scholarly journals Long Noncoding RNA UCA1 Promotes Glutamine-Driven Anaplerosis of Bladder Cancer by Interacting With hnRNP I/L to Upregulate GPT2 Expression

2020 ◽  
Author(s):  
Hua Zhao ◽  
Wenjing Wu ◽  
Xu Li ◽  
Wei Chen
Keyword(s):  
Bladder Cancer ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Metabolic Flux ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Tca Cycle ◽  
Metabolic Reprogramming ◽  
Luciferase Reporter ◽  
Flux Analysis

Abstract Background: Glutamine-driven anaplerosis maintains the tricarboxylic acid (TCA) cycle by replenishing its carbon source of intermediates with the glutamine-derived carbons in cancer cells. Long noncoding RNA urothelial cancer associated 1 (UCA1), initially identified in bladder cancer, is associated with multiple cellular processes, including metabolic reprogramming. However, its characteristics in the anaplerosis context of bladder cancer (BLCA) remains elusive. Methods: The mechanism of UCA1 bound to and facilitated the combination of hnRNP I/L to the promoter of GPT2 gene was investigated by RNA pulldown, qRT-PCR, western blot, dual luciferase reporter assays, immunohistochemical staining, chromatin immunoprecipitation and chromatin isolation by RNA purification. Metabolomics analysis and metabolic flux analysis were conducted to assess the effects of UCA1, hnRNP I/L, and GPT2 on metabolic reprogramming of BLCA.Results: We identified UCA1 as a binding partner of heterogeneous nuclear ribonucleoproteins (hnRNPs) I and L, RNA-binding proteins with no previously known role in metabolic reprogramming. UCA1 and hnRNP I/L profoundly affected glycolysis, TCA cycle, glutaminolysis, and viability of BLCA cells. Importantly, UCA1 specifically bound to and facilitated the combination of hnRNP I/L to the promoter of glutamic pyruvate transaminase 2 (GPT2) gene, resulting in upregulated expression of GPT2 and enhanced glutamine-derived carbons in the TCA cycle. We also systematically confirmed the influence of UCA1, hnRNP I/L, and GPT2 on metabolism and proliferation via glutamine-driven anaplerosis in BLCA cells. Conclusions: Our study reveals the critical mechanism by which UCA1 forms a functional UCA1-hnRNP I/L complex that upregulates GPT2 expression to promote glutamine-driven TCA cycle anaplerosis, providing novel evidence that lncRNA regulates metabolic reprogramming in tumor cells.

scholarly journals HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade

2020 ◽  
Vol 11 (7) ◽  
Author(s):  
Jessica Rea ◽  
Valentina Menci ◽  
Paolo Tollis ◽  
Tiziana Santini ◽  
Alexandros Armaos ◽  
...  
Keyword(s):  
Neuronal Differentiation ◽  
Cell Fate ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Regulatory Networks ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulatory Cascade ◽  
Expression Control ◽  
Gene Expression Control

Abstract Neuronal differentiation is a timely and spatially regulated process, relying on precisely orchestrated gene expression control. The sequential activation/repression of genes driving cell fate specification is achieved by complex regulatory networks, where transcription factors and noncoding RNAs work in a coordinated manner. Herein, we identify the long noncoding RNA HOTAIRM1 (HOXA Transcript Antisense RNA, Myeloid-Specific 1) as a new player in neuronal differentiation. We demonstrate that the neuronal-enriched HOTAIRM1 isoform epigenetically controls the expression of the proneural transcription factor NEUROGENIN 2 that is key to neuronal fate commitment and critical for brain development. We also show that HOTAIRM1 activity impacts on NEUROGENIN 2 downstream regulatory cascade, thus contributing to the achievement of proper neuronal differentiation timing. Finally, we identify the RNA-binding proteins HNRNPK and FUS as regulators of HOTAIRM1 biogenesis and metabolism. Our findings uncover a new regulatory layer underlying NEUROGENIN 2 transitory expression in neuronal differentiation and reveal a previously unidentified function for the neuronal-induced long noncoding RNA HOTAIRM1.

scholarly journals A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

2015 ◽  
Author(s):  
Ailone Tichon ◽  
Noa Gil ◽  
Yoav Lubelsky ◽  
Tal Havkin Solomon ◽  
Doron Lemze ◽  
...  
Keyword(s):  
Cell Division ◽  
Human Genome ◽  
Chromosome Segregation ◽  
Binding Sites ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Levels ◽  
Pumilio Proteins

AbstractThousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionary conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD – an abundant and highly conserved cytoplasmic lncRNA. Most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two Pumilio homologs in mammals. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA binding proteins, an activity which positions them at key junctions of cellular signaling pathways.

scholarly journals Long Noncoding RNA MALAT1 Acts as a Competing Endogenous RNA to Regulate TGF-β2 Induced Epithelial-Mesenchymal Transition of Lens Epithelial Cells by a MicroRNA-26a-Dependent Mechanism

2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Ning Dong
Keyword(s):  
Epithelial Cells ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Epithelial Mesenchymal Transition ◽  
Luciferase Reporter ◽  
Lens Epithelial Cells ◽  
Mesenchymal Transition ◽  
Reporter Assays ◽  
Dependent Mechanism

The aim of the present study was to characterize whether the long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1)/miR-26a/Smad4 axis is involved in epithelial–mesenchymal transition (EMT) of lens epithelial cells (LECs). Primary human LECs were separated and cultured. Microarray analysis showed that a total of 568 lncRNAs are differentially expressed in primary HLECs in the presence of TGF-β2 and MALAT1 is mostly significantly dysregulated lncRNAs, which is increased by nearly 17-fold. In addition, upregulation of MALAT1 and downregulation of miR-26a were detected in human posterior capsule opacification (PCO) attached LECs and the LECs obtained from patients with anterior polar cataracts by quantitative RT-PCR (qRT-PCR). Next, our results showed that TGF-β2 induces overexpression of EMT markers in primary HLECs via a MALAT1-dependent mechanism. The mechanism is that MALAT1 negatively regulates miR-26a and miR-26a directly targets Smad4 by luciferase reporter assays and RNA-binding protein immunoprecipitation assay. In summary, TGF-β2 induces MALAT1 overexpression, which in turn MALAT1 acts as a ceRNA targeting Smad4 by binding miR-26a and promotes the progression of EMT of LECs.

Long noncoding RNA LINC00342 promotes growth of infantile hemangioma by sponging miR-3619-5p from HDGF

2019 ◽  
Vol 317 (4) ◽  
pp. H830-H839 ◽  
Author(s):  
Zhen Liu ◽  
Zhenming Kang ◽  
Yujian Dai ◽  
Huiming Zheng ◽  
Yingjun Wang
Keyword(s):  
Cell Proliferation ◽  
Endothelial Cells ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Micro Rna ◽  
Luciferase Reporter ◽  
Proliferation And Apoptosis

Infantile hemangiomas (IH) are a type of benign vascular neoplasm that may cause permanent scarring. Hemangioma-derived endothelial cells (HemECs) are commonly used as an in vitro model to study IH. Long noncoding RNA is a type of RNA transcript longer than 200 nucleotides that does not encode any protein. LINC00342 was discovered to regulate proliferation and apoptosis in nonsmall cell lung cancer. However, the role of LINC00342 in IH has never been reported before. Expressions of LINC00342 and miR-3619-5p were detected in proliferating versus normal skin tissues. Colony formation and Cell-Couting Kit 8 assays were carried out to study the effects on cell proliferation after knockdown and overexpression of LINC00342, respectively. Meanwhile caspase-3 activity and nucleosomal fragmentation assay were applied to detect cell apoptosis. Micro-RNA binding sites on LINC00342 and hepatoma-derived growth factor (HDGF) were predicted and confirmed via dual-luciferase reporter assay. Biotin RNA pulldown assay was used to verify the direct binding between RNA molecules. LINC00342 enhanced proliferation and inhibited apoptosis in HemECs. MiR-3619-5p targeted both LINC00342 and HDGF, where LINC00342 sponged miR-3619-5p and positively regulated HDGF. HDGF knockdown rescued the effects of LINC00342 on HemECs. The LINC00342-miR-3619-5p-HDGF signaling pathway could regulate cell proliferation and apoptosis in HemECs. NEW & NOTEWORTHY The role of LINC00342 in infantile hemangiomas has not yet been elucidated. This paper highlights the regulatory role of LINC00342 in cell proliferation and apoptosis in hemangioma-derived endothelial cells and the underlying molecular mechanisms. The findings would provide potential target for treatment of infantile hemangiomas.

Long Noncoding RNA LINC00707 Accelerates Tumorigenesis and Progression of Bladder Cancer via Targeting miR-145/CDCA3 Regulatory Loop

2021 ◽  
pp. 1-15
Author(s):  
Tongbin Gao ◽  
Yongjian Ji
Keyword(s):  
Bladder Cancer ◽  
Western Blot ◽  
Long Noncoding Rna ◽  
Colony Formation ◽  
Noncoding Rna ◽  
Cell Counting ◽  
In Vitro Assays ◽  
Luciferase Reporter ◽  
Rt Pcr ◽  
The Impact

<b><i>Introduction:</i></b> Growing studies reveal that long noncoding RNA is involved in oncogenesis and progression. Previous studies have demonstrated that long intergenic noncoding RNA 00707 (LINC00707) stimulated tumor progress in numerous neoplasm types; however, the function of LINC00707 in bladder cancer (BC) was not yet clear. Our researches aimed to determine whether LINC00707 was dysregulated in BC and further study its biological functions. <b><i>Methods:</i></b> LINC00707 levels in BC tissues and cells were measured using reverse transcription-PCR (RT-PCR), and the associations between the levels of LINC00707 and clinicopathological features and the months of survival were also examined. Then, Cell Counting Kit-8 assays, flow cytometry, colony formation assays, and Transwell assays were applied for the assessment of the impact of LINC00707 on the abilities of BC cells. The interaction between LINC00707 and miR-145 or cell division cycle associated 3 was determined by luciferase reporter system and RT-PCR. Protein expressions of Wnt/β-catenin signaling were examined using RT-PCR and Western blot. <b><i>Results:</i></b> We found that LINC00707 expressions were notably upregulated in BC samples and cells. Higher expressions of LINC00707 were associated with T stage, grade, and shorter overall survival in BC patients. LINC00707 was also an independent prognostic factor for BC. In vitro assays confirmed that silencing LINC00707 expressions suppressed cell proliferation, colony formation, and metastasis. Mechanistic studies elucidated that LINC00707 was directly targeted to miR-145/CDCA3. Western blot assays revealed that Wnt/β-catenin signaling was inactivated by LINC00707 knockdown. <b><i>Conclusion:</i></b> Our work offers new insight into the function of LINC00707 in the tumorigenesis of BC.

The Oncogenic Capacities of Long Noncoding RNA SNHG1 in Bladder Cancer by inducing proliferation and repressing apoptosis via upregulation of microRNA-9-3p-targeted MDM2

2021 ◽  
Author(s):  
Weizhang Xu ◽  
Yun Hu ◽  
Haifei Xu ◽  
Haofeng Liu ◽  
Xiaolin Wang ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Cancer Cell ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Bladder Cancer Cell ◽  
Luciferase Reporter ◽  
Mechanistic Investigation ◽  
Gene Assay ◽  
Cancer Tissues

Abstract Background The involvement of long noncoding RNA small nucleolar RNA host gene 1 (lncRNA SNHG1) was documented in numerous cancers, including bladder, pancreatic and prostate cancers. However, the further mechanistic investigation of SNHG1 in bladder is still needed to conduct. With this purpose, tissue, cell, and animal experiments were implemented in our research to figure out the specific mechanism of SNHG1 in bladder cancer via microRNA-9-3p (miR-9-3p). Methods In harvested bladder cancer tissues, RNA-FISH and RT-qPCR were adopted for SNHG1 expression measurement and RT-qPCR for miR-9-3p expression determination. The impacts of SNHG1, miR-9-3p, MDM2, and PPARγ on cell viability, proliferation, and apoptosis were evaluated by gain- and loss-of-function approaches. RT-qPCR and western blot analysis were performed to detect expression of MDM2, PPARγ, and apoptosis-related factors. RNA pull-down, RIP, dual luciferase reporter gene assay, and IP experiment were utilized to assess the modulatory relationship among SNHG1, miR-9-3p, MDM2, and PPARγ. Tumorigenic ability of bladder cancer cells was measured in vivo. Results High SNHG1 and poor miR-9-3p expression was identified in bladder cancer tissues and cells. Mechanistically, SNHG1 bound to miR-9-3p which negatively targeted MDM2. MDM2 augmented PPARγ ubiquitination to downregulate PPARγ. Bladder cancer cell proliferation was diminished and cell apoptosis was enhanced by silencing SNHG1 or MDM2 or overexpressing miR-9-3p. Similarly, SNHG1 silencing orchestrated miR-9-3p/MDM2/PPARγ axis to depress bladder cancer cell tumorigenesis in vivo. Conclusion In summary, the obtained data provided the novel insight of the anti-oncogenic mechanism of silencing SNHG1 in bladder cancer by activating PPARγ via downregulation of miR-9-3p-targeted MDM2.

scholarly journals Long noncoding RNA HOTAIR interacts with Y-Box Protein-1 (YBX1) to regulate cell proliferation

2021 ◽  
Vol 4 (9) ◽  
pp. e202101139
Author(s):  
Siting Li ◽  
Qian Xiong ◽  
Minghai Chen ◽  
Bing Wang ◽  
Xue Yang ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Protein Interaction ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Rna Binding ◽  
Fluorescent Protein ◽  
Nuclear Translocation ◽  
Rna Binding Proteins ◽  
Protein Localization

HOTAIR is a long noncoding RNA (lncRNA) which serves as an important factor regulating diverse processes linked with cancer development. Here, we used comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) to explore the HOTAIR-protein interactome. We were able to identify 348 proteins interacting with HOTAIR, allowing us to establish a heavily interconnected HOTAIR-protein interaction network. We further developed a novel near-infrared fluorescent protein (iRFP)-trimolecular fluorescence complementation (TriFC) system to assess the interaction between HOTAIR and its interacting proteins. Then, we determined that HOTAIR specifically binds to YBX1, promotes YBX1 nuclear translocation, and stimulates the PI3K/Akt and ERK/RSK signaling pathways. We further demonstrated that HOTAIR exerts its effects on cell proliferation, at least in part, through the regulation of two YBX1 downstream targets phosphoenolpyruvate carboxykinase 2 (PCK2) and platelet derived growth factor receptor β. Our findings revealed a novel mechanism, whereby an lncRNA is able to regulate cell proliferation via altering intracellular protein localization. Moreover, the imaging tools developed herein have excellent potential for future in vivo imaging of lncRNA–protein interaction.

scholarly journals Chromosome-associated RNA–protein complexes promote pairing of homologous chromosomes during meiosis in Schizosaccharomyces pombe

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Da-Qiao Ding ◽  
Kasumi Okamasa ◽  
Yuki Katou ◽  
Eriko Oya ◽  
Jun-ichi Nakayama ◽  
...  
Keyword(s):  
Phase Separation ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Homologous Pairing ◽  
Homologous Chromosomes ◽  
Rna Protein Complexes ◽  
Chromosomal Loci

AbstractPairing of homologous chromosomes in meiosis is essential for sexual reproduction. We have previously demonstrated that the fission yeast sme2 RNA, a meiosis-specific long noncoding RNA (lncRNA), accumulates at the sme2 chromosomal loci and mediates their robust pairing in meiosis. However, the mechanisms underlying lncRNA-mediated homologous pairing have remained elusive. In this study, we identify conserved RNA-binding proteins that are required for robust pairing of homologous chromosomes. These proteins accumulate mainly at the sme2 and two other chromosomal loci together with meiosis-specific lncRNAs transcribed from these loci. Remarkably, the chromosomal accumulation of these lncRNA–protein complexes is required for robust pairing. Moreover, the lncRNA–protein complexes exhibit phase separation properties, since 1,6-hexanediol treatment reversibly disassembled these complexes and disrupted the pairing of associated loci. We propose that lncRNA–protein complexes assembled at specific chromosomal loci mediate recognition and subsequent pairing of homologous chromosomes.

scholarly journals Long noncoding RNA pncRNA-D reduces cyclin D1 gene expression and arrests cell cycle through RNA m6A modification

2020 ◽  
Vol 295 (17) ◽  
pp. 5626-5639 ◽  
Author(s):  
Ryoma Yoneda ◽  
Naomi Ueda ◽  
Kousuke Uranishi ◽  
Masataka Hirasaki ◽  
Riki Kurokawa
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Osmotic Stress ◽  
Cyclin D1 ◽  
Hela Cells ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Arginine Methylation

pncRNA-D is an irradiation-induced 602-nt long noncoding RNA transcribed from the promoter region of the cyclin D1 (CCND1) gene. CCND1 expression is predicted to be inhibited through an interplay between pncRNA-D and RNA-binding protein TLS/FUS. Because the pncRNA-D–TLS interaction is essential for pncRNA-D–stimulated CCND1 inhibition, here we studied the possible role of RNA modification in this interaction in HeLa cells. We found that osmotic stress induces pncRNA-D by recruiting RNA polymerase II to its promoter. pncRNA-D was highly m6A-methylated in control cells, but osmotic stress reduced the methylation and also arginine methylation of TLS in the nucleus. Knockdown of the m6A modification enzyme methyltransferase-like 3 (METTL3) prolonged the half-life of pncRNA-D, and among the known m6A recognition proteins, YTH domain-containing 1 (YTHDC1) was responsible for binding m6A of pncRNA-D. Knockdown of METTL3 or YTHDC1 also enhanced the interaction of pncRNA-D with TLS, and results from RNA pulldown assays implicated YTHDC1 in the inhibitory effect on the TLS–pncRNA-D interaction. CRISPR/Cas9-mediated deletion of candidate m6A site decreased the m6A level in pncRNA-D and altered its interaction with the RNA-binding proteins. Of note, a reduction in the m6A modification arrested the cell cycle at the G0/G1 phase, and pncRNA-D knockdown partially reversed this arrest. Moreover, pncRNA-D induction in HeLa cells significantly suppressed cell growth. Collectively, these findings suggest that m6A modification of the long noncoding RNA pncRNA-D plays a role in the regulation of CCND1 gene expression and cell cycle progression.

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