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

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.

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Acknowledgments

The authors thank National Natural Science Foundation of China for funding. This work is supported by the National Natural Science Foundation of China [31171383, 31100934, 31201075, 31371478, 31371334].

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Correspondence to Qiong Wu.

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J. Lv, Z. Huang, H. Liu and H. B. Liu contributed equally to this work.

Communicated by S. Hohmann.

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Lv, J., Huang, Z., Liu, H. et al. Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. Mol Genet Genomics 289, 1225–1235 (2014). https://doi.org/10.1007/s00438-014-0882-9

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  • DOI: https://doi.org/10.1007/s00438-014-0882-9

Keywords

  • Next-generation sequencing
  • Liver development
  • Mouse
  • Transcriptome
  • RNA-sequencing