LncRNA OIP5-AS1/cyrano suppresses GAK expression to control mitosis

Pivotal functions and impact of long con-coding RNAs on cellular processes and genome integrity

Recent advances in uncovering the mysteries of the human genome suggest that long non-coding RNAs (lncRNAs) are important regulatory components. Although lncRNAs are known to affect gene transcription, their mechanisms and biological implications are still unclear. Experimental research has shown that lncRNA synthesis, subcellular localization, and interactions with macromolecules like DNA, other RNAs, or proteins can all have an impact on gene expression in various biological processes. In this review, we highlight and discuss the major mechanisms through which lncRNAs function as master regulators of the human genome. Specifically, the objective of our review is to examine how lncRNAs regulate different processes like cell division, cell cycle, and immune responses, and unravel their roles in maintaining genomic architecture and integrity.

Stoichiometry of long noncoding RNA interactions with other RNAs: Insights from OIP5-AS1

Long noncoding (lnc)RNAs modulate gene expression programs in a range of developmental processes in different organs. In skeletal muscle, lncRNAs have been implicated in myogenesis, the process whereby muscle precursor cells form muscle fibers during embryonic development and regenerate muscle fibers in the adult. Here, we discuss OIP5-AS1, a lncRNA that is highly expressed in skeletal muscle and is capable of coordinating protein expression programs during myogenesis. Given that several myogenic functions of OIP5-AS1 involve interactions with MEF2C mRNA and with the microRNA miR-7, it was critical to carefully evaluate the precise levels of OIP5-AS1 during myogenesis. We discuss the approaches used to examine lncRNA copy number using OIP5-AS1 as an example, focusing on quantification by quantitative PCR analysis with reference to nucleic acids of known abundance, by droplet digital (dd)PCR measurement, and by microscopic visualization of individual lncRNAs in cells. We discuss considerations of RNA stoichiometry in light of developmental processes in which lncRNAs are implicated. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

LncRNA OIP5-AS1/miR-410-3p/Wnt7b axis promotes the proliferation of rheumatoid arthritis fibroblast-like synoviocytes via regulating the Wnt/β-catenin pathway

LncRNA OIP5-AS1 has a common gene imbalance in various cancers and tumours, which plays an important role in regulating its biological function. However, there are few studies on lncRNA OIP5-AS1 in rheumatoid arthritis (RA). The purpose of the present study was to investigate the role of lncRNA OIP5-AS1 in the pathogenesis of RA. In the present study, we established an adjuvant arthritis (AA) rat model to obtain primary fibroblast-like synoviocytes (FLSs);The subcellular localisation of lncRNA OIP5-AS1 was detected by fluorescence in situ hybridisation (FISH) assay; Cell proliferation of FLSs was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide(MTT) assay;IL-1β, IL-6 and TNF-α concentrations were measured by enzyme-linked immunosorbent assay (ELISA);Quantitative real-time PCR (qRT-PCR), Western blots(WB) and immunofluorescence were used to detect the expression of lncRNA OIP5-AS1/miR-410-3p/wnt7b signal axis and Wnt/β-catenin signal pathway related indicators in FLSs. FISH assay confirmed the presence of lncRNA OIP5-AS1 in the cytoplasm, suggesting that it acts as a competing endogenous RNA (ceRNA). qRT-PCR showed that the expression of lncRNA OIP5-AS1 was upregulated in FLSs, while the expression of miR-410-3p was downregulated in FLSs. We also found that lncRNA OIP5-AS1 knockdown inhibited the proliferation and inflammation of FLSs. Moreover, the expression of Wnt7b, the downstream target gene of miR-410-3p, and the activation of the Wnt/β-catenin signalling pathway were also inhibited by lncRNA OIP5-AS1 knockdown. These results suggested that lncRNA OIP5-AS1 promotes the activation of the Wnt/β-catenin signalling pathway by regulating the miR-410-3p/Wnt7b signalling axis, thereby participating in the occurrence and development of RA.

DYRK1A inhibitors for disease therapy: Current status and perspectives

Dual-specificity tyrosine phosphorylation-regulated kinase 1 A (DYRK1A) is a conserved protein kinase that plays essential roles in various biological processes. It is located in the region q22.2 of chromosome 21, which is involved in the pathogenesis of Down syndrome (DS). Moreover, DYRK1A has been shown to promote the accumulation of amyloid beta (Aβ) peptides leading to gradual Tau hyperphosphorylation, which contributes to neurodegeneration. Additionally, alterations in the DRK1A expression are also associated with cancer and diabetes. Recent years have witnessed an explosive increase in the development of DYRK1A inhibitors. A variety of novel DYRK1A inhibitors have been reported as potential treatments for human diseases. In this review, the latest therapeutic potential of DYRK1A for different diseases and the novel DYRK1A inhibitors discoveries are summarized, guiding future inhibitor development and structural optimization.

Long non-coding RNA OIP5-AS1 (Cyrano): A context-specific regulator of normal and disease processes

Long non-coding (lnc) RNAs have been implicated in a plethora of normal biological functions, and have also emerged as key molecules in various disease processes. OIP5-AS1, also commonly known by the alias Cyrano, is a lncRNA that displays broad expression across multiple tissues, with significant enrichment in particular contexts including within the nervous system and skeletal muscle. Thus far, this multifaceted lncRNA has been found to have regulatory functions in normal cellular processes including cell proliferation and survival, as well as in the development and progression of a myriad disease states. These widespread effects on normal and disease states have been found to be mediated through context-specific intermolecular interactions with dozens of miRNAs and proteins identified to date. This review explores recent studies to highlight OIP5-AS1's contextual yet pleiotropic roles in normal homeostatic functions as well as disease oetiology and progression, which may influence its utility in the generation of future theranostics.

Long Non-Coding RNAs, Novel Offenders or Guardians in Multiple Sclerosis: A Scoping Review

Multiple sclerosis (MS), a chronic inflammatory demyelinating disease of the central nervous system, is one of the most common neurodegenerative diseases worldwide. MS results in serious neurological dysfunctions and disability. Disturbances in coding and non-coding genes are key components leading to neurodegeneration along with environmental factors. Long non-coding RNAs (lncRNAs) are long molecules in cells that take part in the regulation of gene expression. Several studies have confirmed the role of lncRNAs in neurodegenerative diseases such as MS. In the current study, we performed a systematic analysis of the role of lncRNAs in this disorder. In total, 53 studies were recognized as eligible for this systematic review. Of the listed lncRNAs, 52 lncRNAs were upregulated, 37 lncRNAs were downregulated, and 11 lncRNAs had no significant expression difference in MS patients compared with controls. We also summarized some of the mechanisms of lncRNA functions in MS. The emerging role of lncRNAs in neurodegenerative diseases suggests that their dysregulation could trigger neuronal death via still unexplored RNA-based regulatory mechanisms. Evaluation of their diagnostic significance and therapeutic potential could help in the design of novel treatments for MS.

LncRNA AFAP1-AS1/miR-27b-3p/VEGF-C axis modulates stemness characteristics in cervical cancer cells

Background:

Long non-coding RNA (lncRNA) actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) functions as a competing endogenous RNA to regulate target genes expression by sponging microRNAs (miRs) to play cancer-promoting roles in cancer stem cells. However, the regulatory mechanism of AFAP1-AS1 in cervical cancer (CC) stem cells is unknown. The present study aimed to provide a new therapeutic target for the clinical treatment of CC.

Methods:

Hyaluronic acid receptor cluster of differentiation 44 variant exon 6 (CD44v6)(+) CC cells were isolated by flow cytometry (FCM). Small interfering RNAs of AFAP1-AS1 (siAFAP1-AS1) were transfected into the (CD44v6)(+) cells. The levels of AFAP1-AS1 were measured by quantitative real-time PCR (qRT-PCR). Sphere formation assay, cell cycle analysis, and Western blotting were used to detect the effect of siAFAP1-AS1. RNA pull-down and luciferase reporter assay were used to verify the relationship between miR-27b-3p and AFAP1-AS1 or vascular endothelial growth factor (VEGF)-C.

Results:

CD44v6(+) CC cells had remarkable stemness and a high level of AFAP1-AS1. However, AFAP1-AS1 knockdown with siAFAP1-AS1 suppressed the cell cycle transition of G(1)/S phase and inhibited self-renewal of CD44v6(+) CC cells, the levels of the stemness markers octamer-binding transcription factor 4 (OCT4), osteopontin (OPN), and cluster of differentiation 133 (CD133), and the epithelial-mesenchymal transition (EMT)-related proteins Twist1, matrix metalloprotease (MMP)-9, and VEGF-C. In the mechanism study, miR-27b-3p/VEGF-C signaling was demonstrated to be a key downstream of AFAP1-AS1 in the CD44v6(+) CC cells.

Conclusions:

LncRNA AFAP1-AS1 knockdown inhibits the CC cell stemness by upregulating miR-27b-3p to suppress VEGF-C.

Deciphering the Long Non-Coding RNAs and MicroRNAs Coregulation Networks in Ovarian Cancer Development: An Overview

Non-coding RNAs are emergent elements from the genome, which do not encode for proteins but have relevant cellular functions impacting almost all the physiological processes occurring in eukaryotic cells. In particular, microRNAs and long non-coding RNAs (lncRNAs) are a new class of small RNAs transcribed from the genome, which modulate the expression of specific genes at transcriptional and posttranscriptional levels, thus adding a new regulatory layer in the flux of genetic information. In cancer cells, the miRNAs and lncRNAs interactions with its target genes and functional pathways are deregulated as a consequence of epigenetic and genetic alterations occurring during tumorigenesis. In this review, we summarize the actual knowledge on the interplay of lncRNAs with its cognate miRNAs and mRNAs pairs, which interact in coregulatory networks with a particular emphasis on the mechanisms underlying its oncogenic behavior in ovarian cancer. Specifically, we reviewed here the evidences unraveling the relevant roles of lncRNAs/miRNAs pairs in altered regulation of cell migration, angiogenesis, therapy resistance, and Warburg effect. Finally, we also discussed its potential clinical implications in ovarian cancer and related endocrine disease therapies.

Long Noncoding RNA OIP5-AS1 Promotes Cell Apoptosis and Cataract Formation by Blocking POLG Expression Under Oxidative Stress

Purpose

Cataract, a clouding of the intraocular lens, is the leading cause of blindness. The lens-expressed long noncoding RNA OIP5-AS1 was upregulated in lens epithelial cells from patients with cataracts, suggesting its pathogenic role in cataracts. We investigated the regulatory role of OIP5-AS1 in the development of cataracts as well as potential RNA binding proteins, downstream target genes, and upstream transcription factors.

Methods

Clinical capsules and ex vivo and in vitro cataract models were used to test OIP5-AS1 expression. Cell apoptosis was detected using Western blots, JC-1 staining, and flow cytometry. Ribonucleoprotein immunoprecipitation-qPCR was performed to confirm the interaction of OIP5-AS1 and POLG. Chromatin immunoprecipitation-qPCR was used to determine the binding of TFAP2A and the OIP5-AS1 promoter region.

Results

OIP5-AS1 was upregulated in cataract lenses and B3 cells under oxidative stress. OIP5-AS1 knockdown protected B3 cells from H₂O₂-induced apoptosis and alleviated lens opacity in the ex vivo cataract model. HuR functioned as a scaffold carrying OIP5-AS1 and POLG mRNA and mediated the decay of POLG mRNA. POLG was downregulated in the cataract lens and oxidative-stressed B3 cells, and POLG depletion decreased the mtDNA copy number and MMP, increased reactive oxygen species production, and sensitized B3 cells to oxidative stress-induced apoptosis. POLG overexpression reversed these effects. TFAP2A bound the OIP5-AS1 promoter and contributed to OIP5-AS1 expression.

Conclusions

We demonstrated that OIP5-AS1, activated by TFAP2A, contributed to cataract formation by inhibiting POLG expression mediated by HuR, thus leading to increased apoptosis of lens epithelial cells and aggravated lens opacity, suggesting that OIP5-AS1 is a potential target for cataract treatment.

Long Noncoding RNAs at the Crossroads of Cell Cycle and Genome Integrity

The cell cycle is controlled by guardian proteins that coordinate the process of cell growth and cell division. Alterations in these processes lead to genome instability, which has a causal link to many human diseases. Beyond their well-characterized role of influencing protein-coding genes, an increasing body of evidence has revealed that long noncoding RNAs (lncRNAs) actively participate in regulation of the cell cycle and safeguarding of genome integrity. LncRNAs are versatile molecules that act via a wide array of mechanisms. In this review, we discuss how lncRNAs are implicated in control of the cell cycle and maintenance of genome stability and how changes in lncRNA-regulatory networks lead to proliferative diseases such as cancer.

A review on the role of oncogenic lncRNA OIP5-AS1 in human malignancies

OIP5-AS1 is a long non-coding transcript with high expression in nervous system, but crucial functions in the neoplastic transformation. This lncRNA partake in the regulation of cell cycle transition at different points. Moreover, it acts a competing endogenous RNA for tens of microRNAs among them are miR-338-3p, miR-204-5p, miR-641, miR-422a, miR-367-3p, miR-153-3p, miR-186, miR-369-3p, miR-137, miR-342-3p, miR‑429, miR-3163, miR-363-3p, miR-186a-5p, hsa-miR-26a-3p, miR‑300, miR-217, miR-378a-3p and miR-448. OIP5-AS1 influence the carcinogenesis via different routes among them is modulation of epithelial-mesenchymal transition. Expression of OIP5-AS1 has been elevated in nearly all kinds of neoplastic tissues except for multiple myeloma. Moreover, in bladder, gastric cancer and lung cancers, assessment of its expression in clinical samples has led to conflicting results. In the current paper, we have provided a comprehensive collection of research papers that evaluated function of OIP5-AS1 in diverse cancer types.

Interaction of OIP5-AS1 with MEF2C mRNA promotes myogenic gene expression

Long noncoding (lnc)RNAs potently regulate gene expression programs in physiology and disease. Here, we describe a key function for lncRNA OIP5-AS1 in myogenesis, the process whereby myoblasts differentiate into myotubes during muscle development and muscle regeneration after injury. In human myoblasts, OIP5-AS1 levels increased robustly early in myogenesis, and its loss attenuated myogenic differentiation and potently reduced the levels of the myogenic transcription factor MEF2C. This effect relied upon the partial complementarity of OIP5-AS1 with MEF2C mRNA and the presence of HuR, an RNA-binding protein (RBP) with affinity for both transcripts. Remarkably, HuR binding to MEF2C mRNA, which stabilized MEF2C mRNA and increased MEF2C abundance, was lost after OIP5-AS1 silencing, suggesting that OIP5-AS1 might serve as a scaffold to enhance HuR binding to MEF2C mRNA, in turn increasing MEF2C production. These results highlight a mechanism whereby a lncRNA promotes myogenesis by enhancing the interaction of an RBP and a myogenic mRNA.

Long non-coding RNA OIP5-AS1 promotes cell proliferation and aerobic glycolysis in gastric cancer through sponging miR-186

INTRODUCTION

Long non-coding RNAs (lncRNAs) play vital roles in tumour initiation and progression. LncRNA OIP5-AS1 is a potential oncogene in many types of human malignancies, but its biological functions in gastric cancer (GC) remain to be further elucidated.

MATERIAL AND METHODS

The expression levels of OIP5-AS1 and miR-186 in GC tissues and cell lines were detected by RT-qPCR analysis. CCK-8 assay and colony formation assay were performed to investigate the proliferation of GC cells in vitro, and a nude mouse tumour model was established to validate the role of OIP5-AS1 in GC tumorigenesis in vivo. The glucose consumption and lactate production of GC cells were detected by ELISA assay. Interaction between OIP5-AS1 and miR-186 was determined using dual luciferase reporter assay.

RESULTS

The results demonstrated that OIP5-AS1 was upregulated in GC tissues and cell lines and that its high expression was notably correlated with aggressive clinicopathological features of GC patients. Functionally, knockdown of OIP5-AS1 inhibited GC cell proliferation and enhanced cell apoptosis in vitro, and inhibited GC xenograft growth in vivo. In addition, knockdown of OIP5-AS1 reduced the glucose consumption and lactate production in GC cells. In particular, OIP5-AS1 may function as a ceRNA for miR-186, and inhibition of miR-186 blocks the effects of OIP5-AS1 knockdown on aerobic glycolysis in GC cells.

CONCLUSIONS

Accordingly, our findings suggested that the OIP5-AS1/miR-186 axis might be considered as a potential therapeutic target for GC patients.

Long Non-Coding RNA OIP5-AS1 Contributes to Gallbladder Cancer Cell Invasion and Migration by miR-143-3p Suppression

Objective

This study was designed to investigate the effect of long non-coding RNA (lncRNA) OIP5-AS1 on cell migration and invasion of gallbladder cancer (GBC) and its specific mechanism.

Methods

The expressions of lncRNA OIP5-AS1 and miR-143-3p in GBC cell lines (GBC-SD, SGC996 and NOZ) and gallbladder epithelial cells (HGBE cells) were measured by qRT-PCR. After loss- and gain-of-function experiments for OIP5-AS1 and miR-143-3p in GBC-SD cells, CCK-8 was applied to examine cell viability, cell scratch assay to measure cell migration, and transwell chamber to inspect cell invasion capacity. The interaction between OIP5-AS1 and miR-143-3p was predicted by StarBase. Then, luciferase reporter gene assay and RNA pull-down were used to verify the targeting relationship between miR-143-3p and OIP5-AS1.

Results

OIP5-AS1 was highly expressed and miR-143-3p was downregulated in GBC cell lines, when compared with HGBE cells. Overexpression of OIP5-AS1 or downregulation of miR-143-3p facilitated GBC-SD cell invasion, proliferation and migration, while different expression patterns were found in GBC-SD cells in response to OIP5-AS1 suppression or miR-143-3p overexpression. OIP5-AS1 negatively mediated miR-143-3p. MiR-143-3p upregulation partially reversed the inhibitory effect of OIP5-AS1 knockdown on GBC-SD cell activities.

Conclusion

LncRNA OIP5-AS1 accelerates the progression of GBC by suppressing miR-143-3p.

Prognostic and clinicopathologic significance of long non-coding RNA opa-interacting protein 5-antisense RNA 1 in multiple human cancers

Background: OIP5-AS1 has been reported to be aberrantly expressed in multiple cancers and associated with clinical outcomes. We conducted this study to assess the generalized prognostic value of OIP5-AS1 in cancers.Methods: PubMed, Web of science, and Cochrane Library were searched for eligible studies. Hazards ratios (HRs) or odd ratios (ORs) with 95% confidence intervals (CIs) were pooled to estimate the prognostic value of OIP5-AS1 in cancers, including overall survival (OS), age, gender, tumor size, clinical stage, and lymph node metastasis (LNM). Publication bias was measured by Begg's test and funnel plot. Sensitivity analysis were used to detect the stability of pooled results.Results: Overall, eleven studies containing 713 patients were eventually enrolled. The pooled results showed that high OIP5-AS1 expression was correlated with shorter OS (HR = 0.48, 95%CI: 0.35-0.64), regardless of the sample size, tumor type and follow-up time. Furthermore, elevated expression of OIP5-AS1 indicated advanced clinical stage (OR = 2.12, 95% CI: 1.06-4.23), but not associated with age, gender, tumor size and LNM. No publication bias was detected.Conclusion: High expression of lncRNA OIP5-AS1 may predict a poor OS and advanced clinical stage, implicating that OIP5-AS1 may be a possible prognostic factor in cancers.

The emerging role of lncRNAs in multiple sclerosis

Multiple sclerosis (MS) is the most common inflammatory demyelinating disease of the central nervous system (CNS) with various clinical manifestations. The characteristic of MS is that myelin is attacked by the body's immune system and increases the electrical capacity of axons, and is the primary pathophysiological mechanism of the transmission block. Studies have shown that epigenetic factors participate in the development of MS. LncRNAs are highly abundant and heterogeneous linear RNA transcripts with lengths exceeding 200 nucleotides and no protein-coding potential. Currently, pieces of evidence have demonstrated that lncRNAs have fundamental actions in multiple cellular pathways, including immune system regulation, epithelial-mesenchymal transition (EMT), cancer cell growth and metastasis, cellular homeostasis, and embryo development. It has been demonstrated that epigenetic mechanisms have an abundant role in the pathogenesis of MS in which the role of lncRNAs as epigenetic regulatory molecules in molecular processes has been proven. In this paper, we have focused on the correlation between MS and lncRNAs, the role of lncRNA in the pathogenesis of the disease, and the diagnostic and prognostic potential of lncRNA in MS.

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

Genome stability relies on proper coordination of mitosis and cytokinesis, where dynamic microtubules capture and faithfully segregate chromosomes into daughter cells. With a high-content RNAi imaging screen targeting more than 2,000 human lncRNAs, we identify numerous lncRNAs involved in key steps of cell division such as chromosome segregation, mitotic duration and cytokinesis. Here, we provide evidence that the chromatin-associated lncRNA, linc00899, leads to robust mitotic delay upon its depletion in multiple cell types. We perform transcriptome analysis of linc00899-depleted cells and identify the neuronal microtubule-binding protein, TPPP/p25, as a target of linc00899. We further show that linc00899 binds TPPP/p25 and suppresses its transcription. In cells depleted of linc00899, upregulation of TPPP/p25 alters microtubule dynamics and delays mitosis. Overall, our comprehensive screen uncovers several lncRNAs involved in genome stability and reveals a lncRNA that controls microtubule behaviour with functional implications beyond cell division.

Short-lived long noncoding RNAs as surrogate indicators for chemical stress in HepG2 cells and their degradation by nuclear RNases

Long noncoding RNAs (lncRNAs) are non-protein-coding transcripts >200 nucleotides in length that have been shown to play important roles in various biological processes. The mechanisms underlying the induction of lncRNA expression by chemical exposure remain to be determined. We identified a novel class of short-lived lncRNAs with half-lives (t_1/2) ≤4 hours in human HeLa Tet-off cells, which have been suggested to express many lncRNAs with regulatory functions. As they may affect various human biological processes, short-lived lncRNAs may be useful indicators of the degree of stress on chemical exposure. In the present study, we identified four short-lived lncRNAs, designated as OIP5-AS1, FLJ46906, LINC01137, and GABPB1-AS1, which showed significantly upregulated expression following exposure to hydrogen peroxide (oxidative stress), mercury II chloride (heavy metal stress), and etoposide (DNA damage stress) in human HepG2 cells. These lncRNAs may be useful indicators of chemical stress responses. The levels of these lncRNAs in the cells were increased because of chemical stress-induced prolongation of their decay. These lncRNAs were degraded by nuclear RNases, which are components of the exosome and XRN2, and chemical exposure inhibited the RNase activities within the cells.

Long noncoding RNA OIP5-AS1 in cancer

Long noncoding RNAs (lncRNAs) can be over two hundred nucleotides in length and lack an obvious open reading frame (ORF). Interestingly, these RNAs form a group of nucleic acids involved in a variety of diverse cellular mechanisms involving proliferation, differentiation, apoptosis,and senescence. Given these characteristics, it is not unexpected that the aberrant expression of certain lncRNAs is strongly linked to oncogenesis and tumor advancement. OIP5-AS1, a prominent tumor-associated lncRNA, contributes to intricate cellular mechanisms during the evolution of malignant tumors. For example, it not only represses cyclin G-associated kinase (GAK) expression thus impacting mitosis, but also regulates cell proliferation and apoptosis in many cancers, including lung adenocarcinoma, breast, glioma and hepatoblastoma. In this paper, we review our current understanding of OIP5-AS1 in carcinogenesis and its potential application as a clinical biomarker or therapeutic target in malignancy.

Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment

Transfer of genetic material from parents to progeny via fusion of gametes is a way to ensure flow of information from one generation to the next. Apart from the genetic material, gametes provide a rich source of other factors such as RNA and proteins which can control traits of the embryo. Non-coding RNAs are not only carriers of regulatory information but can also encode memory of events of parental life. Here, we explore the possibility of parental inheritance of non-coding RNAs, especially long non-coding RNAs. Meta-analysis of RNA-seq data revealed several non-coding RNAs present in zebrafish oocyte, sperm and 2cell-stage. The embryo is transcriptionally silent at this stage, we rationalize that all the RNAs detectable at 2cell-stage are deposited either by sperm or oocyte or both and thus inherited. In the inherited pool, we noticed a conserved lncRNA, Cyrano previously known for zebrafish brain development. Knockdown of inherited Cyrano by miR-7 without changing zygotic Cyrano altered brain morphology at 24 hpf and 48 hpf. This defect could be partially rescued by injecting full length Cyrano lncRNA or a mutant resilient to knock-down by miR-7. In future, there is ample scope to check the possibility of inherited lncRNAs as carriers of memory of parental life events and building blocks that set up an initial platform for development.

Research Progress on Long Non-Coding RNA and Radiotherapy

Long non-coding RNAs (lncRNAs), a group of non-protein-coding RNAs longer than 200 nucleotides, are involved in multiple biological and pathological processes, such as proliferation, apoptosis, migration, invasion, angiogenesis, and immune escape. Many studies have shown that lncRNAs participate in the complex network of cancer and play vital roles as oncogenes or tumor-suppressor genes in a variety of cancers. Moreover, recent research has shown that abnormal expression of lncRNAs in malignant tumor cells before and after radiotherapy may participate in the progression of cancers and affect the radiation sensitivity of malignant tumor cells mediated by specific signaling pathways or cell cycle regulation. In this review, we summarize the published studies on lncRNAs in radiotherapy regarding the biological function and mechanism of human cancers, including esophageal cancer, pancreatic cancers, nasopharyngeal carcinoma, hepatocellular carcinoma, cervical cancer, colorectal cancer, and gastric cancer.

Clathrin heavy chain phosphorylated at T606 plays a role in proper cell division

Clathrin regulates mitotic progression, in addition to membrane trafficking. However, the detailed regulatory mechanisms of clathrin during mitosis remain elusive. Here, we demonstrate novel regulation of clathrin during mitotic phase of the cell cycle. Clathrin heavy chain (CHC) was phosphorylated at T606 by its association partner cyclin G-associated kinase (GAK). This phosphorylation was required for proper cell proliferation and tumor growth of cells implanted into nude mice. Immunofluorescence analysis showed that the localization of CHC-pT606 signals changed during mitosis. CHC-pT606 signals localized in the nucleus and at the centrosome during interphase, whereas CHC signals were mostly cytoplasmic. Co-immunoprecipitation suggested that CHC formed a complex with GAK and polo-like kinase 1 (PLK1). Depletion of GAK using siRNA induced metaphase arrest and aberrant localization of CHC-pT606, which abolished Kiz-pT379 (as a phosphorylation target of PLK1) signals on chromatin at metaphase. Taken together, we propose that the GAK_CHC-pT606_PLK1_Kiz-pT379 axis plays a role in proliferation of cancer cells.

LncRNA OIP5-AS1 predicts poor prognosis and regulates cell proliferation and apoptosis in bladder cancer

Opa-interacting protein 5 antisense RNA 1 (OIP5-AS1) is a long intergenic noncoding RNA, which has been suggested to be dysregulated in human cancers and served as tumor suppressor or promoter depending on tumor types. However, the role of OIP5-AS1 in bladder cancer was still unknown. In our study, OIP5-AS1 was overexpressed in bladder cancer, and associated with clinical progression and short overall survival. The loss-of-function studies suggested downregulation of OIP5-AS1 expression decreased cell viability, induced cell-cycle arrest and promoted cell apoptosis in bladder cancer. There was a positive association between OIP5-AS1 expression and OIP5 expression in bladder cancer tissues. Moreover, downregulation of OIP5-AS1 expression reduced messenger RNA and protein levels of OIP5 in bladder cancer cell lines. In conclusion, OIP5-AS1 is a useful biomarker for predicting clinical progression and poor prognosis and promotes cell proliferation through modulating OIP5 expression.

Integrative analysis of OIP5-AS1/HUR1 to discover new potential biomarkers and therapeutic targets in multiple sclerosis

Multiple sclerosis (MS) is a devastating autoimmune disease of the central nervous system associated with demyelination and axonal injury. This study was designed to find potential lncRNAs and their targets that are associated with the molecular basis of MS pathogenesis. In this study, peripheral blood samples were obtained from 50 relapsing-remitting MS (RR-MS) patients and 50 healthy controls. lncRNAs and their target were selected for validation using TaqMan Real-Time PCR. Interactions were studied based on approaches that used to investigation biological functions and signaling pathways affected by differentially expressed messenger RNAs (mRNAs). The results of this study indicate an increase in the expression of HUR1 (p = 0.0001), CPSF7 (p = 0.02), and reduction of CSTF2 expression (p = 0.04). Also, an increase in the expression of OIP5-AS1 (p = 0.01) was observed in men less than 30 years old. We performed a comparative analysis of the long noncoding RNAs (lncRNAs), and then we ranked them as candidate biomarkers according to a decreasing area under the receiver operating characteristic (ROC) curve (AUC) and plotted the results. Dysregulation of lncRNA expression has been linked to diseases. Further studies on the HUR1 gene can be used as diagnostic tools for the identification of high-risk individuals in families with a history of disease before, during, and even after treatment. Our data uncovered the expression profiles of lncRNAs and mRNAs in MS patients, which will help delineate the molecular mechanisms in MS pathogenesis. However, further studies need to determine the precise role of these genes in the pathological process in MS.

Oncogenic KSHV-encoded interferon regulatory factor upregulates HMGB2 and CMPK1 expression to promote cell invasion by disrupting a complex lncRNA-OIP5-AS1/miR-218-5p network

Kaposi's sarcoma (KS), a highly disseminated tumor of hyperproliferative spindle endothelial cells, is the most common AIDS-associated malignancy caused by infection of Kaposi's sarcoma-associated herpesvirus (KSHV). KSHV-encoded viral interferon regulatory factor 1 (vIRF1) is a viral oncogene but its role in KSHV-induced tumor invasiveness and motility remains unknown. Here, we report that vIRF1 promotes endothelial cell migration, invasion and proliferation by down-regulating miR-218-5p to relieve its suppression of downstream targets high mobility group box 2 (HMGB2) and cytidine/uridine monophosphate kinase 1 (CMPK1). Mechanistically, vIRF1 inhibits p53 function to increase the expression of DNA methyltransferase 1 (DNMT1) and DNA methylation of the promoter of pre-miR-218-1, a precursor of miR-218-5p, and increases the expression of a long non-coding RNA OIP5 antisense RNA 1 (lnc-OIP5-AS1), which acts as a competing endogenous RNA (ceRNA) of miR-218-5p to inhibit its function and reduce its stability. Moreover, lnc-OIP5-AS1 increases DNA methylation of the pre-miR-218-1 promoter. Finally, deletion of vIRF1 from the KSHV genome reduces the level of lnc-OIP5-AS1, increases the level of miR-218-5p, and inhibits KSHV-induced invasion. Together, these results define a novel complex lnc-OIP5-AS1/miR-218-5p network hijacked by vIRF1 to promote invasiveness and motility of KSHV-induced tumors.

Downregulation of long non-coding RNA Opa interacting protein 5-antisense RNA 1 inhibits breast cancer progression by targeting sex-determining region Y-box 2 by microRNA-129-5p upregulation

Several studies have shown an important role for long non‐coding RNA (lncRNA) in breast cancer progression. The present study investigated the role of lncRNA Opa interacting protein 5‐antisense RNA 1 (OIP5‐AS1) in the progression of breast cancer. OIP5‐AS1 was significantly upregulated in breast cancer tissues and in breast cancer cell lines, and OIP5‐AS1 downregulation inhibited the malignant behavior of breast cancer in vitro and in vivo. For in‐depth exploration of the mechanism of OIP5‐AS1 in breast cancer, we found that expression of microRNA‐129‐5p(miR‐129‐5p), which was found to bind sites in the sequence of OIP5‐AS1, in breast cancer tissues was negatively correlated with OIP5‐AS1. Also, luciferase assays indicated that OIP5‐AS1 acted as a miR‐129‐5p sponge, resulting in upregulated expression of the sex‐determining region Y‐box 2 (SOX2) transcription factor. Our study showed that OIP5‐AS1 plays a critical role in promoting breast cancer progression and that OIP5‐AS1 downregulation targets SOX2 by miR‐129‐5p upregulation.

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions

LncRNA-protein interactions play important roles in post-transcriptional gene regulation, poly-adenylation, splicing and translation. Identification of lncRNA-protein interactions helps to understand lncRNA-related activities. Existing computational methods utilize multiple lncRNA features or multiple protein features to predict lncRNA-protein interactions, but features are not available for all lncRNAs or proteins; most of existing methods are not capable of predicting interacting proteins (or lncRNAs) for new lncRNAs (or proteins), which don’t have known interactions. In this paper, we propose the sequence-based feature projection ensemble learning method, “SFPEL-LPI”, to predict lncRNA-protein interactions. First, SFPEL-LPI extracts lncRNA sequence-based features and protein sequence-based features. Second, SFPEL-LPI calculates multiple lncRNA-lncRNA similarities and protein-protein similarities by using lncRNA sequences, protein sequences and known lncRNA-protein interactions. Then, SFPEL-LPI combines multiple similarities and multiple features with a feature projection ensemble learning frame. In computational experiments, SFPEL-LPI accurately predicts lncRNA-protein associations and outperforms other state-of-the-art methods. More importantly, SFPEL-LPI can be applied to new lncRNAs (or proteins). The case studies demonstrate that our method can find out novel lncRNA-protein interactions, which are confirmed by literature. Finally, we construct a user-friendly web server, available at http://www.bioinfotech.cn/SFPEL-LPI/.

LncRNA-protein interactions play important roles in post-transcriptional gene regulation, poly-adenylation, splicing and translation. Identification of lncRNA-protein interactions helps to understand lncRNA-related activities. In this paper, we propose a novel computational method “SFPEL-LPI” to predict lncRNA-protein interactions. SFPEL-LPI makes use of lncRNA sequences, protein sequences and known lncRNA-protein associations to extract features and calculate similarities for lncRNAs and proteins, and then combines them with a feature projection ensemble learning frame. SFPEL-LPI can predict unobserved interactions between lncRNAs and proteins, and also can make predictions for new lncRNAs (or proteins), which have no interactions with any proteins (or lncRNAs). SFPEL-LPI produces high-accuracy performances on the benchmark dataset when evaluated by five-fold cross validation, and outperforms state-of-the-art methods. The case studies demonstrate that SFPEL-LPI can find out novel associations, which are confirmed by literature. To facilitate the lncRNA-protein interaction prediction, we develop a user-friendly web server, available at http://www.bioinfotech.cn/SFPEL-LPI/.

Long noncoding RNA: multiple players in gene expression

Previously considered as a component of transcriptional noise, long noncoding RNAs (lncRNAs) were neglected as a therapeutic target, however, recently increasing evidence has shown that lncRNAs can participate in numerous biological processes involved in genetic regulation including epigenetic, transcriptional, and post-transcriptional regulation. In this review, we discuss the fundamental functions of lncRNAs at different regulatory levels and their roles in metabolic balance. Typical examples are introduced to illustrate their diverse molecular mechanisms. The comprehensive investigation and identification of key lncRNAs will not only contribute to insights into diseases, such as breast cancer and type II diabetes, but also provide promising therapeutic targets for related diseases. [BMB Reports 2018; 51(6): 280-289].

LncRNA OIP5-AS1 regulates radioresistance by targeting DYRK1A through miR-369-3p in colorectal cancer cells

OBJECT

This study aimed to investigate the role of lncRNA OIP5-AS1 in regulating radioresistance of colorectal cancer (CRC) cells.

METHODS

Microarray analysis was used to screen out lncRNAs differentially expressed in radio-resistant CRC cell lines. Expression levels of OIP5-AS1, miR-369-3p and DYRK1A in CRC cell lines were measured by qRT-PCR. Protein expression of DYRK1A was determined by western blot. The target relationships among OIP5-AS1, miR-369-3p and DYRK1A were validated by dual luciferase reporter assay. Impacts of OIP5-AS1 or DYRK1A on CRC cellular activity and apoptosis were investigated by MTT assay, clonogenic survival assay and flow cytometry to analyze OIP5-AS1 or DYRK1A's effect on radioresistance of CRC cells.

RESULTS

LncRNA OIP5-AS1 and DYRK1A were down-regulated in radio-resistant CRC cell lines. OIP5-AS1 suppressed the expression of miR-369-3p, thus up-regulating DYRK1A, the downstream gene of miR-369-3p. OIP5-AS1 and DYRK1A impaired cell clonogenic survival and promoted cell apoptosis after irradiation, improving radiosensitivity of CRC cells.

CONCLUSION

LncRNA OIP5-AS1 suppressed cell viability, promoted radio-induced apoptosis, and enhanced the radiosensitivity of CRC cells by regulating DYRK1A expression through miR-369-3p.

Cytoplasmic functions of long noncoding RNAs

Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides found throughout the cell that lack protein-coding function. Their functions are closely linked to their interaction with RNA-binding proteins (RBPs) and nucleic acids. Nuclear lncRNAs have been studied extensively, revealing complexes with structural and regulatory roles that enable gene organization and control transcription. Cytoplasmic lncRNAs are less well understood, but accumulating evidence indicates that they also form complexes with diverse structural and regulatory functions. Here, we review our current knowledge of cytoplasmic lncRNAs and the different levels of gene regulation controlled by cytoplasmic lncRNA complexes, including mRNA turnover, translation, protein stability, sponging of cytosolic factors, and modulation of signaling pathways. We conclude by discussing areas of future study needed to elucidate comprehensively the biology of lncRNAs, to further understand the impact of lncRNAs on physiology and design lncRNA-centered therapeutic strategies. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Long noncoding RNA complementarity and target transcripts abundance

Eukaryotic mRNA metabolism regulates its stability, localization, and translation using complementarity with counter-part RNAs. To modulate their stability, small and long noncoding RNAs can establish complementarity with their target mRNAs. Although complementarity of small interfering RNAs and microRNAs with target mRNAs has been studied thoroughly, partial complementarity of long noncoding RNAs (lncRNAs) with their target mRNAs has not been investigated clearly. To address that research gap, our lab investigated whether the sequence complementarity of two lncRNAs, lincRNA-p21 and OIP5-AS1, influenced the quantity of target RNA expression. We predicted a positive correlation between lncRNA complementarity and target mRNA quantity. We confirmed this prediction using RNA affinity pull down, microarray, and RNA-sequencing analysis. In addition, we utilized the information from this analysis to compare the quantity of target mRNAs when two lncRNAs, lincRNA-p21 and OIP5-AS1, are depleted by siRNAs. We observed that human and mouse lincRNA-p21 regulated target mRNA abundance in complementarity-dependent and independent manners. In contrast, affinity pull down of OIP5-AS1 revealed that changes in OIP5-AS1 expression influenced the amount of some OIP5-AS1 target mRNAs and miRNAs, as we predicted from our sequence complementarity assay. Altogether, the current study demonstrates that partial complementarity of lncRNAs and mRNAs (even miRNAs) assist in determining target RNA expression and quantity.