Effect Of XBP1 Deficiency In Cartilage On The Regulatory Network Of LncRNA/circRNA-miRNA-mRNA

Xiaoli Li; Yuyou Yang; Li Liang; Mengtian Fan; Xingyue Li; Naibo Feng; Yiming Pan; Qiaoyan Tan; Qingbo Xu; Yangli Xie; Fengjin Guo

doi:10.7150/ijbs.64054

Effect Of XBP1 Deficiency In Cartilage On The Regulatory Network Of LncRNA/circRNA-miRNA-mRNA

Int J Biol Sci. 2022 Jan 1;18(1):315-330. doi: 10.7150/ijbs.64054. eCollection 2022.

Authors

Xiaoli Li¹, Yuyou Yang¹, Li Liang¹, Mengtian Fan¹, Xingyue Li¹, Naibo Feng¹, Yiming Pan¹, Qiaoyan Tan², Qingbo Xu³, Yangli Xie², Fengjin Guo¹

Affiliations

¹ Department of Cell Biology and Genetics, Core Facility of Development Biology, Chongqing Medical University, Chongqing 400016, China.
² Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing 400042, China.
³ Cardiovascular Division, King's College London BHF Centre, London, United Kingdom.

Abstract

X-box binding protein 1(XBP1) is a critical component for unfolded protein response (UPR) in ER stress. According to previous studies performed with different XBP1-deficient mice, the XBP1 gene affects mouse cartilage development and causes other related diseases. However, how the complete transcriptome, including mRNA and ncRNAs, affects the function of cartilage and other tissues when XBP1 is deficient in chondrocytes is unclear. In this study, we aimed to screen the differentially expressed (DE) mRNAs, circRNAs, lncRNAs and miRNAs in XBP1 cartilage-specific knockout (CKO) mice using high throughput sequencing and construct the circRNA-miRNA-mRNA and lncRNA-miRNA-mRNA regulatory networks. DE LncRNAs (DE-LncRNAs), circRNAs (DE-circRNAs), miRNAs (DE-miRNAs), and mRNAs [differentially expressed genes (DEGs)] between the cartilage tissue of XBP1 CKO mice and controls were identified, including 441 DE-LncRNAs, 15 DE-circRNAs, 6 DE-miRNAs, and 477 DEGs. Further, 253,235 lncRNA-miRNA-mRNA networks and 1,822 circRNA-miRNA-mRNA networks were constructed based on the correlation between lncRNAs/circRNAs, miRNAs, mRNAs. The whole transcriptome analysis revealed that XBP1 deficiency in cartilage affects the function of cartilage and other different tissues, as well as associated diseases. Overall, our findings may provide potential biomarkers and mechanisms for the diagnosis and treatment of cartilage and other related diseases.

Keywords: XBP1; cartilage; circRNA-miRNA-mRNA; lncRNA-miRNA-mRNA; whole transcriptome analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cartilage / metabolism*
Gene Expression Profiling
Mice
MicroRNAs / metabolism*
RNA, Circular / metabolism*
RNA, Long Noncoding / metabolism*
RNA, Messenger / metabolism*
X-Box Binding Protein 1 / deficiency*

Substances

MicroRNAs
RNA, Circular
RNA, Long Noncoding
RNA, Messenger
X-Box Binding Protein 1
Xbp1 protein, mouse