A novel antisense long noncoding RNA regulates the expression of MDC1 in bladder cancer

Xue, Yue; Ma, Gaoxiang; Zhang, Zhensheng; Hua, Qiuhan; Chu, Haiyan; Tong, Na; Lin, Yuan; Qin, Chao; Chen, Yin; Wang, Meilin

doi:10.18632/oncotarget.2861

Cited by 53 publications

(46 citation statements)

References 32 publications

(31 reference statements)

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“…Derrien et al [6] also reported a majority of positive co-expressions for lncRNA-mRNA pairs in an anti-sense orientation. The mechanisms that underlie such positive co-expression seem to be complex and act at distinct regulatory levels including the translation, splicing and transcription levels [55–58]. …”

Section: Resultsmentioning

confidence: 99%

Long noncoding RNA repertoire in chicken liver and adipose tissue

et al. 2017

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BackgroundImproving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity. To predict lncRNAs, we used a recently developed tool called FEELnc, which also classifies them with respect to their distance and strand orientation to the closest protein-coding genes. Moreover, to confidently identify the genes/transcripts expressed in each tissue (a complex task for weakly expressed molecules such as lncRNAs), we probed a particularly large number of biological replicates (16 per tissue) compared to common multi-tissue studies with a larger set of tissues but less sampling.ResultsWe predicted 2193 lncRNA genes, among which 1670 were robustly expressed across replicates in the liver and/or adipose tissue and which were classified into 1493 intergenic and 177 intragenic lncRNAs located between and within protein-coding genes, respectively. We observed similar structural features between chickens and mammals, with strong synteny conservation but without sequence conservation. As previously reported, we confirm that lncRNAs have a lower and more tissue-specific expression than mRNAs. Finally, we showed that adjacent lncRNA-mRNA genes in divergent orientation have a higher co-expression level when separated by less than 1 kb compared to more distant divergent pairs. Among these, we highlighted for the first time a novel lncRNA candidate involved in lipid metabolism, lnc_DHCR24, which is highly correlated with the DHCR24 gene that encodes a key enzyme of cholesterol biosynthesis.ConclusionsWe provide a comprehensive lncRNA repertoire in the chicken liver and adipose tissue, which shows interesting patterns of co-expression between mRNAs and lncRNAs. It contributes to improving the structural and functional annotation of the chicken genome and provides a basis for further studies on energy storage and mobilization traits in the chicken.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0275-0) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Long noncoding RNA repertoire in chicken liver and adipose tissue

et al. 2017

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“…Recent studies have revealed that lncRNAs were found to be deregulated in several human cancers including bladder cancer [15,16]. Understanding the molecular mechanism of lncRNAs may help to explore new promising therapeutic strategy for the treatment of bladder cancer.…”

Section: Discussionmentioning

confidence: 99%

Double‐negative feedback loop between long non‐coding RNA TUG1 and miR‐145 promotes epithelial to mesenchymal transition and radioresistance in human bladder cancer cells

et al. 2015

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a b s t r a c tLncRNAs have a critical role in the regulation of cellular processes such as cancer progression and metastasis. In the present study, we confirmed that TUG1 was overexpressed in bladder cancer tissues and established cell lines. Knockdown of TUG1 inhibited bladder cancer cell metastasis both in vitro and in vivo. Furthermore, we found that TUG1 promoted cancer cell invasion and radioresistance through inducing epithelial-to-mesenchymal transition (EMT). Interestingly, TUG1 decreased the expression of miR-145 and there was a reciprocal repression between TUG1 and miR-145 in an Argonaute2-dependent manner. ZEB2 was identified as a down-stream target of miR-145 and TUG1 exerted its function through the miR-145/ZEB2 axis. In summary, our data indicated that blocking TUG1 function may be an effective anti-cancer therapy.

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“…9 Additionally, different classes of lncRNAs can regulate critical cancer genes through a variety of mechanisms. For instance, antisense lncRNAs typically regulate protein-coding genes in close proximity 60,61 whereas cytoplasmic competing endogenous RNAs (ceRNAs) will compete with cancer genes harboring similar microRNA binding sites to modulate expression. 62 Therefore, given the broad and expanding range of lncRNA functions, our comprehensive study importantly hones in on critical onco-lncRNAs and provides an initial framework for dissecting their emerging regulatory roles with oncogenes and tumor suppressors.…”

Section: Discussionmentioning

confidence: 99%