A large scale expression study associates uc.283-plus lncRNA with pluripotent stem cells and human glioma

Galasso, Marco; Dama, Paola; Previati, Maurizio; Sandhu, Sukhinder K.; Palatini, Jeff; Coppola, Vincenzo; Warner, Sarah; Sana, Maria Elena; Zanella, Riccardo; Abujarour, Ramzey; Desponts, Caroline; Teitell, Michael A.; Garzon, Ramiro; Calin, George A.; Croce, Carlo M.; Volinia, Stefano

doi:10.1186/s13073-014-0076-4

Cited by 34 publications

(30 citation statements)

References 41 publications

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“…The main molecular mechanism of T-UCE activity described to date is its ‘decoy’ function. By acting as natural sponges, these lncRNAs can sequester miRNAs via sequence complementarity [ 107 – 110 ]. Decoy binding sites within T-UCEs also act through chromatin remodeling by interplaying with distinct regulatory molecules including epigenetic modifiers, transcription factors, and catalytic proteins [ 111 , 112 ].…”

Section: Transcribed Ucesmentioning

confidence: 99%

“…More recent large-scale efforts, employing genome-wide sequencing of multiple tissues, identified T-UC.283+ as the T-UCE most expressed in ESCs, iPSCs and in several embryonic and extra-embryonic tissues. Although no specific function of T-UC283+ has been elucidated, it has been suggested that it may be involved in pluripotency maintenance but also during the first-cell lineage specification [ 107 ].…”

Section: Transcribed Ucesmentioning

confidence: 99%

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Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation

Fico

Fiorenzano

Pascale

et al. 2019

Cell. Mol. Life Sci.

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LncRNAs have recently emerged as new and fundamental transcriptional and post-transcriptional regulators acting at multiple levels of gene expression. Indeed, lncRNAs participate in a wide variety of stem cell and developmental processes, acting in cis and/or in trans in the nuclear and/or in the cytoplasmic compartments, and generating an intricate network of interactions with RNAs, enhancers, and chromatin-modifier complexes. Given the versatility of these molecules to operate in different subcellular compartments, via different modes of action and with different target specificity, the interest in this research field is rapidly growing. Here, we review recent progress in defining the functional role of lncRNAs in stem cell biology with a specific focus on the underlying mechanisms. We also discuss recent findings on a new family of evolutionary conserved lncRNAs transcribed from ultraconserved elements, which show perfect conservation between human, mouse, and rat genomes, and that are emerging as new player in this complex scenario.

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Section: Transcribed Ucesmentioning

confidence: 99%

Section: Transcribed Ucesmentioning

confidence: 99%

Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation

Fico

Fiorenzano

Pascale

et al. 2019

Cell. Mol. Life Sci.

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“…The noncoding panorama is a real opportunity to reveal new biomarkers or potential targets: in this landscape long noncoding RNAs (lncRNAs) are an emerging class of key regulatory RNAs that do not code for protein and are not translated [5]. lncRNAs are crucial players in various key biological processes that include dosage compensation, genomic imprinting, chromatin organization, gene regulation, and alternative splicing [6]. lncRNA mechanism of action need still to be widely revealed [7].…”

Section: Introductionmentioning

confidence: 99%

Profiling of the Predicted Circular RNAs in Ductal In Situ and Invasive Breast Cancer: A Pilot Study

Galasso

Costantino

Pasquali

et al. 2016

International Journal of Genomics

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The recent advantage obtained by next generation sequencing allows a depth investigation of a new “old” kind of noncoding transcript, the circular RNAs. Circular RNAs are nontranslated RNAs, typically nonpolyadenylated, with a resistance to exonucleases that gives them the ability to be more stable than the common linear RNA isoforms. We used a bioinformatic detection tool (CIRCexplorer) to research predictive circRNAs from the next generation sequenced data of five samples of ductal in situ carcinoma (DCIS) and matched adjacent invasive ductal carcinoma (IDC). Furthermore, we also investigated the circular RNAs expressed in MCF7, an invasive breast ductal carcinoma cell line. We described the genomic context of the predicted circular RNAs and we address the hypothetical possible functional roles. This study showed a perspective of a panel of predictive circRNAs identified and the function that circRNAs could exert.

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“…Another similar finding was the association of methylated Uc283 with the improvement of clinical outcome. Recently, Galasso et al showed that Uc283 is highly expressed in pluripotent embryonic stem cells (ESCs) inducing pluripotency while it is overexpressed in gliomas and prostate cancer and less expressed in CRC [28]. In addition, a group led by Dr Esteller showed that Uc283 binds to pri-miRNA-195, leading to downregulation of mature miRNA-195 [29], a miRNA that is known to suppress metastasis and proliferation of CRC [30].…”

Section: Discussionmentioning

confidence: 99%

Differentially Methylated Ultra-Conserved Regions Uc160 and Uc283 in Adenomas and Adenocarcinomas Are Associated with Overall Survival of Colorectal Cancer Patients

Κοττόρου

Dimitrakopoulos

Antonacopoulou

et al. 2020

Cancers

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Deregulation of the transcribed ultra-conserved regions (T-UCRs) Uc160, Uc283, and Uc346 has been reported in colorectal cancer (CRC) recently. Here, we investigated promoter methylation of these T-UCRs during the adenoma–carcinoma sequence and their clinical significance in CRC patients. Methylation levels were assessed in CRC, adenomas, infiltrated lymph nodes, and metastatic tissue specimens. In situ hybridization was performed in representative tissue specimens. T-UCRs expression levels were also evaluated in HT-29 colon cancer cells before and after the acquired resistance to 5-fluorouracil (5-FU) and oxaliplatin. A gradual increase in T-UCRs methylation levels from hyperplastic polyps to adenomas and to in situ carcinomas (ISC) and a gradual decrease from ISC to infiltrative and metastatic carcinomas was observed (p < 0.001 for Uc160 and Uc283, p = 0.018 for Uc346). Uc160 and Uc283 methylation was associated with the grade of dysplasia in adenoma specimens (p = 0.034 and p = 0.019, respectively). Furthermore, higher Uc160 methylation, mainly in stage III and IV patients, was related to improved overall survival (OS) in univariate (p = 0.009; HR, 0.366) and multivariate analysis (p = 0.005; HR, 0.240). Similarly, higher methylation of Uc283 was associated with longer OS (p = 0.030). Finally, T-UCRs expression was significantly reduced in HT-29 cells after resistance to chemotherapy. This study suggests that promoter methylation of Uc160, Uc283, and Uc346 is altered during CRC development and that Uc160 and Uc283 methylation may have prognostic significance for CRC patients.

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A large scale expression study associates uc.283-plus lncRNA with pluripotent stem cells and human glioma

Cited by 34 publications

References 41 publications

Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation

Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation

Profiling of the Predicted Circular RNAs in Ductal In Situ and Invasive Breast Cancer: A Pilot Study

Differentially Methylated Ultra-Conserved Regions Uc160 and Uc283 in Adenomas and Adenocarcinomas Are Associated with Overall Survival of Colorectal Cancer Patients

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