Expression profiling of preadipocyte microRNAs by deep sequencing on chicken lines divergently selected for abdominal fatness

PLoS One. 2015 Feb 12;10(2):e0117843. doi: 10.1371/journal.pone.0117843. eCollection 2015.

Abstract

Through posttranscriptional gene regulation, microRNA (miRNA) is linked to a wide variety of biological processes, including adipogenesis and lipid metabolism. Although miRNAs in mammalian adipogenesis have been worked on extensively, their study in chicken adipogenesis is still very limited. To find miRNAs potentially important for chicken preadipocyte development, we compared the preadipocyte miRNA expression profiles in two broiler lines divergently selected for abdominal fat content, by sequencing two small RNA libraries constructed for primary preadipocytes isolated from abdominal adipose tissues. After bioinformatics analyses, from chicken miRNAs deposited in miRBase 20.0, we identified 225 miRNAs to be expressed in preadipocytes, 185 in the lean line and 200 in the fat line (derived from 208 and 203 miRNA precursors, respectively), which corresponds to 114 miRNA families. The let-7 family miRNAs were the most abundant. Furthermore, we validated the sequencing results of 15 known miRNAs by qRT-PCR, and confirmed that the expression levels of most miRNAs correlated well with those of Solexa sequencing. A total of 33 miRNAs was significantly differentially expressed between the two chicken lines (P<0.05). Gene ontology analysis revealed that they could target genes enriched in the regulation of gene transcription and chromatin function, response to insulin stimulation, and IGF-1 signaling pathways, which could have important roles in preadipocyte development. Therefore, a valuable information and resource of miRNAs on chicken adipogenesis were provided in this study. Future functional investigations on these miRNAs could help explore related genes and molecular networks fundamental to preadipocyte development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abdominal Fat / cytology*
  • Abdominal Fat / metabolism*
  • Adipogenesis / genetics*
  • Animals
  • Chickens / genetics*
  • Computational Biology / methods
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • Genome
  • Genomics
  • High-Throughput Nucleotide Sequencing*
  • MicroRNAs / genetics*
  • Molecular Sequence Annotation
  • Reproducibility of Results

Substances

  • MicroRNAs

Associated data

  • SRA/SRR1562981
  • SRA/SRR1563007

Grant support

This study was supported by the National 863 project of China (No. 2013AA102501), National Basic Research Program of China (No. 2009CB941604), and China Agriculture Research System (No. CARS-42). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.