Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken

Tao Zhang; Xiangqian Zhang; Kunpeng Han; Genxi Zhang; Jinyu Wang; Kaizhou Xie; Qian Xue; Xiaomei Fan

doi:10.1371/journal.pone.0172389

Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken

PLoS One. 2017 Feb 15;12(2):e0172389. doi: 10.1371/journal.pone.0172389. eCollection 2017.

Authors

Tao Zhang^{1

2}, Xiangqian Zhang^{1

2}, Kunpeng Han^{1

2}, Genxi Zhang^{1

2}, Jinyu Wang^{1

2}, Kaizhou Xie^{1

2}, Qian Xue^{1

2}, Xiaomei Fan³

Affiliations

¹ College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.
² Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China.
³ Vazyme Biotech Co.,Ltd., Economic and Technological Development Zone, Nanjing, Jiangsu, China.

Abstract

Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison. These 7,433 differentially expressed genes were grouped into 11 clusters based on their expression patterns by K-means clustering. Using Weighted Gene Coexpression Network Analysis, we identified four stage-specific modules positively related to I0, I2, I4, and I6 stages and two stage-specific modules negatively related to I0 and I2 stages, respectively. Many well-known and novel pathways associated with intramuscular preadipocyte differentiation were identified. We also identified hub genes in each stage-specific module and visualized them in Cytoscape. Our analysis revealed many highly-connected genes, including XLOC_058593, BMP3, MYOD1, and LAMP3. This study provides a valuable resource for chicken lncRNA study and improves our understanding of the biology of preadipocyte differentiation in chicken.

MeSH terms

Adipocytes / cytology
Adipocytes / metabolism
Animals
Cell Differentiation
Cells, Cultured
Chickens / genetics
Cluster Analysis
Gene Expression
Gene Expression Profiling
Gene Regulatory Networks
RNA, Long Noncoding / chemistry
RNA, Long Noncoding / genetics
RNA, Long Noncoding / metabolism*
RNA, Messenger / chemistry
RNA, Messenger / genetics
RNA, Messenger / metabolism*
Sequence Analysis, RNA

Substances

RNA, Long Noncoding
RNA, Messenger

Grants and funding

Support was provided by the National Broiler Industrial and Technology Sestem: nycytx-42-G1-05 and the Priority Academic Program Development of Jiangsu Higher Education Institutions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.