Comprehensive CircRNA expression profile and selection of key CircRNAs during priming phase of rat liver regeneration

Abstract

BackgroundRat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic.ResultsTo investigate the regulatory mechanism of circRNA during priming phase of rat LR, high-throughput RNA sequencing technology was performed to unbiasedly profile the expression of circRNA during priming phase of rat LR. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis was conducted to predict the functions of differentially expressed circRNAs and their host linear transcripts. Co-expression networks of circRNA-miRNA were constructed based on the correlation analysis between the differentially expressed LR-related circRNAs and the condition of their miRNA binding sites. To excavate the key circRNAs in the early phase of rat LR, we comprehensively evaluated and integrated the relationship of expression level between the circRNAs and the linear transcripts as well as the distribution of miRNA binding sites in circRNA sequences.ConclusionsThis paper is the first to employ the comprehensive circRNA expression profile and to investigate circRNA-miRNA interactions during priming phase of rat LR. Two thousand four hundred twelve circRNAs were detected, and 159 circRNAs deriving from 116 host linear transcripts differentially expressed (p < 0.05). Six significantly changed circRNAs during priming phase of rat LR were screened as key circle molecules, and then were validated by qRT-PCR. This study will lay the foundation for revealing the functional roles of circRNAs during rat LR and help solve the remaining clinical problems.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3476-6) contains supplementary material, which is available to authorized users.

Differential expression of circular RNAs in hepatic tissue in a model of liver fibrosis and functional analysis of their target genes

“…The existing papers mainly focus on the field of primary liver cancer . However, other studies have found that circRNA is associated with non‐alcoholic fatty liver and liver regeneration mechanisms . Recently, Chen et al .…”

“…4 However, other studies have found that circRNA is associated with non-alcoholic fatty liver and liver regeneration mechanisms. 5,6 Recently, Chen et al reported for the first time that circRNA is involved in HSC activation. The researchers used microarray technology to analyze the differentially expressed circRNAs in a model of radiation-induced HSC activation and found that, compared with the normal control group, there were 179 upregulated circRNAs and 630 downregulated circRNAs in the experimental group.…”

Comprehensive circRNA expression profile and construction of circRNA‐associated ceRNA network in fur skin

“…The relationships between circRNAs and the brain, liver and heart have been recognized. Recently, the role of circRNAs in cancer was also highlighted.…”

Large-scale quantitative genomics analyzes the circRNA expression profile and identifies the key circRNA in regulating cell proliferation during the proliferation phase of rat LR

“…It has been verified that circRNAs work through various ways including acting as miRNAs sponge, regulating transcription by interacting with small nuclear ribonucleoproteins (snRNP), recruiting RNA polymeraseII, interacting with proteins, and coding protein [7]. We had shown that 159 circRNAs were differentially expressed (DE) in the priming phase after PH [8]. In the present study, we aimed primarily to investigate the potential mechanism of circRNAs regulating the proliferation phase after 2/3 PH in rats.…”