Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii.

Zhiqiang Hao,Juanjuan Guo,Guanglin Li,Jingang Li,Jianping He,Mingfang Han

doi:10.3390/cimb43030132

Abstract

Subterranean rodents could maintain their normal activities in hypoxic environments underground. Eospalax fontanierii, as one kind of subterranean rodent found in China can survive very low oxygen concentration in labs. It has been demonstrated that long non-coding RNAs (lncRNAs) have important roles in gene expression regulations at different levels and some lncRNAs were found as hypoxia-regulated lncRNAs in cancers. We predicted thousands of lncRNAs in the liver and heart tissues by analyzing RNA-Seq data in Eospalax fontanierii. Those lncRNAs often have shorter lengths, lower expression levels, and lower GC contents than mRNAs. Majors of lncRNAs have expression peaks in hypoxia conditions. We found 1128 DE-lncRNAs (differential expressed lncRNAs) responding to hypoxia. To search the miRNA regulation network for lncRNAs, we predicted 471 and 92 DE-lncRNAs acting as potential miRNA target and target mimics, respectively. We also predicted the functions of DE-lncRNAs based on the co-expression networks of lncRNA-mRNA. The DE-lncRNAs participated in the functions of biological regulation, signaling, development, oxoacid metabolic process, lipid metabolic/biosynthetic process, and catalytic activity. As the first study of lncRNAs in Eospalax fontanierii, our results show that lncRNAs are popular in transcriptome widely and can participate in multiple biological processes in hypoxia responses.

Highlights

Subterranean rodents suffer from adverse environmental factors underground, such as hypoxia and hypercapnia
By comparing the numbers of long non-coding RNAs (lncRNAs) with peak expression levels in the heart and liver tissues, we found that the number of lncRNAs with peak expression levels in the liver were larger than that in heart, while the numbers of mRNAs with peak expression levels were considerable in the two tissues (Figure 2D)
We predicated the lncRNAs in E. fontanierii in two tissues heart and liver

Summary

Introduction

Subterranean rodents suffer from adverse environmental factors underground, such as hypoxia and hypercapnia. They have evolved and adapted in a long-term period. They can survive under 3% O2 for more than 11 h without obvious damage, while rats survive only 2.5 h under the same condition [1]. Mice or rats serve as model animals for medical research, they are limited in hypoxia studies as they are sensitive under severe hypoxia. Blind mole rats and naked mole rats attract scientists’ attention for their cancer-resistant, long-lived, and hypoxia-adaptive traits. AS with blind mole rats, Eospalax fontanierii (E. fontanierii) are strictly subterranean rodents that survive in habitats poor in oxygen and rich in carbon dioxide and ammonia

Methods

Results

Conclusion