Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches

Qian, Xingyang; Zhao, Jieyu; Yeung, Pui Yan; Zhang, Qiangfeng Cliff; Kwok, Chun Kit

doi:10.1016/j.tibs.2018.09.012

Cited by 332 publications

(251 citation statements)

References 171 publications

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“…In post-transcriptional regulation, LncRNAs can act as competing endogenous RNAs (ceRNAs) by interacting with miRNAs to influence the stability of their targets [10,18,19]. Their function is usually determined by their sequence, structure and location [20]. LncRNAs are involved in physiological and pathological processes such as cancer progression [10], organ development [14], immune regulation [21], stem cell maintenance [22] and pathogen infection [23,24].…”

Section: Ivyspringmentioning

confidence: 99%

LncRNA NRON promotes the proliferation, metastasis and EMT process in bladder cancer

Xiong

Huang

et al. 2020

J. Cancer

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Background: Bladder cancer (BC) is one of the most common malignancies worldwide with high morbidity and mortality. Long noncoding RNAs (lncRNAs) are thought to play a critical role in cancer development. LncRNA NRON, a repressor of activated T-cell nuclear factor (NFAT), has been shown to be dysregulated in many cancer types. However, the clinical significance and molecular mechanism of NRON in bladder cancer is still unknown. Methods: The expression levels of NRON in BC tissues and cell lines were tested by RT-qPCR. Survival analysis was performed to detect the correlation between NRON expression and clinical outcomes in patients with BC. The biological role of NRON in BC cells proliferation and metastasis was examined in vitro and in vivo. Results: The expression of NRON was significantly upregulated in BC specimens and cell lines compared with paired adjacent normal tissues and normal cell lines. The upregulation of NRON in bladder cancer patients was significantly associated with the depth of bladder tumor invasion and poor prognosis. Knockdown of NRON inhibited BC cells proliferation, migration, invasion and tumorigenicity. Furthermore, NRON promoted epithelial-mesenchymal transition (EMT) progression, and NRONinduced EZH2 expression contributed to this process. Conclusion: In conclusion, our results suggested that NRON acted as an oncogene and tumor biomarker for BC.

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Section: Ivyspringmentioning

confidence: 99%

LncRNA NRON promotes the proliferation, metastasis and EMT process in bladder cancer

Xiong

Huang

et al. 2020

J. Cancer

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“…Studies reported that lncRNAs can activate post-transcriptional gene regulation, splicing, and translation by binding to proteins (Zhang et al,. 2018c;Li et al, 2019a) Therefore, identifying possible lncRNA-protein interactions (LPIs) is essential for unraveling lncRNA-related activities (Qian et al, 2018;Zhang et al, 2018c;Zhao et al, 2018c). Wet experiments validated parts of LPIs, but experimental methods remain costly and time-consuming.…”

Section: Introductionmentioning

confidence: 99%

Probing lncRNA–Protein Interactions: Data Repositories, Models, and Algorithms

Peng

Liu

Yang³

et al. 2020

Front. Genet.

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Identifying lncRNA-protein interactions (LPIs) is vital to understanding various key biological processes. Wet experiments found a few LPIs, but experimental methods are costly and time-consuming. Therefore, computational methods are increasingly exploited to capture LPI candidates. We introduced relevant data repositories, focused on two types of LPI prediction models: network-based methods and machine learning-based methods. Machine learning-based methods contain matrix factorization-based techniques and ensemble learning-based techniques. To detect the performance of computational methods, we compared parts of LPI prediction models on Leave-One-Out cross-validation (LOOCV) and fivefold cross-validation. The results show that SFPEL-LPI obtained the best performance of AUC. Although computational models have efficiently unraveled some LPI candidates, there are many limitations involved. We discussed future directions to further boost LPI predictive performance.Keywords: lncRNA-protein interaction, computational method, network-based method, machine learning-based method, data repositories

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“…Thus, delving into the potential molecular mechanism in PCa for a deep understanding is of vital importance. Long noncoding RNAs (lncRNAs) are a group of transcripts greater than 200nts in length with no protein-coding capacity [4]. For the last few years, quantities of lncRNAs have been reported to be crucial regulators in cellular processes of various cancers [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

LINC01006 facilitates cell proliferation, migration and invasion in prostate cancer through targeting miR-34a-5p to up-regulate DAAM1

Wang

et al. 2020

Preprint

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Background: Prostate cancer (PCa) is a kind of malignancy occurring in the prostate gland. Substantial researches have proved the major role of long noncoding RNAs (lncRNAs) in PCa. However, the role of long intergenic non-protein coding RNA 1006 (LINC01006) in PCa has not been investigated yet.Methods: RT-qPCR was used to examine the expression levels of LINC01006 and its downstream targets. The function of LINC01006 in PCa was tested by in vitro and in vivo assays. With application of RNA pull down, RNA immunoprecipitation (RIP) and luciferase reporter assays, the interaction among LINC01006, miR-34a-5p and disheveled associated activator of morphogenesis 1 (DAAM1) were verified.Results: LINC01006 expression presented high in PCa cell lines. LINC01006 silencing suppressed cell proliferative, migratory, invasive capacities while accelerated apoptotic rate. Besides, LINC01006 knockdown also suppressed tumor growth and metastasis in vivo. Furthermore, miR-34a-5p, a tumor suppressor in PCa, was sponged by LINC01006. Moreover, DAAM1 was targeted by miR-34a-5p and promoted PCa progression. More intriguingly, rescue assays suggested that the inhibitory effect of LINC01006 knockdown on PCa development was offset by DAAM1 overexpression.Conclusions: LINC01006 promoted PCa progression by sponging miR-34a-5p to up-regulate DAAM1, providing a novel target for PCa therapy.

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Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches

Cited by 332 publications

References 171 publications

LncRNA NRON promotes the proliferation, metastasis and EMT process in bladder cancer

LncRNA NRON promotes the proliferation, metastasis and EMT process in bladder cancer

Probing lncRNA–Protein Interactions: Data Repositories, Models, and Algorithms

LINC01006 facilitates cell proliferation, migration and invasion in prostate cancer through targeting miR-34a-5p to up-regulate DAAM1

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