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Genome-wide identification and characterization of long non-coding RNAs during differentiation of visceral preadipocytes in rabbit

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Abstract

Emerging evidence suggests that long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes, including adipogenesis. Despite being considered an ideal animal model for studying adipogenesis, little is known about the roles of lncRNAs in the regulation of rabbit preadipocyte differentiation. In the present study, visceral preadipocytes isolated from newborn rabbits were cultured in vitro and induced for differentiation, and global lncRNA expression profiles of adipocytes collected at days 0, 3, and 9 of differentiation were analyzed by RNA-seq. A total of 2066 lncRNAs were identified from nine RNA-seq libraries. Compared to protein-coding transcripts, lncRNA transcripts exhibited characteristics of a longer length and lower expression level. Furthermore, 486 and 357 differentially expressed (DE) lncRNAs were identified when comparing day 3 vs. day 0 and day 9 vs. day 3, respectively. Target genes of DE lncRNAs were predicted by the cis-regulating approach. Prediction of functions revealed that DE lncRNAs when comparing day 3 vs. day 0 were involved in gene ontology (GO) terms of developmental growth, growth, developmental cell growth, and stem cell proliferation, and involved in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of PI3K-Akt signaling pathway, fatty acid biosynthesis, and the insulin signaling pathway. The DE lncRNAs when comparing day 9 vs. day 3 were involved in GO terms that associated with epigenetic modification and were involved in the KEGG pathway of cAMP signaling pathway. This study provides further insight into the regulatory function of lncRNAs in rabbit visceral adipose and facilitates a better understanding of different stages of preadipocyte differentiation.

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Funding

This work was supported by the earmarked fund for China Agriculture Research System (CARS-44-A-2).

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  1. Kun Du and Guo-Ze Wang contributed equally to this work.

Authors and Affiliations

  1. Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, China

    Kun Du, Guo-Ze Wang, An-yong Ren, Ming-cheng Cai, Gang Luo, Xian-bo Jia, Shen-qiang Hu, Jie Wang, Shi-Yi Chen & Song-Jia Lai

  2. College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China

    Guo-Ze Wang

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  1. Kun Du
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Contributions

Conceptualization: Song-Jia Lai.

Formal analysis: Kun Du, Guo-Ze Wang.

Resource: An-yong Ren, Ming-cheng Cai, Gang Luo, Xian-bo Jia, Shen-qiang Hu, Jie Wang, Shi-Yi Chen, Song-Jia Lai.

Writing: Kun Du.

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Correspondence to Song-Jia Lai.

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Electronic supplementary material

Table S1.

Primers of genes used in RT-qPCR (docx format). (DOCX 15 kb)

Table S2.

Summary of RNA-seq data and reads mapping (docx format). (DOCX 16 kb)

Table S3.

Differentially expressed analysis when comparing day 3 vs. day 0 (xlsx format). (XLSX 50 kb)

Table S4.

Differentially expressed analysis when comparing day 9 vs. day 3 (xlsx format). (XLSX 39 kb)

Table S5.

FPKM of lncRNA transcripts (xlsx format). (XLSX 209 kb)

Table S6.

Result of GO enrichment between day 0 and day 3 of rabbit adipogenesis (xlsx format). (XLSX 23 kb)

Table S7.

Result of KEGG pathway analysis between day 0 and day 3 of rabbit adipogenesis (xlsx format). (XLSX 12 kb)

Table S8.

Result of GO enrichment between day 3 and day 9 of rabbit adipogenesis (xlsx format). (XLSX 22 kb)

Table S9.

Result of KEGG pathway analysis between day 3 and day 9 of rabbit adipogenesis (xlsx format). (XLSX 11 kb)

Table S10.

DE LncRNAs in key pathways that might regulate rabbit adipogenesis (xlsx format). (XLSX 10 kb)

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Du, K., Wang, GZ., Ren, Ay. et al. Genome-wide identification and characterization of long non-coding RNAs during differentiation of visceral preadipocytes in rabbit. Funct Integr Genomics 20, 409–419 (2020). https://doi.org/10.1007/s10142-019-00729-5

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