A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

Cesana, Marcella; Cacchiarelli, Davide; Legnini, Ivano; Santini, Tiziana; Sthandier, Olga; Chinappi, Mauro; Tramontano, Anna; Bozzoni, Irene

doi:10.1016/j.cell.2011.09.028

Cited by 2,295 publications

(1,894 citation statements)

References 52 publications

Supporting

Mentioning

1,854

Contrasting

Unclassified

Order By: Relevance

“…Sequencing-based approaches for high-throughput structure mapping have been employed by several previous studies. [40][41][42][43][44][45][46] These pioneer works showed that the HTS-based approaches were highly efficient for interrogating RNA secondary structures on a global scale. 47 Here, we would like to introduce dsRNA-seq and ssRNA-seq by illustrating their use for the studies on miRNA structures.…”

Section: Srna-seqmentioning

confidence: 99%

“…Usually, ssRNA-seq was used in combination with dsRNA-seq for high-throughput probing the RNA structurome of an organism. 40,44 The "loop" structure of a miRNA precursor is a locally unpaired region. Theoretically, this region could be identified by ssRNA-seq.…”

Section: Srna-seqmentioning

confidence: 99%

“…In animals, certain long non-coding RNAs were identified to act as competing endogenous RNAs (ceRNAs) to compete with the genuine targets for the binding of specific miRNAs. 40,87 Thus, a portion of functional miRNAs could be sequestered by the ceRNAs, adding another layer of post-transcriptional regulation of the miRNA activities. These ceRNAs were also called miRNA decoys or sponges, indicating their ability of trapping mature miRNAs.…”

Section: Degradome-seqmentioning

confidence: 99%

See 2 more Smart Citations

The use of high-throughput sequencing methods for plant microRNA research

Tang

Qin³

et al. 2015

RNA Biology

View full text Add to dashboard Cite

Section: Srna-seqmentioning

confidence: 99%

Section: Srna-seqmentioning

confidence: 99%

Section: Degradome-seqmentioning

confidence: 99%

See 1 more Smart Citation

The use of high-throughput sequencing methods for plant microRNA research

Tang

Qin³

et al. 2015

RNA Biology

View full text Add to dashboard Cite

“…Different species of RNA transcripts can communicate with each other, which have been symbolically referred to as letters of a new language. The competing regulation of lncRNA, miRNA, and gene is not only of fundamental importance in physiological conditions (Cesana et al ., 2011), but also relevant in various cancers (Wang et al ., 2015) and may also influence genes associated with drug responses and the development of resistance to cancer therapy (Ling et al ., 2013). For example, Cao et al .…”

Section: Introductionmentioning

confidence: 99%

Inferences of individual drug responses across diverse cancer types using a novel competing endogenous RNA network

Zhang

Zhou

et al. 2018

Molecular Oncology

View full text Add to dashboard Cite

Differences in individual drug responses are an obstacle to progression in cancer treatment, and predicting responses would help to plan treatment. The accumulation of cancer molecular profiling and drug response data provides opportunities and challenges to identify novel molecular signatures and mechanisms of tumor responsiveness to drugs. This study evaluated drug responses with a competing endogenous RNA (ceRNA) system that depended on competition between diverse RNA species. We identified drug response‐related ceRNA (DRCEs) by combining the sequence and expression data of long noncoding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA), and the survival data of cancer patients treated with drugs. We constructed a patient–drug two‐layer integrated network and used a linear weighting method to predict individual drug responses. DRCEs were found to be significantly enriched in known cancer and drug‐associated data resources, involved in biological processes known to mediate drug responses, and correlated to drug activity in cancer cell lines. The dysregulation of DRCE expression influenced drug response‐associated functions and pathways, suggesting DRCEs as potential therapeutic targets affecting drug responses. A further case study in breast invasive carcinoma (BRCA) found that DRCE expression was consistent with the drug response pattern and the aberrant expression of the two NEAT1‐related DRCEs may lead to poor response to tamoxifen therapy for patients with TP53 mutations. In summary, this study provides a framework for ceRNA‐based evaluation of clinical drug responses across multiple cancer types. Understanding the underlying molecular mechanisms of drug responses will allow improved response to chemotherapy and outcomes of cancer treatment.

show abstract

“…However, the majority of the mammalian genome is transcribed into non-coding RNAs (ncRNAs), including the small ncRNAs (< 200 bp) and long ncRNAs (lncRNAs) (> 200 bp)[5]. LncRNAs are the major regulators of gene expression and are involved in multiple biological processes, including genomic imprinting, embryonic development, cell differentiation, tumor metastasis and regulation of cell cycle [6–10]. LncRNAs regulate gene expression at the epigenetic, transcriptional and post-transcriptional levels in diverse biological contexts[6].…”

Section: Introductionmentioning

confidence: 99%

Deep sequencing of the mouse lung transcriptome reveals distinct long non-coding RNAs expression associated with the high virulence of H5N1 avian influenza virus in mice

Hu¹,

Hu²,

Wang³

et al. 2018

Virulence

View full text Add to dashboard Cite

Long non-coding RNAs (lncRNAs) play multiple key regulatory roles in various biological processes. However, their function in influenza A virus (IAV) pathogenicity remains largely unexplored. Here, using next generation sequencing, we systemically compared the whole-transcriptome response of the mouse lung infected with either the highly pathogenic (A/Chicken/Jiangsu/k0402/2010, CK10) or the nonpathogenic (A/Goose/Jiangsu/k0403/2010, GS10) H5N1 virus. A total of 126 significantly differentially expressed (SDE) lncRNAs from three replicates were identified to be associated with the high virulence of CK10, whereas 94 SDE lncRNAs were related with GS10. Functional category analysis suggested that the SDE lncRNAs-coexpressed mRNAs regulated by CK10 were highly related with aberrant and uncontrolled inflammatory responses. Further canonical pathway analysis also confirmed that these targets were highly enriched for inflammatory-related pathways. Moreover, 9 lncRNAs and 17 lncRNAs-coexpressed mRNAs associated with a large number of targeted genes were successfully verified by qRT-PCR. One targeted lncRNA (NONMMUT011061) that was markedly activated and correlated with a great number of mRNAs was selected for further in-depth analysis, including predication of transcription factors, potential interacting proteins, genomic location, coding ability and construction of the secondary structure. More importantly, NONMMUT011061 was also distinctively stimulated during the highly pathogenic H5N8 virus infection in mice, suggesting a potential universal role of NONMMUT011061 in the pathogenesis of different H5 IAV. Altogether, these results provide a subset of lncRNAs that might play important roles in the pathogenesis of influenza virus and add the lncRNAs to the vast repertoire of host factors utilized by IAV for infection and persistence.

show abstract

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

Cited by 2,295 publications

References 52 publications

The use of high-throughput sequencing methods for plant microRNA research

The use of high-throughput sequencing methods for plant microRNA research

Inferences of individual drug responses across diverse cancer types using a novel competing endogenous RNA network

Deep sequencing of the mouse lung transcriptome reveals distinct long non-coding RNAs expression associated with the high virulence of H5N1 avian influenza virus in mice

Contact Info

Product

Resources

About