Molecular Genetics and Genomics

, Volume 289, Issue 6, pp 1225–1235 | Cite as

Identification and characterization of long intergenic non-coding RNAs related to mouse liver development

  • Jie Lv
  • Zhijun Huang
  • Hui Liu
  • Hongbo Liu
  • Wei Cui
  • Bao Li
  • Hongjuan He
  • Jing Guo
  • Qi Liu
  • Yan Zhang
  • Qiong Wu
Original Paper

Abstract

Long non-coding RNAs (lncRNAs) have been studied extensively over the last few years. Liver is an important organ that plays a crucial role in glucose metabolism and homeostasis; however, there are few reports of the identification and functional characterization of lncRNAs with important roles in liver development. Therefore, it is necessary to systematically identify lncRNAs that are involved in liver development. In this paper, we assembled the transcriptome using published RNA-seq data across three mouse liver developmental stages and identified 4,882 putative long intergenic non-coding RNAs (lincRNAs) expressed in at least one of the investigated stages. Combining these with Ensembl lincRNAs, we established a reference catalog of 6,602 transcribed lincRNAs in the mouse liver. We then analyzed all the lincRNAs in this reference catalog systematically and revealed that liver lincRNAs carry different genomic signatures from protein-coding genes, while the putative lincRNAs are generally comparable with known Ensembl lincRNAs. In addition, putative lincRNAs are functionally associated with essential biological processes, including RNA splicing, protein localization and fatty acid metabolic process, implying that they may play an important role in regulating liver development. The validation of selected lincRNAs that are specifically expressed in developing liver tissues further suggested the effectiveness of our approach. Our study shows that lincRNAs that are differentially expressed during three liver developmental stages could have important regulatory roles in liver development. The identified putative lincRNAs are a valuable resource for further functional studies.

Keywords

Next-generation sequencing Liver development Mouse Transcriptome RNA-sequencing 

Supplementary material

438_2014_882_MOESM1_ESM.pdf (178 kb)
Supplementary material 1 (PDF 177 kb)
438_2014_882_MOESM2_ESM.xlsx (7.4 mb)
Supplementary material 2 (XLSX 7566 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Jie Lv
    • 1
  • Zhijun Huang
    • 1
  • Hui Liu
    • 1
  • Hongbo Liu
    • 1
  • Wei Cui
    • 1
  • Bao Li
    • 1
  • Hongjuan He
    • 1
  • Jing Guo
    • 1
  • Qi Liu
    • 1
  • Yan Zhang
    • 2
  • Qiong Wu
    • 1
  1. 1.School of Life Science and Technology, State Key Laboratory of Urban Water Resource and EnvironmentHarbin Institute of TechnologyHarbinChina
  2. 2.College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina

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