Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs) Functional Analysis

Sacco, Letizia Da; Baldassarre, Antonella; Masotti, Andrea

doi:10.3390/ijms13010097

Cited by 94 publications

(77 citation statements)

References 83 publications

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“…However, different ncRNA-specific databases are now publicly accessible, and these are of great help in their study: lncRNAdb (Amaral et al 2011;Quek et al 2015), providing detailed information about lncRNA, which includes sequences, functions, expression patterns, cellular location, and interacting proteins; NONCODE (Xie et al 2014), which accounts for other types of sequences than lncRNAs and with similar information as the p r e v i o u s m e n t i o n e d ( C h e n e t a l . 2 0 1 3 ) ; LncRNADisease , presenting data that associate lncRNAs with diseases, namely, with cancer ; and other lesser known databases (Da Sacco et al 2012). Nevertheless, these databases are scarce regarding the information about satncRNAs, and the NONCODE database is the only one with data regarding these sequences.…”

Section: The Analysis Of Satncrnas-experimental Approachesmentioning

confidence: 98%

Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer

et al. 2015

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For several decades, transcriptional inactivity was considered as one of the particular features of constitutive heterochromatin and, therefore, of its major component, satellite DNA sequences. However, more recently, succeeding evidences have demonstrated that these sequences can indeed be transcribed, yielding satellite non-coding RNAs with important roles in the organization and regulation of genomes. Since then, several studies have been conducted, trying to understand the function(s) of these sequences not only in the normal but also in cancer genomes. It is thought that the association between cancer and satncRNAs is mostly due to the influence of these transcripts in the genome instability, a hallmark of cancer. The few reports on satellite DNA transcription in cancer contexts point to its overexpression; however, this scenario may be far more complex, variable, and influenced by a number of factors and the exact role of satncRNAs in the oncogenic process remains poorly understood. The greater is the knowledge on the association of satncRNAs with cancer, the greater would be the opportunity to assist cancer treatment, either by the design of effective therapies targeting these molecules or by using them as biomarkers in cancer diagnosis, prognosis, and with predictive value.

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Section: The Analysis Of Satncrnas-experimental Approachesmentioning

confidence: 98%

Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer

et al. 2015

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“…It has been shown that the transcription of lncRNAs can affect the expression of nearby coding genes (Da Sacco et al, 2012). LncRNAs can recruit chromatinmodifying enzymes to regulate the expression of genes, either in cis (near the site of lncRNA production) or in trans (when the genes involved are distant) through a phenomenon called transvection (Da Sacco et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

“…LncRNAs can recruit chromatinmodifying enzymes to regulate the expression of genes, either in cis (near the site of lncRNA production) or in trans (when the genes involved are distant) through a phenomenon called transvection (Da Sacco et al, 2012). In our study, the lncRNAs that displayed the greatest decrease in expression in H2 were the lincRNAs TSPAN8 and CALCA; the nearby genes encoding TSPAN8 and CALCB mRNA were also differentially expressed in the H2 and LM3 cell lines and the fold change in their expression was equally high (48.58408 and 74.100555, respectively).…”

Section: Discussionmentioning

confidence: 99%

Long Non-coding RNAs are Differentially Expressed in Hepatocellular Carcinoma Cell Lines with Differing Metastatic Potential

Fang

Sun²,

Chen³

et al. 2015

Asian Pacific Journal of Cancer Prevention

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(Talmadge and Fidler, 2010). A salient feature of metastasis is the ability of cancer cells to colonize specific organ sites (Hanahan and Weinberg, 2011). For instance, HCC cells metastasize to the lung more frequently than the lymph nodes. It is well recognized that the probability of metastatic seeding and growth is determined by both intrinsic genetic properties of the cancer cells involved and characteristics of the stromal microenvironment that surrounds them (Lu and Kang, 2007;Nguyen et al., 2009). Functional genomic analysis of HCC cell lines with different organ-specific metastatic potential may provide new opportunities for identifying diagnostic biomarkers and developing therapies to combat HCC metastasis.Large-scale genomic studies have demonstrated that the mammalian genome encodes many thousands Ting-Ting Fang et al

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“…lncRNAs are popular in molecular studies due to their critical functions in regulating diverse biological behaviors [7]. In addition, it has been disclosed that lncRNAs are also key regulators in various cardiovascular diseases (heart failure in particular); these lncRNAs include lncRNA CHRF [8], lncRNA H19 [1], lncRNA HOTAIR [9], and others.…”

Section: Introductionmentioning

confidence: 99%

lncRNA UCA1 Is a Novel Regulator in Cardiomyocyte Hypertrophy through Targeting the miR-184/HOXA9 Axis

Zhou

Feng

et al. 2018

Cardiorenal Med

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Cardiac hypertrophy is closely associated with a series of cardiovascular diseases, including heart failure and sudden death in particular. An in-depth comprehension of the pathogenesis of cardiac hypertrophy will improve the diagnosis and therapy of cardiac hypertrophy. It has been acknowledged that long noncoding RNAs/microRNAs (lncRNAs/miRNAs) are crucial regulators in diverse biological processes, including various cardiovascular diseases, in multiple manners. Nevertheless, the biological roles of lncRNA UCA1 and miR-184 in cardiac hypertrophy are scarcely reported. In this paper, qRT-PCR analysis exhibited that lncRNA UCA1 was highly expressed in mice heart treated with transverse aortic constriction (TAC) and the cardiomyocytes treated with phenylephrine (PE). On the contrary, miR-184 was downregulated under the same conditions. In addition, it was deduced that lncRNA UCA1 was reversely related with miR-184 in PE-triggered hypertrophic cardiomyocytes, confirmed by the Spearman correlation analysis. The knockdown of UCA1 or the overexpression of miR-184 lessened the enlarged surface area of cardiomyocytes and the elevated expressions of fetal genes (ANP and BNP) induced by PE. Later, it was determined that miR-184 was a direct target of UCA1, whereas the mRNA HOXA9 was a target of miR-184. Rescue assays indicated that UCA1 promoted the progression of cardiac hypertrophy through competitively binding with miR-184 to enhance the expression of HOXA9.

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Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs) Functional Analysis

Cited by 94 publications

References 83 publications

Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer

Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer

Long Non-coding RNAs are Differentially Expressed in Hepatocellular Carcinoma Cell Lines with Differing Metastatic Potential

lncRNA UCA1 Is a Novel Regulator in Cardiomyocyte Hypertrophy through Targeting the miR-184/HOXA9 Axis

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