Databases for lncRNAs: a comparative evaluation of emerging tools

Fritah, Sabrina; Niclou, Simone P.; Azuaje, Francisco

doi:10.1261/rna.044040.113

Cited by 82 publications

(62 citation statements)

References 76 publications

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“…Websites reviewed in (Fritah, et al 2014 (Rehmsmeier, et al 2004) has been used to examine miRNA/lncRNA interaction (Zhou, et al 2017a) http://bibiserv.techfak.unibielefeld.de/rnahybrid/ Increased by androgens in prostate cancer cells (Salameh, et al 2015) Suppressed by ERβ PCa-specific urine biomarker (Laxman, et al 2008 Represses onco-miR-21 (Zhang, et al 2013) inhibited miR-103 in EC cells (Guo, et al 2015) inhibited activation of the AKT/mTOR pathway in PC3 PCa cells (Xue, et al 2016a) Low expression correlated with poor prognosis in thyroid cancer tissues, co-immunoprecipitates with PI3K in HEC-1B EC cells Downregulated in breast , prostate , endometrial Sun et al 2017a), and PTC (Murugan et al 2017) tumors…”

Section: Declaration Of Interest and Fundingmentioning

confidence: 99%

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

Klinge

2018

Endocrine-Related Cancer

100

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Abstract:The human genome is 'pervasively transcribed' leading to a complex array of noncoding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~ 22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation. Long non-coding RNAs (lncRNAs) are classified as >200 nucleotides in length, but range up to several kb and are heterogeneous in genomic origin and function.LncRNAs fold into structures that interact with DNA, RNA, and proteins to regulate chromatin dynamics, protein complex assembly, transcription, telomere biology, and splicing. Some lncRNAs act as sponges for miRNAs and decoys for proteins. Nuclear-encoded lncRNAs can be taken up by mitochondria and lncRNAs are transcribed from mtDNA. Both miRNAs and lncRNAs are dysregulated in endocrine cancers. This review provides an overview on the current understanding of the regulation and function of selected lncRNAs and miRNAs, and their interaction, in endocrine-related cancers: breast, prostate, endometrial, and thyroid.

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Section: Declaration Of Interest and Fundingmentioning

confidence: 99%

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

Klinge

2018

Endocrine-Related Cancer

100

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“…The length of long non-coding RNA (lncRNA) is greater than 200 nucleotides [4-6]. Because of its role in gene transcription, epigenetic, and post transcriptional regulation, lncRNA received more and more concerned by researchers [7, 8].…”

Section: Introductionmentioning

confidence: 99%

LncRNA HOTAIR is a Prognostic Biomarker for the Proliferation and Chemoresistance of Colorectal Cancer via MiR-203a-3p-Mediated Wnt/ß-Catenin Signaling Pathway

Xiao

Chen

et al. 2018

Cell Physiol Biochem

134

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Background/Aims: HOX transcript antisense RNA (HOTAIR) plays a vital role in carcinogenesis. However, its functional and regulatory roles remain unclear. In this study, we aimed to investigate its biological function and clinical significance in human colorectal cancer (CRC). Methods: We examined the expression levels of lncRNA HOTAIR and miR-203a-3p in CRC tissues and CRC cell lines by qRT-PCR. Gain and loss-of-function assays were performed to examine the effects of HOTAIR and miR-203a-3p on the proliferation and chemoresistance of CRC cells. The possible mechanisms of HOTAIR were also explored by fluorescence reporter assay and Western blot. Results: The expressions of HOTAIR were upregulated in CRC tissue tissues compared to adjacent control tissues. We also found HOTAIR was downregulated by miR-203a-3p in CRC cell lines. Both HOTAIR knockdown and miR-203a-3p overexpression in CRC cell lines led to inhibited cell proliferation and reduced chemoresistance. We also determined that β-catenin and GRG5 were inhibitory targets of miR-203a-3p, and that Wnt/β-catenin signaling was inhibited by both HOTAIR knockdown and miR-203a-3p overexpression. Significantly, we found that increased expression of miR-203a-3p is essential for cell proliferation repression, chemoresistance reduction, and Wnt/β-catenin signaling inhibition induced by HOTAIR knockdown. Conclusions: Our study demonstrated that the lncRNA HOTAIR could regulate the progression and chemoresistance of CRC via modulating the expression levels of miR-203a-3p and the activity of Wnt/β-catenin signaling pathway.

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“…Recently, a two-stage case-control study revealed that patients with the rs7958904 CC genotype exhibited a significantly decreased risk of both Dukes' stage I and II colorectal cancer compared with those exhibiting the GG genotype, indicating that genetic variations in the HOTAIR gene are associated with the risk of colorectal cancer (21). An additional study indicated that HOTAIR and lncRNA-422 may be involved in The known functions of lncRNAs may be obtained from the listed databases (9).…”

Section: Cancer-related Lncrnasmentioning

confidence: 99%

LncRNAs and cancer

Zhang

et al. 2016

Oncology Letters

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Abstract. Long non-coding RNAs (lncRNAs) are a group of non-coding RNAs composed of >200 nucleotides. Recent studies have revealed that lncRNAs exert an important role in the development and progression of cancer. In this review, the involvement of the most extensively investigated lncRNAs in cancers of the digestive, respiratory, reproductive, urinary and central nervous systems are discussed. LncRNAs function via molecular and biochemical mechanisms that include cis-and trans-regulation of gene expression, epigenetic modulation in the nucleus and post-transcriptional control in the cytoplasm. Although the detailed biological functions and molecular mechanisms of the majority of lncRNAs remain to be elucidated, this review aims to provide a novel insight into the diagnosis and treatment of cancer using lncRNAs.

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Databases for lncRNAs: a comparative evaluation of emerging tools

Cited by 82 publications

References 76 publications

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

LncRNA HOTAIR is a Prognostic Biomarker for the Proliferation and Chemoresistance of Colorectal Cancer via MiR-203a-3p-Mediated Wnt/ß-Catenin Signaling Pathway

LncRNAs and cancer

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