Abstract
BackgroundLong noncoding RNAs (lncRNAs) are a class of ubiquitous noncoding RNAs and have been found to act as tumor suppressors or oncogenes, which dramatically altered our understanding of cancer. Naked mole rat (NMR, Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent; however, whether lncRNAs play roles in cancer resistance in this seductive species remains unknown.ResultsIn this study, we developed a pipeline and identified a total of 4422 lncRNAs across the NMR genome based on 12 published transcriptomes. Systematic analysis revealed that NMR lncRNAs share many common characteristics with other vertebrate species, such as tissue specificity and low expression. BLASTN against with 1057 human cancer-related lncRNAs showed that only 5 NMR lncRNAs displayed homology, demonstrating the low sequence conservation between NMR lncRNAs and human cancer-related lncRNAs. Further correlation analysis of lncRNAs and protein-coding genes indicated that a total of 1295 lncRNAs were intensively coexpressed (r ≥ 0.9 or r ≤ −0.9, cP value ≤ 0.01) with potential tumor-suppressor genes in NMR, and 194 lncRNAs exhibited strong correlation (r ≥ 0.8 or r ≤ −0.8, cP value ≤ 0.01) with four high-molecular-mass hyaluronan related genes that were previously identified to play key roles in cancer resistance of NMR.ConclusionIn this study, we provide the first comprehensive genome-wide analysis of NMR lncRNAs and their possible associations with cancer resistance. Our results suggest that lncRNAs may have important effects on anticancer mechanism in NMR.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0101-5) contains supplementary material, which is available to authorized users.
Highlights
Long noncoding RNAs are a class of ubiquitous noncoding RNAs and have been found to act as tumor suppressors or oncogenes, which dramatically altered our understanding of cancer
With the rapid development of next-generation sequencing (NGS) techniques and in silico analysis, large sets of Long noncoding RNAs (lncRNAs) have been identified in many species; it has yet to be applied in naked mole rat (NMR)
long noncoding RNA (LncRNA) showed a significant lower expression level than protein-coding gene (PCG) by comparing the fragments per kilobase of exon per million fragments mapped (FPKM) values (Fig. 2d), which has been observed in other species such as rainbow trout [15] and pacific oyster [16]
Summary
Long noncoding RNAs (lncRNAs) are a class of ubiquitous noncoding RNAs and have been found to act as tumor suppressors or oncogenes, which dramatically altered our understanding of cancer. Naked mole rat (NMR, Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent; whether lncRNAs play roles in cancer resistance in this seductive species remains unknown. Naked mole rats (NMRs; Heterocephalus glaber) are small, nearly hairless, subterranean rodents that are renowned for their longevity and cancer resistance [1, 2]. Recent studies indicated that lncRNAs have become new players in cancer [11] and attracted plenty of attention in scientific community due to their altered expressions and dysregulated functions as tumor suppressors or oncogenes in various human cancer types [12, 13]. Considering the close connections between lncRNAs and cancers, it becomes urgent and necessary to identify and feature lncRNAs in the attractive cancerresistant rodent, NMR
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