes of neurodegenerative diseases. Specifically, we focus on how lncRNA dysfunctions are involved in the pathogenesis of Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and amyotrophic lateral sclerosis.

LincRNA-1614 coordinates Sox2/PRC2-mediated repression of developmental genes in pluripotency maintenance.

Large-intergenic noncoding RNAs (lincRNAs) cooperate with core transcription factors to coordinate the pluripotency network of embryonic stem cells. The mechanisms by which lincRNAs affect chromatin structure and gene transcription remain mostly unknown. Here, we identified that a lincRNA (linc1614), occupied by pluripotency factors at its promoter, was indispensable for both maintenance and acquisition of pluripotency. Linc1614 served as a specific partner of core factor Sox2 in maintaining pluripotency, primarily by mediating the function of Sox2 in the repression of developmental genes. Moreover, Ezh2, an essential subunit of polycomb repressive complex 2 (PRC2), physically interacted with linc1614 and contributed to lincRNA-mediated transcriptional silencing. Thus, we propose that the interplay of linc1614 with Sox2 implicates this lincRNA as a recruitment platform that mediates transcriptional silencing by guiding the PRC2 complex to the loci of developmental genes.

Long Non-Coding RNA lincRNA-ROR Promotes the Progression of Colon Cancer and Holds Prognostic Value by Associating with miR-145.

Large intergenic non-coding RNA ribonucleic acids-ROR (lincRNA-ROR) has been reported to exert impacts on the maintenance of induced pluripotent stem cells and embryonic stem cells, and play important roles in human hepatocellular cancer. It contributes to tumorigenesis and metastasis and functions as a competing endogenous RNA (ceRNA) by sponging miR-145 in breast cancer. However, its clinical significance and prognostic value in colon cancer remain unknown. The aim of the present study was to clarify the clinicopathological role and prognostic value of lincRNA-ROR and miR-145 in colon cancer. In the present study, qRT-PCR was performed to measure the expression levels of lincRNA-ROR in colon cancer tissues and cell lines. Then, the clinicopathological significance and prognostic value of lincRNA-ROR were analyzed. LincRNA-ROR expression correlated with pT stage, pN stage, AJCC stage and vascular invasion. Knockdown of lincRNA-ROR restored the expression of miR-145, and had a significant influence on colon cancer cell proliferation, migration and invasion. Patients of the high lincRNA-ROR/low miR-145 group had significantly poorer outcomes than those of the low lincRNA-ROR/high miR-145 group. Taken together, Overexpression of lincRNA-ROR combined with depletion of miR-145 may exert crucial impact on colon cancer prognosis evaluation and treatment.

Linc-ROR induces epithelial-mesenchymal transition and contributes to drug resistance and invasion of breast cancer cells.

We aimed to investigate the role of large intergenic noncoding RNA regulator of reprogramming (linc-ROR) in the chemotherapy resistance of human breast cancer (BC) cells and its mechanism. A total of 142 patients diagnosed with BC in the First Affiliated Hospital, Zhejiang University between January 2012 and January 2014 were enrolled in our study. The BC tissues and the adjacent normal tissues (5cm away from tumor tissue) of the enrolled patients were selected, and human BC cell lines (MCF10A, SK-BR-3, MCF-7, Bcap-37, MDA-MB-231, and T47D) were also selected. Quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, 3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt (MTS) assay, and Transwell were applied in our study. Expression level of linc-ROR messenger RNA (mRNA) in BC tissues was clearly higher than that in adjacent normal tissues, and significant difference was found between expression level of linc-ROR mRNA and lymph node metastasis (all P < 0.05). Linc-ROR was highly expressed in others BC cell lines compared with that in immortalized mammary epithelial cells (MECs) MCF10A (both P < 0.05), while MDA-MB231 cell presented the higher expression (P < 0.001). Under different concentrations of 5-FU and paclitaxel in MDA-MB231 cell, E-cadherin mRNA and protein expressions increased gradually with the increase of concentrations, and Vimentin and N-cadherin mRNA and protein expressions decreased gradually with the decrease of concentrations (all P < 0.05). Compared with shCtrl group, MDA-MB231 cell in shROR group presented higher sensibility of 5-FU and paclitaxel with increased E-cadherin expression, decreased Vimentin and N-cadherin expression and invasion ability (all P < 0.05). Compared with vector cell, overexpressed linc-ROR cell presented decreased sensibility of 5-FU and paclitaxel with decreased E-cadherin expression, increased Vimentin, N-cadherin expression, and invasion ability (all P < 0.05). Our study demonstrated that linc-ROR is an important marker for multidrug resistance of BC, and its up-regulation is important for chemotherapy tolerance and invasion of BC.

Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss).

Long noncoding RNAs (lncRNAs) have been recognized in recent years as key regulators of diverse cellular processes. Genome-wide large-scale projects have uncovered thousands of lncRNAs in many model organisms. Large intergenic noncoding RNAs (lincRNAs) are lncRNAs that are transcribed from intergenic regions of genomes. To date, no lincRNAs in non-model teleost fish have been reported. In this report, we present the first reference catalog of 9674 rainbow trout lincRNAs based on analysis of RNA-Seq data from 15 tissues. Systematic analysis revealed that lincRNAs in rainbow trout share many characteristics with those in other mammalian species. They are shorter and lower in exon number and expression level compared with protein-coding genes. They show tissue-specific expression pattern and are typically co-expressed with their neighboring genes. Co-expression network analysis suggested that many lincRNAs are associated with immune response, muscle differentiation, and neural development. The study provides an opportunity for future experimental and computational studies to uncover the functions of lincRNAs in rainbow trout.