Expression profiles and regulatory network of microRNA, long non-coding RNA and circular RNA in rat chronic stress depression model based on whole transcriptome technology

MENG Pan; ZHANG Xi; LIU Tong-Tong; ZHAO Hong-Qing; YANG Hui; LIU Jian; FANG Rui; WANG Yu-Hong; GE Jin-Wen; WANG Xiao-Ye

doi:10.16098/j.issn.0529-1356.2023.04.005

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Acta Anatomica Sinica ›› 2023, Vol. 54 ›› Issue (4) : 405-413. DOI: 10.16098/j.issn.0529-1356.2023.04.005

Expression profiles and regulatory network of microRNA, long non-coding RNA and circular RNA in rat chronic stress depression model based on whole transcriptome technology

MENG Pan¹ ZHANG Xi ² YANG Hui³ LIU Jian³ FANG Rui⁴ WANG Xiao-ye^2* GE Jin-wen^1,4* LIU Tong-tong⁵ ZHAO Hong-qing⁵ WANG Yu-hong⁵#br#

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Abstract

Objective To explore the potential pathophysiological mechanism of depression by screening the expression profiles and competing endogenous RNA (ceRNA) regulatory network microRNA(miRNA), long non\|coding RNA(lncRNA) and circular RNA(circRNA) in the hippocampus of chronic stress depression rat model. Methods Twelve SD rats were divided into blank group and model group. Chronic mild unpredictability stress (CUMS) was used to construct the rat model of depression. The whole transcriptome analysis was performed on the hippocampus of the rats, and the possible regulatory networks among lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA were explored by bioinformatics method. Results According to the |fold change|≥1.5 and P≤0.05, 29 differentially expressed miRNAs (21 up-regulated and 8 down-regulated), 686 differentially expressed lncRNAs (163 up-regulated and 523 down-regulated) and 8 differentially expressed circRNAs (3 up-regulated and 5 down-regulated) were identified. Gene Ontology(GO) and Kytot Encyclopedia of Genes and Genomes(KEGG) pathway analysis showed that the target genes of miRNAs were mainly enriched in the Golgi apparatus and calcium ion binding process in the cell membrane, the functions of lncRNAs target genes involved nucleic acid binding regulation, cytokine and protein ubiquitination, etc, and the functions of host genes of circRNAs were associated with cellular stimulation response, metabolic process, catalytic activity and other processes. The ceRNA network of lncRNAs and circRNAs showed complex interactions between non-coding RNA (ncRNA) and mRNA related to synaptic plasticity, such as protein Wnt-sa(WNT5a) and collagentype Ⅲ alpha1(COL8a1) related to axon orientation and laminin A2(LAMA2) related to neurodevelopment. Conclusion The ceRNA network of lncRNA and circRNA shows that the complex interaction betweens ncRNA and mRNA is highly associated with the neuroplasticity, which support the neuroplasticity hypothesis of depression.

Key words

MicroRNA / Long non-coding RNA / Circular RNA / Depression / Neuroplasticity / Whole transcriptome technology / Rat

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MENG Pan ZHANG Xi YANG Hui LIU Jian FANG Rui WANG Xiao-ye GE Jin-wen LIU Tong-tong ZHAO Hong-qing WANG Yu-hong.

Expression profiles and regulatory network of microRNA, long non-coding RNA and circular RNA in rat chronic stress depression model based on whole transcriptome technology

[J]. Acta Anatomica Sinica. 2023, 54(4): 405-413 https://doi.org/10.16098/j.issn.0529-1356.2023.04.005

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